Language：English   Publisher：Plants  

In Kenya’s rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups—A, B1, and B2—based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.

DOI： 10.3390/plants12040863

Open Access

Scopus

PubMed

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

Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.

DOI： 10.3390/life12111752

Open Access

Scopus

PubMed

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

DOI： 10.3390/agriculture12081141

DOI： 10.3390/agriculture12081141

Open Access

Scopus

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

DOI： 10.3389/fpls.2022.908000

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

DOI： 10.3389/fpls.2022.1002605

Open Access

Scopus

PubMed

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

The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.

DOI： 10.3390/plants10050844

Open Access

Scopus

PubMed

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

DOI： 10.1038/s42003-020-1036-8

Open Access

Web of Science

Scopus

PubMed

Other Link： http://www.nature.com/articles/s42003-020-1036-8

DOI： doi/10.18999/jouica.18.18

DOI： doi/10.18999/jouica.18.18

Publisher：Rice Science  

The quantitative resistance gene pi21 from Sensho was introgressed to an indica breeding line IR63307-4B-13-2, a pyramiding line IRBB4/5/13/21, and a tropical japonica line Kinandang Patong by marker-assisted backcrossing. A total of 192 improved lines at the BC4F3 and BC4F4 generations were developed and confirmed to have the gene introgression via genotyping using a pi21-specific InDel marker. Thirteen randomly selected improved lines, representing all the three genetic backgrounds, demonstrated resistance against leaf blast composites in the field and a broader spectrum resistance against individual isolates compared to the recurrent parents in the glasshouse. Specifically, the tested lines exhibited pi21-acquired resistance against 11 leaf blast isolates that elicited susceptible reactions from the recurrent parents. All the tested lines maintained a comparative heading date, and similar or improved panicle length, number of primary branches per panicle and number of total grains per panicle relative to the recurrent parents. The physical grain characteristics of the recurrent parents were also maintained in the 13 lines tested, although variability in the amylose content and chalkiness degree was observed. The successful marker-assisted introgression of pi21 in diverse genetic backgrounds and the resulting broader spectrum resistance of improved lines against leaf blast indicate the potential of pi21 for deployment in cultivars grown across other rice growing regions in Asia.

DOI： 10.1016/j.rsci.2020.01.002

Open Access

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Scopus

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

Postzygotic reproductive isolation maintains species integrity and uniformity and contributes to speciation by restricting the free gene flow between divergent species. In this study we identify causal genes of two Mendelian factors <italic>S22A</italic> and <italic>S22B</italic> on rice chromosome 2 inducing F₁ pollen sterility in hybrids between <italic>Oryza sativa</italic> japonica-type cultivar Taichung 65 (T65) and a wild relative of rice species <italic>Oryza glumaepatula</italic>. The causal gene of <italic>S22B</italic> in T65 encodes a protein containing DUF1668 and gametophytically expressed in the anthers, designated <italic>S22B_j</italic>. The <italic>O. glumaepatula</italic> allele <italic>S22B-g</italic>, allelic to <italic>S22B_j</italic>, possesses three non-synonymous substitutions and a 2-bp deletion, leading to a frameshifted translation at the S22B C-terminal region. Transcription level of <italic>S22B-j</italic> and/or <italic>S22B_g</italic> did not solely determine the fertility of pollen grains by genotypes at <italic>S22B</italic>. Western blotting of S22B found that one major band with approximately 46 kDa appeared only at the mature stage and was reduced on semi-sterile heterozygotes at <italic>S22B</italic>, implying that the 46 kDa band may associated in hybrid sterility. In addition, causal genes of <italic>S22A</italic> in T65 were found to be <italic>S22A_j1</italic> and <italic>S22A_j3</italic> encoding DUF1668-containing protein. The allele of a wild rice species <italic>Oryza meridionalis</italic> Ng at <italic>S22B</italic>, designated <italic>S22B_m</italic>, is a loss-of-function allele probably due to large deletion of the gene lacking DUF1668 domain and evolved from the different lineage of <italic>O. glumaepatula</italic>. Phylogenetic analysis of DUF1668 suggested that many gene duplications occurred before the divergence of current crops in Poaceae, and loss-of-function mutations of DUF1668-containing genes represent the candidate causal genetic events contributing to hybrid incompatibilities. The duplicated DUF1668-domain gene may provide genetic potential to induce hybrid incompatibility by consequent mutations after divergence.

DOI： 10.3389/fpls.2020.632420

Open Access

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PubMed

Language：English  

DOI： 10.18999/jouica.18.18

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.248.0_99

CiNii Research

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

<p>Problems with carbon assimilate translocation from source organs to sink (grains) during ripening cause yield losses in rice (<i>Oryza sativa</i> L.), especially in high-sink-capacity varieties. We conducted a genetic analysis of traits related to such translocation by using recombinant inbred lines. Shoot weight (SW) of T65, a <i>japonica</i> parent, was retained from heading to late maturity, whereas that of DV85, an <i>aus</i> parent, was greater than that of T65 at 5 days after heading (DAH) and then decreased until 20 DAH. This difference was observed clearly under standard-fertilizer but not low-fertilizer conditions. Non-structural carbohydrate (NSC) contents in the parents showed a tendency similar to that for SW. QTL analysis revealed pleiotropic QTLs on chromosomes 5 and 10, probably by associations with heading date QTLs. A QTL associated with harvest index and NSC at 5 DAH was detected on chromosome 1. By considering the temporal changes of the traits, we found a QTL for decrease in SW on chromosome 11; the DV85 allele of this QTL facilitated assimilate translocation and suppressed biomass growth. A suggestive QTL for NSC decrease was located on chromosome 2. These QTLs could represent potential targets for controlling carbon assimilate translocation in breeding programs.</p>

DOI： 10.1270/jsbbs.18203

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CiNii Research

Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.247.0_110

CiNii Research

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

Publishing type：Part of collection (book)  

DOI： 10.1007/978-981-10-7308-3_3

Scopus

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

DOI： 10.1017/S0007485317000992

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F-2 population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = -0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC1F4 and BC1F5 genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.

DOI： 10.1080/1343943X.2018.1440970

Open Access

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Scopus

Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation (SMF) which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines (BILs) and to identify QTL(s) associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F-2 plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.

DOI： 10.1080/1343943X.2018.1446759

Open Access

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Scopus

Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOCIETY AMERICA  

Reproductive barriers are commonly observed in both animals and plants, in which they maintain species integrity and contribute to speciation. This report shows that a combination of loss-offunction alleles at two duplicated loci, DUPLICATED GAMETOPHYTIC STERILITY 1 (DGS1) on chromosome 4 and DGS2 on chromosome 7, causes pollen sterility in hybrid progeny derived from an interspecific cross between cultivated rice, Oryza sativa, and an Asian annual wild rice, O. nivara. Male gametes carrying the DGS1 allele from O. nivara (DGS1-nivaras) and the DGS2 allele from O. sativa (DGS2-T65s) were sterile, but female gametes carrying the same genotype were fertile. We isolated the causal gene, which encodes a protein homologous to DNA-dependent RNA polymerase (RNAP) III subunit C4 (RPC4). RPC4 facilitates the transcription of 5S rRNAs and tRNAs. The loss-of-function alleles at DGS1-nivaras and DGS2-T65s were caused by weak or nonexpression of RPC4 and an absence of RPC4, respectively. Phylogenetic analysis demonstrated that gene duplication of RPC4 at DGS1 and DGS2 was a recent event that occurred after divergence of the ancestral population of Oryza from other Poaceae or during diversification of AA-genome species.

DOI： 10.1534/g3.117.043943

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PubMed

Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOCIETY AMERICA  

Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.

DOI： 10.1534/g3.116.038190

Open Access

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PubMed

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

Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood.
We conducted an association analysis for the coding sequences of SH3/SH4 in AA-genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O. sativa genetic background.
We found that the loss of seed shattering in O. glaberrima was caused by an SNP resulting in a truncated SH3/SH4 protein. This mutation appears to be endemic and to have spread in the African gene pool by hybridization with some O. barthii accessions. We showed that interaction between the O. sativa and O. glaberrima domestication alleles of SH3 in heterozygotes induces a 'throwback' seed-shattering phenotype similar to that in the wild species.
Identification of the causative SNP provides new insights into the molecular basis of seed shattering in crops and may facilitate investigation of the history of African rice domestication.

DOI： 10.1111/nph.14290

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PubMed

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

DOI： 10.1270/jsbbs.16083

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

DOI： 10.1073/pnas.1604849113

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

DOI： doi:10.1016/j.plantsci.2015.09.008

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

Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glums or S22B-glums) were sterile if produced on a heterozygous plant. No transmission of the S22A-glums allele via pollen was observed, whereas a low frequency of transmission of S22B-glums was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization

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

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DOI： 10.1073/pnas.1019490108

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

Language：Japanese  

J-GLOBAL

Event date： 2024.3

Language：English   Presentation type：Oral presentation (general)  

Venue：東京大学  

Event date： 2023.12

Language：Japanese   Presentation type：Poster presentation  

Venue：名古屋大学  

Event date： 2023.12

Language：Japanese   Presentation type：Poster presentation  

Venue：名城大学  

Event date： 2023.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：東海作物研究  

Event date： 2023.9

Language：English   Presentation type：Poster presentation  

Venue：神戸大学  

Event date： 2023.3

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：静岡大学   Country：Japan  

Event date： 2023.3

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：静岡大学   Country：Japan  

Event date： 2022.12

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Venue：オンライン   Country：Japan  

Event date： 2022.12

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Venue：オンライン   Country：Japan  

Event date： 2022.11

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Venue：オンライン   Country：Japan  

Event date： 2022.11

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Venue：オンライン   Country：Japan  

Event date： 2022.9

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Venue：帯広畜産大学   Country：Japan  

Event date： 2022.9

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Venue：帯広畜産大学   Country：Japan  

Event date： 2022.3

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Venue：オンライン   Country：Japan  

Event date： 2021.12

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Venue：オンライン   Country：Japan  

Event date： 2021.12

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Venue：オンライン   Country：Japan  

Event date： 2021.11

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Venue：オンライン   Country：Japan  

Event date： 2021.11

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Venue：オンライン   Country：Japan  

Event date： 2008.10

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

Event date： 2008.3

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

Event date： 2008.3

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan