Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/age.70038

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1101/2024.09.21.614268

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41598-025-09050-7

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PubMed

Publisher：Cold Spring Harbor Laboratory  

ABSTRACT

Salicylic acid (SA) and jasmonic acid (JA) regulate plant defense against pathogens and herbivores. The SA-JA pathways often interact antagonistically with the induction of one, leading to the suppression of the other. However, the effect of combined SA/JA concentrations on plant responses is unknown. Here, we show transcriptional responses specific to combinations of SA and JA concentrations and develop transcriptomic biomarkers to estimate SA/JA response states. Combinatorial treatments with eight concentrations of SA and JA, combined with large-scale transcriptome analysis, revealed 43 different expression patterns, including not only well-known antagonistic responses but also responses specific to combinations of SA/JA concentrations. Notably, the expression ofCYP94B3, a key enzyme involved in JA-Ile turnover, was finely tuned by specific SA/JA concentration combinations being induced under high SA conditions in a JA dose-dependent manner. In addition, the expression peaks of indole glucosinolate biosynthesis genes were found at approximately 30-fold higher JA concentrations than aliphatic glucosinolate biosynthesis genes. Furthermore, to quantitatively estimate SA/JA response states, we developed transcriptomic biomarkers using a machine learning approach. The marker specifically estimated response states to target phytohormones. Through analysis ofnpr3/4double mutants, we confirmed that the biomarkers were applicable to the analysis of mutants. The biomarkers will allow us to extract insights into phytohormone responses from various large-scale transcriptome data, e.g., field transcriptomics and single-cell RNA-Seq.

DOI： 10.1101/2025.05.29.656841

Publisher：Cold Spring Harbor Laboratory  

Abstract

Plants emit a large amount of volatile organic compounds (VOCs) into the atmosphere, reaching approximately 10⁹tons of carbon per year. These biogenic VOCs exhibit significant chemical diversity, with terpenoids being the dominant group, and isoprene accounting for nearly half of the total biogenic VOCs. Due to its high chemical reactivity, isoprene has a strong impact on atmospheric quality and climate.Quercusspecies (Fagaceae) are known to be the main isoprene emitters in the Northern Hemisphere. However, isoprene synthase is unknown in the entire Fagaceae family. Notably, even within a single genus such asQuercus, both isoprene-emitting and non-emitting species are present, yet the molecular basis of this dichotomy remains unclear. Here, we report the identification of theIspSgene from the isoprene-emitting speciesQuercus serrata(QsIspS1) through seasonal transcriptome analysis and its detailed biochemical characterization. We also identified two genes with high sequence similarity toQsIspS1in the genomes of non-emitting species:Q. glauca(QgIspS1-like) andLethocarpus edulis(LeIspS1-like). We discovered mutations in these sequences that likely impair their function. Biochemical analysis revealed thatQgIspS1-likeis a monoterpene synthase, whereasLeIspS1-likeis a pseudogene incapable of isoprene synthesis, explaining these plants’ inability to emit isoprene. Furthermore, site-directed mutagenesis revealed an amino acid that plays a pivotal role in the substrate and product specificities of isoprene synthase. Our findings provide new insight into the molecular mechanisms of isoprene emission diversity in Fagaceae.

DOI： 10.1101/2025.05.17.654689

Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1126/science.adu8988

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41467-025-57994-1

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PubMed

Other Link： https://www.nature.com/articles/s41467-025-57994-1

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/fwb.70004

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s10126-025-10416-1

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Other Link： https://link.springer.com/article/10.1007/s10126-025-10416-1/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.3390/plants14020241

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/ece3.70795

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/mec.17599

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Lasy-Seq (low-cost and easy RNA-seq) is a high-throughput library preparation method for 3' RNA-seq. Usage of oligo(dT) primers with unique index sequences allows simultaneous reverse transcription (RT) reaction and sample indexing. Therefore, each post-RT step, which was performed on a sample-by-sample basis in a conventional method, can be performed on a large number of samples together in a single tube. With the Lasy-Seq, the sequencing-ready library pool can be prepared from a few to several hundred samples in a few days.

DOI： 10.1007/978-1-0716-4204-7_13

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DeLTa-seq is a high-throughput RNA-seq library preparation method that enables quantification of the expression of hundreds of arbitrarily selected genes without RNA purification. This method involves direct reverse transcription using rice leaf lysate and targeted RNA-seq library preparation. DeLTa-seq enables the precise quantification of gene expression with a small number of sequencing reads. This chapter provides detailed information on the design of gene-specific primers, sampling of rice leaves, preparation of lysates, direct-lysate reverse transcription, targeted RNA-seq library preparation, and bioinformatic analysis of DeLTa-seq data.

DOI： 10.1007/978-1-0716-4204-7_12

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/1442-1984.12502

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41467-024-52374-7

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1186/s12870-024-05591-7

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41540-024-00437-2

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PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1101/2024.08.29.610218

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PubMed

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Capsicum peppers are among the oldest domesticated crops in the Americas. Columbus introduced them to Europe, from where they spread to the Far East via Africa, South Asia, and Southeast Asia. However, the details of how Capsicum peppers were introduced into the Asia–Pacific region and their subsequent dispersal remain unknown. Therefore, we investigated the genetic diversity and relationships of Capsicum frutescens in the Asia–Pacific region through restriction site-associated DNA sequencing (RAD-seq) and the sequencing of a variable chloroplast genome locus. The RAD-seq analysis showed that three accessions from Japan are most closely related to those from the Americas and Micronesia, and are distant from most of those from islands and continental Southeast Asia. Although C. frutescens has two chloroplast haplotypes (T and TC), only the T type was found in the Americas and Japan, whereas both types were distributed in other regions. Therefore, we postulate that some C. frutescens accessions were introduced into the Asia–Pacific region from the Americas via the Pacific dispersal route, whereas only the T type was introduced into Japan. Evidence for this Pacific dispersal route of C. frutescens could lead to a reconsideration of the dispersal routes of other crops native to the Americas.

DOI： 10.1007/s10761-024-00750-w

Other Link： https://link.springer.com/article/10.1007/s10761-024-00750-w/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

<jats:title>Abstract</jats:title><jats:p>The Ogasawara Islands, isolated from the continent throughout their geological history, harbor abundant endemic species. However, 32% of the native plant species are on the Japanese Red List, signaling their endangered status. Among these endangered species, <jats:italic>Calanthe hoshii</jats:italic> stands out as highly susceptible to extinction. Two wild and 89 ex situ individuals were alive in 2020, but the last known wild individual died in October 2021, indicating this species may have become extinct in the wild. Despite the conservation efforts under the Act for the Conservation of Endangered Species of Wild Fauna and Flora, the lack of essential information regarding genetic diversity and population structure among the remaining individuals poses a significant obstacle to developing effective conservation measures. In this research, we conducted a genetic analysis of the wild and ex situ individuals, which revealed notably reduced genetic diversity between individuals, with individual heterozygosity levels (1.0 × 10<jats:sup>−5</jats:sup>) measuring one‐ninth of those observed within a closely related species <jats:italic>Calanthe triplicata</jats:italic> (1.5 × 10<jats:sup>−4</jats:sup>). Comprehensive genetic analysis revealed that <jats:italic>C. hoshii</jats:italic> consisted of three genetic clusters of different sizes: cluster 1 comprised 95% of the total population, while clusters 2 and 3, with few individuals, were only found in the ex situ populations at Koishikawa Botanical Garden. Since extant <jats:italic>C. hoshii</jats:italic> maintains a remarkably low genetic diversity at both individual and population levels, it is necessary to consider future management strategies, such as artificial breeding among different clades identified in this study, to safeguard the stability and resilience of this species.</jats:p>

DOI： 10.1111/1442-1984.12479

Language：English   Publishing type：Research paper (scientific journal)  

Abiotic stress is a major factor affecting crop productivity. Chemical priming is a promising strategy to enhance tolerance to abiotic stress. In this study, we evaluated the use of 1-butanol as an effectual strategy to enhance drought stress tolerance in Arabidopsis thaliana. We first demonstrated that, among isopropanol, methanol, 1-butanol, and 2-butanol, pretreatment with 1-butanol was the most effective for enhancing drought tolerance. We tested the plants with a range of 1-butanol concentrations (0, 10, 20, 30, 40, and 50 mM) and further determined that 20 mM was the optimal concentration of 1-butanol that enhanced drought tolerance without compromising plant growth. Physiological tests showed that the enhancement of drought tolerance by 1-butanol pretreatment was associated with its stimulation of stomatal closure and improvement of leaf water retention. RNA-sequencing analysis revealed the differentially expressed genes (DEGs) between water- and 1-butanol-pretreated plants. The DEGs included genes involved in oxidative stress response processes. The DEGs identified here partially overlapped with those of ethanol-treated plants. Taken together, the results show that 1-butanol is a novel chemical priming agent that effectively enhances drought stress tolerance in Arabidopsis plants, and provide insights into the molecular mechanisms of alcohol-mediated abiotic stress tolerance.

DOI： 10.1007/s11103-024-01479-0

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

<jats:title>Abstract</jats:title><jats:p>A short period of exposure to elevated CO<jats:sub>2</jats:sub> is known to decrease evapotranspiration via stomatal closure. Based on theoretical evaluation of a canopy transpiration model, we hypothesized that this decrease in the evapotranspiration of rice under elevated CO<jats:sub>2</jats:sub> was greater under higher temperature conditions due to an increased sensitivity of transpiration to changes in CO<jats:sub>2</jats:sub> induced by the greater vapour pressure deficit. In a temperature gradient chamber‐based experiment, a 200 ppm increase in CO<jats:sub>2</jats:sub> concentration led to 0.4 mm (−7%) and 1.5 mm (−15%) decreases in 12 h evapotranspiration under ambient temperature and high temperature (+3.7°C) conditions, respectively. Model simulations revealed that the greater vapour pressure deficit under higher temperature conditions explained the variations in the reduction of evapotranspiration observed under elevated CO<jats:sub>2</jats:sub> levels between the temperature treatments. Our study suggests the utility of a simple modelling framework for mechanistic understanding of evapotranspiration and crop energy balance system under changing environmental conditions.</jats:p>

DOI： 10.1111/pce.15013

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s10228-024-00976-y

Other Link： https://link.springer.com/article/10.1007/s10228-024-00976-y/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Zoological Society of Japan  

The east coast of the Indochinese Peninsula is a well-known transition zone from subtropical to tropical systems, yet only a small number of studies have been conducted on the biogeography and phylogeography of aquatic organisms in this region. The Hau Giang medaka, Oryzias haugiangensis, was originally described from the Mekong Delta in southern Vietnam, and later reported also from southeastern Thailand, west of the Mekong Delta region. However, the species' full geographic range and population genetic structures remain unknown. Field surveys showed a widespread distribution of this species along the east coast of the Indochinese Peninsula, as far as northern Vietnam. A mitochondrial gene phylogeny and population genetic structure analysis using genome-wide single nucleotide polymorphisms revealed that the populations of O. haugiangensis are highly structuralized along the east coast of Vietnam, with the southernmost Mekong Delta population clearly separated from three populations north of central Vietnam. Further field collections are necessary to determine the boundary between the southern and northern populations, and the presence or absence of a hybrid zone.

DOI： 10.2108/zs230121

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Climate change profoundly affects the timing of seasonal activities of organisms, known as phenology. The impact of climate change is not unidirectional; it is also influenced by plant phenology as plants modify atmospheric composition and climatic processes. One important aspect of this interaction is the emission of biogenic volatile organic compounds (BVOCs), which link the Earth's surface, atmosphere, and climate. BVOC emissions exhibit significant diurnal and seasonal variations and are therefore considered essential phenological traits. To understand the dynamic equilibrium arising from the interplay between plant phenology and climate, this review presents recent advances in comprehending the molecular mechanisms underpinning plant phenology and its interaction with climate. We provide an overview of studies investigating molecular phenology, genome-wide gene expression analyses conducted in natural environments, and how these studies revolutionize the concept of phenology, shifting it from observable traits to dynamic molecular responses driven by gene-environment interactions. We explain how this knowledge can be scaled up to encompass plant populations, regions, and even the globe by establishing connections between molecular phenology, changes in plant distribution, species composition, and climate. Expected final online publication date for the Annual Review of Plant Biology, Volume 75 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI： 10.1146/annurev-arplant-060223-032108

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in Vigna nakashimae, one of the coastal species in the genus Vigna. Using intraspecific variation, we performed a forward genetic analysis and identified a strong QTL region harboring ~200 genes. To further narrow down the candidate genes, we performed a comparative transcriptome analysis, using the genome sequence of azuki bean (V. angularis) as a reference. However the detected differentially-expressed genes (DEGs) did not include those related to salt tolerance. As we suspected that the target gene in V. nakashimae is missing in V. angularis, we sequenced the whole genome sequence of V. nakashimae with long-reads. By re-analyzing the transcriptome data with the new reference genome, we successfully identified POCO1 as a candidate gene, which was missing not only in V. angularis but also in the salt-sensitive accession of V. nakashimae. Further comparative analysis revealed that the tolerant genotypes conserved the ancestral form of the locus, while the sensitive genotypes did not. We also emphasize the pitfalls in our study, such as position effect in a growth chamber, missing important genes in the reference genome, and limited reproducibility of RNA-seq experiments.

DOI： 10.1270/jsbbs.23053

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.2503/hortj.SZD-002

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency. In this study, we aimed to identify novel genomic regions for the net CO2 assimilation rate (A) by combining genome-wide association study (GWAS) and the newly developed rapid closed gas exchange system MIC-100. Using three MIC-100 systems in the field at the vegetative stage, we measured A of 168 temperate japonica rice varieties with six replicates for three years. We found that the modern varieties exhibited higher A than the landraces, while there was no significant relationship between the release year and A among the modern varieties. Our GWAS scan revealed two major peaks located on chromosomes 4 and 8, which were repeatedly detected in the different experiments and in the generalized linear modelling approach. We suggest that high-throughput gas exchange measurements combined with GWAS is a reliable approach for understanding the genetic mechanisms underlying photosynthetic diversities in crop species.

DOI： 10.1007/s11120-023-01065-3

PubMed

Other Link： https://link.springer.com/article/10.1007/s11120-023-01065-3/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

To cope with seasonal environmental changes, organisms have evolved approximately 1-y endogenous circannual clocks. These circannual clocks regulate various physiological properties and behaviors such as reproduction, hibernation, migration, and molting, thus providing organisms with adaptive advantages. Although several hypotheses have been proposed, the genes that regulate circannual rhythms and the underlying mechanisms controlling long-term circannual clocks remain unknown in any organism. Here, we show a transcriptional program underlying the circannual clock in medaka fish ( Oryzias latipes ). We monitored the seasonal reproductive rhythms of medaka kept under natural outdoor conditions for 2 y. Linear regression analysis suggested that seasonal changes in reproductive activity were predominantly determined by an endogenous program. Medaka hypothalamic and pituitary transcriptomes were obtained monthly over 2 y and daily on all equinoxes and solstices. Analysis identified 3,341 seasonally oscillating genes and 1,381 daily oscillating genes. We then examined the existence of circannual rhythms in medaka via maintaining them under constant photoperiodic conditions. Medaka exhibited approximately 6-mo free-running circannual rhythms under constant conditions, and monthly transcriptomes under constant conditions identified 518 circannual genes. Gene ontology analysis of circannual genes highlighted the enrichment of genes related to cell proliferation and differentiation. Altogether, our findings support the “histogenesis hypothesis” that postulates the involvement of tissue remodeling in circannual time-keeping.

DOI： 10.1073/pnas.2313514120

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.

DOI： 10.1111/mec.17216

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.

DOI： 10.1038/s41598-023-48293-0

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F₂ population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.

DOI： 10.1186/s12284-023-00621-8

Open Access

PubMed

Other Link： https://link.springer.com/article/10.1186/s12284-023-00621-8/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

Abstract

Young seedlings use nutrients stored in the seeds to grow and acquire photosynthetic potential. This process, called seedling establishment, involves a developmental phase transition from heterotrophic to autotrophic growth. Some membrane-trafficking mutants ofArabidopsis thaliana(Arabidopsis), such as thekatamari2(kam2) mutant, exhibit growth arrest during seedling development, with a portion of individuals failing to develop true leaves on sucrose-free solid medium. However, the reason for this seedling arrest is unclear. In this study, we show that seedling arrest is a temporal growth arrest response that occurs not only inkam2but also in wild-type Arabidopsis; however, the threshold for this response is lower inkam2than in the wild type. A subset of the arrestedkam2seedlings resumed growth after transfer to fresh sucrose-free medium. Growth arrest inkam2on sucrose-free medium was restored by increasing the gel concentration of the medium or covering the surface of the medium with a perforated plastic sheet. Wild-type Arabidopsis seedlings were also arrested when the gel concentration of sucrose-free medium was reduced. RNA sequencing revealed that transcriptomic changes associated with the rate of seedling establishment were observed as early as 4 days after sowing. Our results suggest that the growth arrest of bothkam2and wild-type seedlings is an adaptive stress response and is not simply caused by the lack of a carbon source in the medium. This study provides a new perspective on an environmental stress response under unfavorable conditions during the phase transition from heterotrophic to autotrophic growth in Arabidopsis.

DOI： 10.1101/2023.11.05.565727

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Authorea, Inc.  

<p id="p1">The Bonin Islands, comprising of the Mukojima, Chichijima, and HahajimaIslands, are known for their isolated and distinctive habitats, hostinga diverse array of endemic flora and fauna. In these islands, adaptiveradiation has played a remarkable role in speciation, particularlyevident in the Callicarpa genus that is represented by threespecies: Callicarpa parvifolia and Callicarpa glabraexclusive to the Chichijima Islands, and Callicarpa subpubescens,distributed across the entire Bonin Islands. Notably, C.subpubescens exhibits multiple ecotypes, differing in leaf hairdensity, flowering time, and tree size. In this study, we useddouble-digest restriction site–associated DNA sequencing to analyzespecies, ecotypes and geographical variations within Callicarpain the Bonin Islands. We aimed to determine detailed phylogeneticrelationships, investigate species and ecotype diversification patterns,estimate divergence times, and explore cryptic species using genetic andphenotypic data. Genetic analysis revealed that C. parvifolia andC. glabra formed a single, distinct genetic groups. Conversely,C. subpubescens showed seven genetic groups corresponding todifferent ecotypes and regions, with one ecotype derived from thehybridization of two others. Phylogenetic and population demographyanalyses, focusing on six Chichijima and Hahajima Islands–basedspecies/ecotypes, indicated the divergence of an ecotype adapted to tallmesic forests approximately 170 kya, whereas the other fivespecies/ecotypes diverged nearly simultaneously around 73–77 kya.Environmental changes during the glacial period likely contributed tothis process of adaptive radiation. Moreover, leaf morphology, floweringtime, and genetic analyses suggested the presence of two cryptic specieswithin C. subpubescens.</p>

DOI： 10.22541/au.169865467.72711081/v1

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Allium macrostemon Bunge, commonly referred to as "no-biru" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using RAD-Seq. Our analyses distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, groups A and B showed clear evidence of bulb propagation, while group C did not. Group C formed four subgroups: C1, C2, C3, and C4. Hybridization between subgroup C1 and either group A, B, or both, resulted in the emergence of subgroups C2, C3, and C4. Thus, groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status.

DOI： 10.1038/s41598-023-43537-5

Open Access

PubMed

Other Link： https://www.nature.com/articles/s41598-023-43537-5

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of ‘ghost introgression’ in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthys in Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population‐genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorus and A. poptae, but the large time‐lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted.

DOI： 10.1111/jeb.14223

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be developed for large-scale transcriptomic studies such as time-series analysis and genome-wide association studies in allopolyploids. In this study, we employed a 3' RNA-seq utilizing 3' untranslated regions (UTRs) containing frequent mutations among homeologous genes, compared to coding sequence. Among the 3' RNA-seq protocols, we examined a low-cost method Lasy-Seq using an allohexaploid bread wheat, Triticum aestivum. HISAT2 showed the best performance for 3' RNA-seq with the least mapping errors and quick computational time. The number of detected homeologs was further improved by extending 1 kb of the 3' UTR annotation. Differentially expressed genes in response to mild cold treatment detected by the 3' RNA-seq were verified with high-coverage conventional RNA-seq, although the latter detected more differentially expressed genes. Finally, downsampling showed that even a 2 million sequencing depth can still detect more than half of expressed homeologs identifiable by the conventional 32 million reads. These data demonstrate that this low-cost 3' RNA-seq facilitates large-scale transcriptomic studies of allohexaploid wheat and indicate the potential application to other allopolyploid species.

DOI： 10.1093/nargab/lqad067

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall in Japan. Chloroplast DNA variations and genome-wide single-nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal the evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario that assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, and it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.

DOI： 10.1038/s41437-023-00637-2

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

BACKGROUND: Phylogeographical approaches explain the genetic diversity of local organisms in the context of their geological and geographic environments. Thus, genetic diversity can be a proxy for geological history. Here we propose a genus of woodland isopod, Ligidium, as a marker of geological history in relation to orogeny and the Quaternary glacial cycle. RESULTS: Mitochondrial analysis of 721 individuals from 97 sites across Japan revealed phylogenetic divergence between the northeastern and southwestern Japan arcs. It also showed repeated population expansions in northeastern Japan in response to Quaternary glacial and interglacial cycles. Genome-wide analysis of 83 selected individuals revealed multiple genetic nuclear clusters. The genomic groupings were consistent with the local geographic distribution, indicating that the Ligidium phylogeny reflects its regional history. CONCLUSION: Ligidium DNA sequence analysis can provide insight into the geological, geographical, and paleoenvironmental history of the studied region.

DOI： 10.1186/s12862-023-02144-8

Open Access

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.aqrep.2023.101650

Open Access

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

Repeated colonizations and resultant hybridization may increase lineage diversity on an island if introgression occurs only in a portion of the indigenous island lineage. Therefore, to precisely understand how island biodiversity was shaped, it is essential to reconstruct the history of secondary colonization and resultant hybridization both in time and space. In this study, we reconstructed the history of multiple colonizations of the Oryzias woworae species group, a freshwater fish group of the family Adrianichthyidae, from Sulawesi Island to its southeast satellite island, Muna Island. Phylogenetic and species tree analyses using genome-wide single-nucleotide polymorphisms revealed that all local populations on Muna Island were monophyletic, but that there were several genetically distinct lineages within the island. Population structure and phylogenetic network analyses demonstrated that colonization of this island occurred more than once, and that secondary colonization and resultant introgressive hybridization occurred only in one local population on the island. The spatially heterogeneous introgression induced by the multiple colonizations were also supported by differential admixture analyses. In addition, the differential admixture analyses detected reverse colonization from Muna Island to the Sulawesi mainland. Coalescence-based demographic inference estimated that these mutual colonizations occurred during the middle to late Quaternary period, during which sea level repeatedly declined; this indicates that the colonizations occurred via land bridges. We conclude that these mutual colonizations between Muna Island and the Sulawesi mainland, and the resultant spatially heterogeneous introgression shaped the current biodiversity of this species group in this area.

DOI： 10.1016/j.ympev.2023.107804

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s13355-023-00832-x

Other Link： https://link.springer.com/article/10.1007/s13355-023-00832-x/fulltext.html

Publisher：Cold Spring Harbor Laboratory  

Summary

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of both positive and negative effects of mixed planting on plant resistance, called associational resistance and susceptibility. We used genome-wide polymorphisms of the plant speciesArabidopsis thalianato identify genotype pairs that enhance associational resistance to herbivory. By quantifying neighbor interactions among 199 genotypes grown in a randomized block design, we predicted that 823 of the 19,701 candidate pairs could reduce herbivory through associational resistance. We planted such pairs with predicted associational resistance in mixtures and monocultures and found a significant reduction in herbivore damage in the mixtures. Our study highlights the potential application to assemble genotype mixtures with positive biodiversity effects.

DOI： 10.1101/2023.05.19.541411

Language：English   Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications, Ltd  

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and inevitably influenced by surrounding ecological community members, and whether and how ecological communities influence the rice performance under field conditions has been underexplored.

In the present study, we demonstrate an ecological-network-based approach to detect potentially influential, previously ignored organisms for rice (Oryza sativa). First, we established small experimental rice plots, and measured rice growth and monitored ecological community dynamics intensively and extensively using quantitative environmental DNA analysis in 2017 in Japan. We detected more than 1000 species in the rice plots, and nonlinear time series analysis detected 52 potentially influential organisms with lower-level taxonomic information.

The results of the time series analysis were validated in 2019. In 2019, we focused on two species, Globisporangium nunn and Chironomus kiiensis, whose abundance was manipulated in artificial rice plots. The responses of rice, namely, the growth rate and gene expression patterns, were measured before and after the manipulation. We confirmed that, especially in the G. nunn-added treatment, rice growth rate and gene expression pattern were changed.

In the present study, we demonstrated that intensive monitoring of an agricultural system and the application of nonlinear time series analysis were helpful to identify influential organisms under field conditions. Although the effects of the manipulations were relatively small, the research framework presented here has future potential to harness the ecological complexity and utilize it in agriculture. Our proof-of-concept study would be an important basis for the further development of field-basis system management.

DOI： 10.7554/elife.87202.1

Open Access

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

Population sizes of the Japanese red coral Corallium japonicum have been severely affected by poaching and overfishing. Although genetic structure and connectivity patterns are considered important parameters for conservation strategies, there are few studies focusing on the population genetics of C. japonicum in the Northwest Pacific. We examined the genetic population structure of C. japonicum, in the Northwest Pacific. We used restriction-site-associated DNA sequencing (RAD-seq), which can be used to identify genome-wide single-nucleotide polymorphism (SNPs), to reveal detailed within-species genetic variations. Using the variable SNP loci identified from this analysis, we successfully evaluated the population-level genetic diversity and patterns of gene flow among multiple populations of C. japonicum around Japan. The results of genetic analysis basically showed that gene flow is widely maintained in the geographic range examined in this study, but the analysis in combination with larval dispersal simulations revealed several populations that were genetically distinct from the other populations, suggesting geographically limited gene flows. The information obtained from this study will be useful for the design of effective management schemes for C. japonicum, which is under threat from overfishing.

DOI： 10.3389/fmars.2023.1052033

Open Access

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

Abstract

The importance of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite accumulated knowledge concerning adult hybrid variations, how hybridization affects ontogenetic allometry is less well understood. Herein, we assessed the effects of hybridization on the postnatal ontogenetic allometry in skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with various degrees of admixture, formed by male migration of Japanese to Taiwanese macaques. Hybridization parallelly shifted the ontogenetic trajectories of the overall skull shape in an almost additive manner. Transgressive variations in the overall skull shape were observed mainly in non-allometric components. Hybridization lifted the restriction found in Japanese macaques on the growth rate of the maxillary sinus (the hollow space in the face), producing hybrids with a mosaic pattern, i.e., the maxillary sinus is as large as that in Taiwanese macaques, although the overall skull shape is intermediate. Our findings suggest that the transgressive variations can be caused by prenatal shape modifications and the lifting of the genetic restriction on the regional growth rate, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

DOI： 10.1101/2023.04.19.536293

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

PREMISE: The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula. METHODS: We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses. RESULTS: The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance. CONCLUSIONS: The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.

DOI： 10.1002/ajb2.16166

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s10592-023-01517-2

Other Link： https://link.springer.com/article/10.1007/s10592-023-01517-2/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Severe genetic redundancy is particularly clear in gene families encoding plant hormone receptors, each subtype sharing redundant and specific functions. Genetic redundancy of receptor family members represents a major challenge for the functional dissection of each receptor subtype. A paradigmatic example is the perception of the hormone (+)-7-iso-jasmonoyl-L-isoleucine, perceived by several COI1-JAZ complexes; the specific role of each receptor subtype still remains elusive. Subtype-selective agonists of the receptor are valuable tools for analyzing the responses regulated by individual receptor subtypes. We constructed a stereoisomer library consisting of all stereochemical isomers of coronatine (COR), a mimic of the plant hormone (+)-7-iso-jasmonoyl-L-isoleucine, to identify subtype-selective agonists for COI1-JAZ co-receptors in Arabidopsis thaliana and Solanum lycopersicum. An agonist selective for the Arabidopsis COI1-JAZ9 co-receptor efficiently revealed that JAZ9 is not involved in most of the gene downregulation caused by COR, and the degradation of JAZ9-induced defense without inhibiting growth.

DOI： 10.1038/s42003-023-04709-1

Open Access

PubMed

Other Link： https://www.nature.com/articles/s42003-023-04709-1

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

The glucosinolate–myrosinase defense system (GMDS), characteristic of Brassicales, is involved in plant defense. Previous single-cell transcriptomic analyses have reported the expression profiles of multiple GMDS-related cell types (i.e. myrosinase-rich myrosin idioblasts and multiple types of potential glucosinolate synthetic cells as well as a candidate S-cell for glucosinolate accumulation). However, differences in plant stages and cell-type annotation methods have hindered comparisons among studies. Here, we used the single-cell transcriptome profiles of extended Arabidopsis leaves and verified the distribution of previously used markers to refine the expression profiles of GMDS-associated cell types. Moreover, we performed beta-glucuronidase promoter assays to confirm the histological expression patterns of newly obtained markers for GMDS-associated candidates. As a result, we found a set of new specific reporters for myrosin cells and potential glucosinolate-producing cells.

DOI： 10.1093/pcp/pcac167

PubMed

Other Link： https://academic.oup.com/pcp/article-pdf/64/2/234/49377821/pcac167.pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared with other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between 2 rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in 2 reciprocal backcross populations. Markers showing either of the 2 types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between 2 backcross families and 2 developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane’s rule in terms of hybrid inviability does not hold. Additionally, quantitative trait loci (QTL) mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step toward a comprehensive understanding of speciation and morphological diversification of rockfishes.

DOI： 10.1093/jhered/esad007

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing β-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the root apoplastic fraction of ichg mutants, the isoflavone glycosides contents were significantly increased while isoflavone aglycone contents were decreased, indicating that ICHG hydrolyzes isoflavone glycosides into aglycones in the root apoplast. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and WTs. Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions, either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential in isoflavone-mediated plant-microbe interactions.

DOI： 10.1093/pcp/pcad012

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

As biodiversity loss continues, there is an urgent need to develop efficient conservation measures to protect diversity with limited conservation resources. Conservation targets have generally been selected based on their population size, but more detailed assessments clarifying the phylogenetic genetic status, history, and phylogenetic uniqueness of rare species is crucial to set more appropriate and effective conservation measures. In Japan, the Act on Conservation of Endangered Species of Wild Fauna and Flora designated endangered plants with high conservation priority, but &amp;gt;40% of these species also grow overseas. We conducted comparative analyses based on ddRADseq and MIG-seq to evaluate the population conservation status and value of Vaccinium emarginatum and Elatostema platyphyllum which are growing across national borders at the eastern edge of their species distribution range. The analyses revealed contrasting conservation status between the two species; the Japanese population of V. emarginatum had lower genetic diversity at the individual level and phylogenetically differentiated from Taiwanese populations, while that of E. platyphyllum had higher diversity at the individual level and is a relatively recent migrant with little phylogenetical differentiation from Taiwanese populations. The two species, which share the common feature of being critically rare in Japan, showed contrasting genetic/phylogenetic characteristics. This study provided useful information for appropriate conservation measures based on species’ phylogenetic traits and genetic diversity.

DOI： 10.3389/fevo.2023.1093321

Open Access

Publishing type：Research paper (scientific journal)   Publisher：Informa UK Limited  

DOI： 10.1080/1343943x.2022.2160362

Open Access

Language：English   Publishing type：Research paper (scientific journal)  

The sensation of pungency generated by capsaicinoids is a characteristic trait of chili peppers (Capsicum spp.), and the presence or absence of pungency is central in determining its usage as a spice or a vegetable. In the present study, we aimed to clarify the heredity and genetic factors involved in the deficiency of pungency (quite low pungency) that is uniquely observed in the Japanese chili pepper 'Shishito' (Capsicum annuum). First, the F2 population ('Shishito' × pungent variety 'Takanotsume') was used for segregation analysis, and pungency level was investigated using capsaicinoid quantification with high-performance liquid chromatography. Also, restriction site associated DNA sequencing of the F2 population was performed, and genetic map construction and quantitative trait locus (QTL) mapping were implemented. The results indicated that the F2 population showed varying capsaicinoid content and two major QTLs were detected, Shql3 and Shql7, which explained 39.8 and 19.7% of the genetic variance, respectively. According to these results, the quite low pungency of 'Shishito' was a quantitative trait that involved at least the two loci. Further, this trait was completely separate from general non-pungent traits controlled by individual recessive genes, as described in previous studies. The present study is the first report to investigate the genetic mechanism of pungency deficiency in Japanese chili peppers, and our results provide new insights into the genetic regulation of pungency in chili pepper.

DOI： 10.1007/s00438-022-01975-2

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

The long‐term dynamics of the transcriptome under natural field conditions remain unclear. We conducted comprehensive gene expression analyses of rice leaves and roots grown under natural field conditions for a long period, from the tillering stage to the ripening stage. In this experiment, changes in the transcriptome were captured in relation to microclimatic parameters, particularly potential evaporation (Ep), which is a multiple meteorological factor and acts as an indicator of transpirational demand. The results indicated  that many genes were regulated by changes in temperature and Ep in both leaves and roots. Furthermore, the correlation between gene expression and meteorological factors differed significantly between the vegetative and reproductive stages. Since Ep triggers transpiration, we analyzed aquaporin gene expression, which is responsible for water transport, and found that many aquaporin genes in leaves were positively correlated with Ep throughout the growth period, whereas in roots, two plasma membrane intrinsic aquaporins, PIP2;4 and PIP2;5 were strongly correlated with Ep during reproductive growth. Other genes closely related to productivity, such as those involved in nutrient absorption and photosynthesis, exhibited different responses to meteorological factors at different growth stages. The stage‐dependent shift in the microclimate response provides an important perspective on crop physiology in light of climate change.

DOI： 10.1111/pce.14439

PubMed

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/pce.14439

Language：English   Publishing type：Research paper (scientific journal)  

Nitrogen (N) is an important macronutrient for plant growth and development. Currently, N fertilizers are required for the efficient production of modern crops such as rice due to their limited capacity to take up N when present at low concentrations. Wild rice represents a useful genetic resource for improving crop responses to low nutrient stress. Here, we describe the isolation and characterization of an introgression line, KRIL37, that carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari (KH) background. This line was found to grow better under low N conditions and have similar or lower C/N ratios in aerial portions compared to those in the parental KH cultivar, suggesting that KRIL37 has a higher capacity to take up and assimilate N when present at low concentrations. KRIL37 performance in the field was also better than that of KH cultivated without N and fertilizer (-F). Transcriptome analyses of 3-week-old seedlings based on RNA-sequencing revealed that KH induced a wider suite of genes than the tolerant line KRIL37 in response to low N conditions. Some ammonium transporters and N assimilation genes were found to be induced under low N in KRIL37, but not in KH. Our findings suggest that the superior growth performance of KRIL37 under limited N conditions could be due to the expression of wild alleles influencing N uptake and assimilation. Our study demonstrates the potential to use wild rice genomes to improve modern crops for low nutrient tolerance.

DOI： 10.1093/pcp/pcac097

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Water scarcity is a serious agricultural problem causing significant losses to crop yield and product quality. The development of technologies to mitigate the damage caused by drought stress is essential for ensuring a sustainable food supply for the increasing global population. We herein report that the exogenous application of ethanol, an inexpensive and environmentally friendly chemical, significantly enhances drought tolerance in Arabidopsis thaliana, rice and wheat. The transcriptomic analyses of ethanol-treated plants revealed the upregulation of genes related to sucrose and starch metabolism, phenylpropanoids and glucosinolate biosynthesis, while metabolomic analysis showed an increased accumulation of sugars, glucosinolates and drought-tolerance-related amino acids. The phenotyping analysis indicated that drought-induced water loss was delayed in the ethanol-treated plants. Furthermore, ethanol treatment induced stomatal closure, resulting in decreased transpiration rate and increased leaf water contents under drought stress conditions. The ethanol treatment did not enhance drought tolerance in the mutant of ABI1, a negative regulator of abscisic acid (ABA) signaling in Arabidopsis, indicating that ABA signaling contributes to ethanol-mediated drought tolerance. The nuclear magnetic resonance analysis using 13C-labeled ethanol indicated that gluconeogenesis is involved in the accumulation of sugars. The ethanol treatment did not enhance the drought tolerance in the aldehyde dehydrogenase (aldh) triple mutant (aldh2b4/aldh2b7/aldh2c4). These results show that ABA signaling and acetic acid biosynthesis are involved in ethanol-mediated drought tolerance and that chemical priming through ethanol application regulates sugar accumulation and gluconeogenesis, leading to enhanced drought tolerance and sustained plant growth. These findings highlight a new survival strategy for increasing crop production under water-limited conditions.

DOI： 10.1093/pcp/pcac114

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s10681-022-03073-1

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing, we found sex chromosomes in nine species that all had XY systems, with a species being possibly modified by multiple loci. Seven species (O. woworae, O. asinua, O. wolasi, O. matanensis, O. celebensis, O. hadiatyae, and O. dopingdopingensis) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of O. eversi was LG4, which has not been reported as a sex chromosome in any other medaka species. In O. sarasinorum, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. No significant signatures for sex chromosomes were identified in the other four species (O. marmoratus, O. nigrimas, O. nebulosus, and O. orthognathus). Frequent turnovers and the great diversity of the sex chromosomes will make Sulawesian medaka species a model system for investigating the driving forces and consequences of sex chromosome turnover.

DOI： 10.1111/jeb.14076

PubMed

Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/edn3.337

Open Access

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/edn3.337

Language：English   Publishing type：Research paper (scientific journal)  

KEY MESSAGE: A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F2 and F3 segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.

DOI： 10.1007/s00122-022-04125-9

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/mec.16447

Open Access

Web of Science

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/pce.14319

Web of Science

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a non-brooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.

DOI： 10.1111/mec.16555

PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

The differences between plants grown in field and controlled environments have long been recognised; however, few studies have addressed the underlying molecular mechanisms. Here, we show fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments by utilising SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature, and humidity of field environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening; those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature only affects transcriptome dynamics in the morning. We found upregulation of genes related to biotic and abiotic stress, whose expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results accelerate the understanding of plant responses to field environments for both field and laboratory studies.

DOI： 10.1111/pce.14367

Open Access

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

Sulawesi is a biodiversity hotspot for ricefishes (Adrianichthyidae), with many species endemic to the central part of this island in single ancient lakes or lake systems. Frequent vicariance by lake fragmentation since the Pliocene may be largely responsible for diversification in this family. In this study, we demonstrate that not only lacustrine species but also riverine species in this area are also deeply divergent even within a single river system. A mitochondrial phylogeny revealed that a ricefish population newly discovered from Cerekang River is sister to Oryzias dopingdopingensis Mandagi, Mokodongan, Tanaka, & Yamahira, another riverine species endemic to Doping-doping River. However, the Cerekang Oryzias was genetically isolated from O. dopingdopingensis, despite that Cerekang River and Doping-doping River share a connection across estuarine waters. This separation was supported by phylogenomic trees and population genetic structure analyses based on genome-wide single nucleotide polymorphisms. Coalescent-based demographic inference demonstrated that the ancestral population of these two riverine ricefishes had experienced a substantial population decrease and subsequently diverged into two sub-populations. Because the Cerekang Oryzias was also morphologically distinguished from O. dopingdopingensis, we described it as a new species, O. landangiensis. We infer that O. landangiensis and O. dopingdopingensis are of lake-origin and are relic species which were left in these rivers after the lake disappeared, and that they have lost their dispersal ability when inhabiting the ancient lake. The lost dispersal ability possibly contributed to the formation of the biodiversity hotspot for this fish group on this island.

DOI： 10.1016/j.ympev.2022.107519

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.2141/jpsa.0210037

Open Access

Web of Science

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/tpj.15767

Web of Science

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.envexpbot.2021.104724

Open Access

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/jpy.13233

Web of Science

PubMed

Publisher：Cold Spring Harbor Laboratory  

Abstract

Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

DOI： 10.1101/2022.03.28.486085

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Research Square Platform LLC  

<title>Abstract</title>
Loquat (<italic>Eriobotrya japonica</italic>) is thought to have originated in southeastern China and spread as a cultivated plant worldwide. Many of the loquat genetic resources collected internationally are of unknown origin, and their genetic background requires clarification. This study analyzed the genetic diversity of 95 accessions by using SNP markers obtained by restriction site–associated DNA sequencing. Principal component analysis and multidimensional scaling analysis broadly classified loquat into three groups: 1) Japanese and Chinese cultivars and some Japanese strains (wild plants that are not used for commercial cultivation), 2) Vietnamese, Israeli, Greek, USA, and Mexican cultivars and strains, and 3) other Japanese strains. Group 2 is cultivated mostly outside of East Asia and was clearly distinct from the other groups, indicating that varieties of unknown origin with genetic backgrounds different from those of Japanese and Chinese cultivars may have been introduced to Mediterranean countries and North America (USA and Mexico). The fact that Japanese and Chinese cultivars belong to the same group confirms that the current Japanese cultivars are derived from genetic resources brought from China. Some of group 1 may have been introduced to Japan before excellent varieties were developed in China, while group 3 may have been indigenous to Japan.

DOI： 10.21203/rs.3.rs-1331382/v1

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Other Link： https://www.researchsquare.com/article/rs-1331382/v1.html

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s10681-022-02970-9

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DOI： 10.1371/journal.pone.0265994

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DOI： 10.1093/pcp/pcab088

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DOI： 10.1080/14772000.2021.1971792

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DOI： 10.1007/s10265-021-01339-8

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Other Link： https://link.springer.com/article/10.1007/s10265-021-01339-8/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/jeb.13932

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DOI： 10.1002/ece3.8050

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/ece3.8050

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DOI： 10.1016/j.ympev.2021.107230

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DOI： 10.1038/s41598-021-98822-y

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DOI： 10.1007/s00122-021-03870-7

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DOI： 10.1007/s00438-021-01806-w

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DOI： 10.1071/FP21088

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DOI： 10.1186/s12864-021-07908-4

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Publisher：Cold Spring Harbor Laboratory  

Plants must respond to various environmental factors that change seasonally. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis in a wild population of <italic>Arabidopsis halleri</italic> ssp. <italic>gemmifera</italic>, a sister species of <italic>Arabidopsis thaliana</italic>. To analyze the function of these seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends using <italic>A. thaliana</italic>. <italic>Arabidopsis thaliana</italic> plants were cultured under conditions that mimicked average monthly temperatures and daylengths in a "smart growth chamber mini," a hand-made low-cost small chamber. Under different short-term incubations, the seasonal trends of 1627 seasonally oscillating genes were mimicked. These seasonally oscillating genes had varying temporal responsiveness (constant, transient, and incremental). Our findings suggest that plants perceive and integrate information about environmental stimuli in the field by combining seasonally oscillating genes with temporal responsiveness.

DOI： 10.1101/2021.08.02.454700

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s00338-021-02145-3

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DOI： 10.17660/ActaHortic.2021.1318.26

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DOI： 10.1111/jeb.13874

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DOI： 10.1093/dnares/dsab004

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DOI： 10.1038/s41467-021-23766-w

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DOI： 10.1038/s41438-021-00569-0

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DOI： 10.1038/s41598-021-90791-6

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DOI： 10.1002/ece3.7545

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DOI： 10.1101/2021.05.27.445368

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DOI： 10.1111/jbi.14121

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DOI： 10.3390/genes12050735

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DOI： 10.1038/s41437-021-00417-w

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DOI： 10.1038/s41437-021-00408-x

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DOI： 10.1038/s41598-021-87384-8

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DOI： 10.1093/biolinnean/blab033

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DOI： 10.1038/s41598-021-86983-9

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DOI： 10.1038/s41437-020-00396-4

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DOI： 10.1038/s41437-020-00401-w

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DOI： 10.1093/jxb/eraa546

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DOI： 10.1038/s41467-021-21697-0

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DOI： 10.1007/s10327-021-00980-4

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DOI： 10.1093/jxb/eraa519

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DOI： 10.1093/g3journal/jkab017

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DOI： 10.1038/s41598-021-82731-1

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DOI： 10.1111/evo.14120

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DOI： 10.3389/fpls.2021.618245

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DOI： 10.1371/journal.pone.0245316

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DOI： 10.1007/s00705-020-04838-6

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DOI： 10.1038/s41477-020-00822-9

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DOI： 10.1002/pld3.286

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DOI： 10.1007/s10519-020-10012-0

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DOI： 10.3390/horticulturae6040071

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DOI： 10.1038/s41598-020-74623-7

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

<title>Abstract</title>Using current mRNA quantification methods such as RT-qPCR and RNA-Seq, it is very difficult to examine thousands of tissue samples due to cost and labor of RNA extraction and quantification steps. Here, we developed Direct-RT buffer in which homogenization of tissue samples and direct-lysate reverse transcription can be conducted without RNA purification. We showed that appreciate concentration of DTT prevented RNA degradation but not RT in the lysates of several plants’ tissues, yeast, and zebrafish larvae. Using the buffer, direct reverse transcription on the lysates could produce comparable amount of cDNA with that synthesized from purified RNA. Furthermore, we established DeLTa-Seq (<bold>D</bold>ir<bold>e</bold>ct-<bold>L</bold>ysate reverse transcription and <bold>Ta</bold>rgeted RNA-<bold>Seq</bold>) method. DeLTa-Seq is a cost-effective, high-throughput and highly-precise quantification method for the expressions of hundreds of genes. It enables us to conduct large-scale studies using thousands of samples such as chemical screening, field experiments and studies focusing on individual variability.

DOI： 10.1101/2020.09.15.299180

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/nph.16627

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DOI： 10.1038/s41477-020-00757-1

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/nph.16647

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J-GLOBAL

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1098/rstb.2019.0548

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DOI： 10.1038/s41598-020-69941-9

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DOI： 10.1007/s10592-020-01275-5

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DOI： 10.1093/aob/mcaa072

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Language：English   Publishing type：Research paper (scientific journal)  

RNA-Seq is a powerful method for transcriptome analysis used in varied field of biology. Although several commercial products and hand-made protocols enable us to prepare RNA-Seq library from total RNA, their cost are still expensive. Here, we established a low-cost and multiplexable whole mRNA-Seq library preparation method for illumine sequencers. In order to reduce cost, we used cost-effective and robust commercial regents with small reaction volumes. This method is a whole mRNA-Seq, which can be applied even to non-model organisms lacking the transcriptome references. In addition, we designed large number of 3' PCR primer including 8 nucleotides barcode sequences for multiplexing up to three hundreds samples. To summarize, it is possible with this protocol to prepare 96 directional RNA-Seq libraries from purified total RNA in three days and can be pooled for up to three hundred libraries. This is beneficial for large scale transcriptome analysis in many fields of animals and plant biology.

DOI： 10.21769/BioProtoc.3496

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/aob/mcaa062

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DOI： 10.1371/journal.pone.0234803

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DOI： 10.1038/s41467-020-15896-4

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Language：Japanese  

DOI： 10.1101/2020.05.10.086611

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s12686-018-1050-z

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DOI： 10.1093/aobpla/plz080

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CiNii Research

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DOI： 10.1038/s41396-019-0519-4

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s42003-019-0739-1

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Other Link： http://www.nature.com/articles/s42003-019-0739-1.pdf

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41437-019-0239-6

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DOI： 10.1186/s12870-019-2117-z

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DOI： 10.1534/g3.119.400708

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Language：English   Publishing type：Research paper (other academic)  

DOI： 10.1101/845735

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DOI： 10.1093/jxb/erz304

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DOI： 10.3897/phytokeys.134.38216

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DOI： 10.1111/evo.13821

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DOI： 10.1371/journal.pone.0220981

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DOI： 10.1007/s00248-018-1271-4

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Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Island in 2018. Their genetic diversity is considered lower than that of other Japanese native horse breeds; thus, it needs to be investigated for sustainable conservation of this breed. Historical records revealed that several Taishu individuals were released areas off-Tsushima Island in mid-1980s. At present, Taishu horses living outside of Tsushima Island, hereafter referred to as Non-Tsushima Taishus (NTTs), are tagged. However, the genetic structure of the NTT individuals remains unclear, and such individuals are not included in the current mating plans for Taishu horses. Herein, we examined the genetic structure of 18 NTT individuals by comparing their genomic (SNP) information with that of individuals on Tsushima Island (TT), four other native Japanese breeds, and one Anglo-Arabian breed by using ddRAD-seq. We found that all individuals related to the Taishu can be grouped in one cluster, which was separated from other horse breeds. Patterns of specific and shared SNPs in NTT individuals closely resembled those of TT individuals, suggesting very minor genetic differences. Meanwhile, the heterozygosity of NTT individuals was slightly higher than that of TT individuals, and many NTT individuals were of fertile age, suggesting that the pedigree of NTT individuals would be useful in breed conservation plans for Taishu horses. Based on their genomic information, we also reconstructed the pedigree structures of four NTT individuals with no family information. The inclusion of NTT individuals in future mating plans on Tsushima Island may be an effective and feasible method for conserving the Taishu horse breed in Japan.

DOI： 10.1294/jes.30.33

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1126/science.aau5656

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1098/rsbl.2018.0577

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Other Link： https://royalsocietypublishing.org/doi/pdf/10.1098/rsbl.2018.0577

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41598-019-43600-0

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DOI： 10.1534/g3.119.201011

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DOI： 10.1186/s12870-019-1705-2

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DOI： 10.3382/ps/pey493

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DOI： 10.1038/s41477-019-0381-4

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DOI： 10.1038/s41477-018-0338-z

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DOI： 10.1007/s00122-018-3195-2

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Other Link： http://link.springer.com/content/pdf/10.1007/s00122-018-3195-2.pdf

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DOI： 10.1371/journal.pone.0226116

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DOI： 10.3389/fgene.2019.00787

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DOI： 10.1101/451609

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DOI： 10.1016/j.marenvres.2018.05.021

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Language：English   Publishing type：Research paper (scientific journal)  

OBJECTIVE: Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity within these populations remains unknown. In this study, we estimated the genetic diversity and key quantitative genetic parameters such as heritability and genomic breeding value for body size traits by means of genomic best linear unbiased prediction to assess the genetic health of these populations. RESULTS: Ninety-nine and 83 females from the selective and random groups, respectively, were genotyped at 2350 putative SNPs by means of double digest restriction associated DNA sequencing. The genetic diversity in the selectively bred group was low, as were the estimated heritability and prediction accuracy for length and weight (h2 = 0.26-0.28; accuracy = 0.34), compared to the randomly bred group (h2 = 0.50-0.60; accuracy = 0.51-0.54). Although the tested sample size was small, these results suggest that further selection is difficult for the selectively bred population, while there is some potential for the randomly bred group, especially with the aid of genomic information.

DOI： 10.1186/s13104-018-3663-4

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1104/pp.17.01259

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DOI： 10.1038/s41598-018-26735-4

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DOI： 10.1038/s41467-018-04596-9

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DOI： 10.1093/aob/mcx182

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DOI： 10.1111/mec.14515

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DOI： 10.1093/dnares/dsy005

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DOI： 10.3389/fpls.2018.01880

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DOI： 10.1038/s41467-017-02053-7

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DOI： 10.1111/nph.14744

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Publisher：Cold Spring Harbor Laboratory  

DOI： 10.1101/194118

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.7554/eLife.26845.001

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DOI： 10.1093/dnares/dsx012

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DOI： 10.1093/bioinformatics/btx049

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DOI： 10.1007/s10265-017-0917-5

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DOI： 10.1111/mec.14016

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DOI： 10.1270/jsbbs.16059

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DOI： 10.1038/ncomms13295

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DOI： 10.1093/femsec/fiw176

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DOI： 10.1111/mec.13721

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DOI： 10.3389/fpls.2015.01114

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Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-15H01237/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier B.V.  

DOI： 10.1016/j.plgene.2015.10.003

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English  

DOI： 10.1371/journal.pone.0150788

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DOI： 10.3389/fpls.2016.00087

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Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15J12133/

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DOI： 10.1266/ggs.15-00071

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DOI： 10.1038/srep21411

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DOI： 10.1007/s11295-015-0944-0

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DOI： 10.1016/j.jtbi.2015.09.017

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DOI： 10.1371/journal.pone.0143412

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DOI： 10.1371/journal.pgen.1005361

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Other Link： http://dx.plos.org/10.1371/journal.pgen.1005361

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/srep08695

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/978-1-4939-1743-3_8

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1105/tpc.114.129874

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.3732/apps.1400045

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.plaphy.2013.11.023

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Other Link： http://orcid.org/0000-0001-7891-5049

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DOI： 10.1104/pp.112.207654

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Other Link： http://orcid.org/0000-0001-7891-5049

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.cell.2012.10.048

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DOI： 10.1371/journal.pone.0049103

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DOI： 10.4161/psb.20486

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DOI： 10.1105/tpc.111.083238

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DOI： 10.1093/pcp/pcp157

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DOI： 10.4161/psb.4.9.9377

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DOI： 10.1111/j.1365-313X.2008.03656.x

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DOI： 10.1105/tpc.108.059345

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DOI： 10.1093/pcp/pcn075

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DOI： 10.1093/pcp/pci126

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Language：Japanese   Publisher：東京 : 国立科学博物館  

CiNii Research

Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I033725275

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Language：Japanese  

CiNii Research

J-GLOBAL

Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I033633494

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Language：Japanese   Publisher：岩波書店  

CiNii Research

Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I032728732

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