Journal
MOLECULAR BREEDING
Volume 39, Issue 6, Pages -Publisher
SPRINGER
DOI: 10.1007/s11032-019-0993-4
Keywords
Rice; Seed vigor; QTL mapping; GWAS; RNA-seq; Candidate genes
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Funding
- Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production [2017YFD0100104]
- National Key Technology Research and Development Program of China [2016YFD0102102]
- Science and Technology Project of Guangdong Province [2015B020231011]
- earmarked fund for Modern Agro-Industry Technology Research System [CARS-01-12]
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Seed vigor is an important seed quality trait in rice (Oryza sativa L.) that profoundly affects seedling morphogenesis in different environments. Generally, highly vigorous seeds have many advantages in agricultural production, such as resistance to adverse stresses, rapid emergence, and yield improvement. In the present study, one germplasm collection and one recombinant inbred line (RIL) population were used to identify quantitative trait loci (QTLs) for seed vigor. A total of 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with seed vigor (-log(10)(P) > 6) in the germplasm collection, which consisted of 200 rice cultivars. Nine loci responsible for seed vigor were identified via QTL mapping by using a high-density bin map. To screen the candidate genes more efficiently, we selected six loci that were co-localized in GWAS and QTL mapping, overlapped previous reports, repeat detected across two seasons, or high contribution rate as reliable loci. A total of 44 differentially expressed genes were obtained from the reliable loci via gene expression profile analysis. Among these 44 genes, Os06g0108600, Os06g0110200, Os06g0253100, Os06g0282000, Os07g0583600, Os07g0592600, and Os09g0432300 were the most promising candidates associated with seed vigor.
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