Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (Oryza sativa...

Rice provides poor yields in acidic soils due to several nutrient deficiencies and metal toxicities. The low availability of phosphorus (P) in acidic soils offers a natural condition for screening genotypes for grain yield and phosphorus utilization efficiency (PUE). The objective of this study was to phenotype a subset of indica rice accessions from 3000 Rice Genome Project (3K-RGP) under acidic soils and find associated genes and alleles. A panel of 234 genotypes, along with checks, were grown under low-input acidic soils for two consecutive seasons, followed by a low-P-based hydroponic screening experiment. The heritability of the agro-morphological traits was high across seasons, and Ward's clustering method identified 46 genotypes that can be used as low-P-tolerant donors in acidic soil conditions. Genotypes ARC10145, RPA5929, and K1559-4, with a higher grain yield than checks, were identified. Over 29 million SNPs were retrieved from the Rice SNP-Seek database, and after quality control, they were utilized for a genome-wide association study (GWAS) with seventeen traits. Ten quantitative trait nucleotides (QTNs) for three yield traits and five QTNs for PUE were identified. A set of 34 candidate genes for yield-related traits was also identified. An association study using this indica panel for an already reported 1.84 Mbp region on chromosome 2 identified genes Os02g09840 and Os02g08420 for yield and PUE, respectively. A haplotype analysis for the candidate genes identified favorable allelic combinations. Donors carrying the superior haplotypic combinations for the identified genes could be exploited in future breeding programs.