Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand

• DOI: 10.1186/s12864-018-5317-2
• Publication Date: 2019-01-23T15:01:44Z
• Authors: Chakkree Lekklar; Monnat Pongpanich; Duangjai Suriya-a...; Aumnart Chinpongp...; Helen Tsai; Luca Comai; Supachitra Chadch...; Teerapong Buaboocha
• Keywords: Genome-wide Association Study; Indel; Genetic Association; Panicle

Salt stress, a major plant environmental is critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in improving productivity, especially at flowering stage, remains challenging. Here, we conducted genome-wide association study (GWAS) of based on exome sequencing Thai accessions. Photosynthetic parameters and cell membrane stability under stress stage; yield-related traits 104 (Oryza sativa L.) accessions belonging to indica subspecies were evaluated. The subjected sequencing, resulting 112,565 single nucleotide polymorphisms (SNPs) called with minor allele frequency least 5%. LD decay analysis panel indicates that average SNPs 20 kb distance from each other was 0.34 (r2), which decayed its half value (~ 0.17) around 80 kb. By GWAS performed using mixed linear model, two hundred containing 448 exons identified susceptibility index net photosynthetic rate day 6 after stress; number panicles, filled grains unfilled per plant. One forty six genes, accounted 73% loci, co-localized previously reported quantitative trait (QTLs). top four regions contained high significant found chromosome 8, 12, 1 2. While many are novel, their annotation consistent potential involvement related agronomic traits. These greatly help narrow down region within these QTLs where likely underlying candidate genes can be identified. Insight into contribution this provides further understanding mechanisms improve yield productivity salinity via gene cloning genomic selection.