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

The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.

DOI： 10.3390/plants12040929

PubMed

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

Sorghum is the fifth most important cereal crop. Here we performed molecular genetic analyses of the 'SUGARY FETERITA' (SUF) variety, which shows typical sugary endosperm traits (e.g., wrinkled seeds, accumulation of soluble sugars, and distorted starch). Positional mapping indicated that the corresponding gene was located on the long arm of chromosome 7. Within the candidate region of 3.4 Mb, a sorghum ortholog for maize Su1 (SbSu) encoding a starch debranching enzyme ISA1 was found. Sequencing analysis of SbSu in SUF uncovered nonsynonymous single nucleotide polymorphisms (SNPs) in the coding region, containing substitutions of highly conserved amino acids. Complementation of the rice sugary-1 (osisa1) mutant line with the SbSu gene recovered the sugary endosperm phenotype. Additionally, analyzing mutants obtained from an EMS-induced mutant panel revealed novel alleles with phenotypes showing less severe wrinkles and higher Brix scores. These results suggested that SbSu was the corresponding gene for the sugary endosperm. Expression profiles of starch synthesis genes during the grain-filling stage demonstrated that a loss-of-function of SbSu affects the expression of most starch synthesis genes and revealed the fine-tuned gene regulation in the starch synthetic pathway in sorghum. Haplotype analysis using 187 diverse accessions from a sorghum panel revealed the haplotype of SUF showing severe phenotype had not been used among the landraces and modern varieties. Thus, weak alleles (showing sweet and less severe wrinkles), such as in the abovementioned EMS-induced mutants, are more valuable for grain sorghum breeding. Our study suggests that more moderate alleles (e.g. produced by genome editing) should be beneficial for improving grain sorghum.

DOI： 10.3389/fpls.2023.1114935

PubMed

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

FE UPTAKE-INDUCING PEPTIDE1 (FEP1), also named IRON MAN3 (IMA3) is a short peptide involved in the iron deficiency response in Arabidopsis thaliana. Recent studies uncovered its molecular function, but its physiological function in the systemic Fe response is not fully understood. To explore the physiological function of FEP1 in iron homoeostasis, we performed a transcriptome analysis using the FEP1 loss-of-function mutant fep1-1 and a transgenic line with oestrogen-inducible expression of FEP1. We determined that FEP1 specifically regulates several iron deficiency-responsive genes, indicating that FEP1 participates in iron translocation rather than iron uptake in roots. The iron concentration in xylem sap under iron-deficient conditions was lower in the fep1-1 mutant and higher in FEP1-induced transgenic plants compared with the wild type (WT). Perls staining revealed a greater accumulation of iron in the cortex of fep1-1 roots than in the WT root cortex, although total iron levels in roots were comparable in the two genotypes. Moreover, the fep1-1 mutation partially suppressed the iron overaccumulation phenotype in the leaves of the oligopeptide transporter3-2 (opt3-2) mutant. These data suggest that FEP1 plays a pivotal role in iron movement and in maintaining the iron quota in vascular tissues in Arabidopsis.

DOI： 10.1111/pce.14424

PubMed

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

Rice (Oryza sativaL.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage,sake. The grain used insakebrewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking rice. Chalky grains, such as white-core or white-belly grains, are not ideal as cooking rice. Here, we report that three grain-size quantitative trait loci (QTLs;qGL4-2,qGWh5,qGWh10), derived from the brewing cultivar, Yamadanishiki, affect grain shape, chalky grain rate, and yield, using near isogenic and pyramiding lines in the genetic background of the cooking cultivar, Koshihikari. First, these QTLs influenced multiple components of grain shape, where epistatic effects were detected betweenqGL4-2andqGWh5, for grain width and thickness, and betweenqGL4-2andqGWh10, for grain length. Therefore, these QTLs may coordinate to control grain shape. Second, lines harboringqGWh5orqGWh10at the Yamadanishiki allele exhibited increased WCE, whereas lines withqGL4-2andqGWh10exhibited decreased white-belly grain rate (WBR). Thus, grain shape is associated with the occurrence of chalky grain, where the chalky type depends on the QTL. Finally, we used total panicle weight of plants as a simplified rice yield index, and a promising line pyramidingqGL4-2andqGWh5emerged. In conclusion,qGL4-2would be useful for the breeding of cooking rice, to decrease WBR, whileqGWh5andqGWh10were definitely more beneficial for that of brewing rice, to increase grain weight and WCE.

DOI： 10.1007/s11032-020-01166-0

Web of Science

Scopus

Other Link： https://link.springer.com/article/10.1007/s11032-020-01166-0/fulltext.html

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

Abstract

Agronomically important traits often develop during the later stages of crop growth as consequences of various plant–environment interactions. Therefore, the temporal physiological states that change and accumulate during the crop’s life course can significantly affect the eventual phenotypic differences in agronomic traits among crop varieties. Thus, to improve productivity, it is important to elucidate the associations between temporal physiological responses during the growth of different crop varieties and their agronomic traits. However, data representing the dynamics and diversity of physiological states in plants grown under field conditions are sparse. In this study, we quantified the endogenous levels of five phytohormones — auxin, cytokinins (CKs), ABA, jasmonate and salicylic acid — in the leaves of eight diverse barley (Hordeum vulgare) accessions grown under field conditions sampled weekly over their life course to assess the ongoing fluctuations in hormone levels in the different accessions under field growth conditions. Notably, we observed enormous changes over time in the development-related plant hormones, such as auxin and CKs. Using 3′ RNA-seq-based transcriptome data from the same samples, we investigated the expression of barley genes orthologous to known hormone-related genes of Arabidopsis throughout the life course. These data illustrated the dynamics and diversity of the physiological states of these field-grown barley accessions. Together, our findings provide new insights into plant–environment interactions, highlighting that there is cultivar diversity in physiological responses during growth under field conditions.

DOI： 10.1093/pcp/pcaa046

PubMed

Other Link： http://academic.oup.com/pcp/article-pdf/61/8/1438/33662758/pcaa046.pdf

J-GLOBAL

Event date： 2023.3

Language：Japanese   Presentation type：Oral presentation (general)  

Event date： 2023.3

Language：Japanese   Presentation type：Oral presentation (general)  

Event date： 2023.3

Language：Japanese   Presentation type：Oral presentation (general)  

Event date： 2022.12

Presentation type：Oral presentation (general)  

Event date： 2022.11

Presentation type：Oral presentation (general)