Genome-wide Association Study(GWAS)for Mesocotyl Elongation In Rice(Oryza Sativa L.)under Multiple Culture Conditions

Mesocotyl is a crucial organ for pushing buds out of soil,which plays a vital role in seedling emergence and establishment in dry direct-seeded rice.However,the genetic mechanisms of mesocotyl elongation remains unclear.In our study,208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions,including sand,water and soil.The ranges of genetic variation of mesocotyl lengths were 0-4.88 cm,0-3.99 cm and 0-4.51 cm in sand,water and soil covering,respectively.A total of 2,338,336 SNPs were developed by re-sequencing of 208 rice accessions.Genome-wide association study(GWAS)based on mixed linear model(MLM)was conducted and 16 unique loci were identified on chromosomes 1,2(2),3,4,5(2),6(2),7,8,9(2)and 12(3),respectively,explaining phenotypic variations ranging from 6.3 to 15.9%.Among these loci,12 were stable across two or more environments.Ten out of the sixteen loci coincided with known genes or quantitative trait locus(QTL),whereas the other six were potentially novel loci.Furthermore,five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1,3,5,9 and 12,and all these five genes showed significantly different expression abundance between short-mesocotyl accessions and long-mesocotyl accessions.This study provides new insights into the genetic architecture of rice mesocotyl,the associated SNPs and germplasm with elongated mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.