Genome-wide association study (GWAS) of germination and post-germination related seedling traits in rice

Genome-wide association study (GWAS) has become an accepted and powerful method for understanding the associations between phenotypes and genotypes. In agricultural production, uniform and rapid germination is an important prerequisite in crop production. Here, the genetic diversity of rice (Oryza sativa L.) genotypes was put under scrutiny for germination and post-germination related seedling traits, and a rice GWAS analysis with 33,934 SNPs for eight traits including germination percentage (GP), shoot (SL) and root length (RL), root (RFW) and shoot fresh weight (SFW), root (RDW) and shoot (SDW) dry weight, and number of days to germinate (NDG) was performed to define genomic regions influencing seed germination and post-germination related seedling traits. By GWAS, 52 QTLs tagged to 93 significant trait-associated markers were detected across all rice chromosomes. The detected QTLs explained 5 to 58% of variation of different traits. More important candidate associated genes in the vicinity of the detected QTL regions were: LOC_Os01g26210 (OsWAK6) co-located with a seed vigor QTL, a gene with alpha-glucosidases/starch lyase activity (GH31, LOC_Os07g23944) associated with shoot length, UDP-glucuronic acid 4-epimerase 1 (LOC_Os03g14540) associated with root length, chloroplast outer envelope protein 86 (LOC_Os12g09570) associated with root fresh mass, vacuolar sorting receptor 7 (LOC_Os04g52190) and a gene cluster on chromosome 7 including LOC_Os07g07320 (glutathione S-transferase), LOC_Os07g07340 (glucan endo-1,3-beta-glucosidase) and LOC_Os08g42720 (solute carrier 35) affecting root dry mass, and LOC_Os06g47640 (calmodulin-related calcium sensor protein 29) involveing in the inhibition of ABA during seed germination, associated with germination rate. The associated genes for the studied traits can be generally classified as hydrolytic enzymes, kinases and transferases or transcription factors that can directly or indirectly influence germination and post-germination related seedling traits. Our GWAS results identified several putative candidate genes for germination and seedling traits that will greatly contribute to our understanding of the genetic complexity underlying the corresponding traits.