期刊
FRONTIERS IN PLANT SCIENCE
卷 13, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2022.976669
关键词
rice; shoot length; genome-wide association study; OsCPS1; selection
资金
- Guangdong Provincial International Cooperation Project of Science Technology [2021A0505030048]
- Key Areas Research Projects of Guangdong Province [2020B0202090003]
- Science and Technology Program of Guangzhou [202002030375, 201804020078]
- National Natural Science Foundation of China [31901441]
- Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science [R2021PY-QF001]
- evaluation and operation funds of Guangdong key laboratories [2020B1212060047]
- YouGu Plan of Rice Research Institute of Guangdong Academy of Agricultural Sciences [2021YG001]
This study identified six quantitative trait loci associated with shoot length in rice and characterized OsCPS1 as a candidate gene for shoot length. The 36 bp deletion in the 5' UTR of OsCPS1 was found in accessions with long shoot length and associated with higher levels of bioactive GA(1) and GA(4). The expression of photosynthesis genes was higher in accessions with long shoot length, while genes involved in ABA-activated signal pathway showed lower expression. The findings provide valuable candidate genetic variation for seedling vigor in rice breeding.
High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance index in seedling vigor evaluation. However, information on the identity of rice germplasm with high seedling vigor, and the genetic basis of seedling vigor are not well understood. In this study, we have conducted a genome-wide association study using 302 international diverse rice accessions from the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were found to associate with shoot length (SL). The locus qSL2 was further analyzed for candidate gene characterization. We identified OsCPS1, which encodes CDP synthase and functions in GA (Gibberellins) biosynthesis in rice, exhibits differential expression between long and short SL accessions. Using the Nipponbare genome sequence as the reference, we identified a 36 bp deletion in the 5' UTR of OsCPS1 in long SL accessions, which is absent in short SL accessions. GA content analysis showed that the levels of bioactive GA(1) and GA(4) are considerably higher in long SL accessions than in short SL accessions. Genome-wide gene expression analysis indicated the expression of some photosynthesis genes is higher in long SL accessions than in short SL accessions. In contrast, genes involved in ABA (Abscisic Acid)-activated signal pathway showed lower expression in long SL accessions. Population analysis across wild rice, indica and japonica, suggested that OsCPS1 may be under selection in japonica during domestication. The results suggest that OsCPS1 is a candidate gene underlying qSL2. These data provide a promising source for candidate genetic variation associated with seedling vigor, with practical applications in rice breeding.
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