Dataset Information

QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping.

ABSTRACT: Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.

SUBMITTER: Dang X

PROVIDER: S-EPMC4977947 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping.

Dang Xiaojing X Liu Erbao E Liang Yinfeng Y Liu Qiangming Q Breria Caleb M CM Hong Delin D

Frontiers in plant science 20160809

Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL ...[more]

PMID: 27555858

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Project description:BACKGROUND:Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. RESULTS:The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg- 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg- 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg- 1 (RM7309-135 bp on chromosome 9) to 0.45 mg.mg- 1 (RM297-180 bp on chromosome 2). RM297-180 bp showed the largest phenotypic effect value (0.44 mg.mg- 1 in 2016 and 0.45 mg.mg- 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297-175 bp (0.43 mg.mg- 1 in 2016 and 0.44 mg.mg- 1 in 2017). CONCLUSION:Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

Dataset Information

QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping.

Publications

QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping.

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