Detecting Marker-Trait Associations for Total Milled Rice, Head Rice, and Rice Chalky Grain Percentages

High total milling yield and head rice percentages and low chalky grain percentage, are desired grain quality traits in rice. Identifying functional DNA markers leads to effective marker-assisted selection for favorable grain quality traits. The objectives of this study were to detect single nucleotide polymorphisms (SNPs) associated with these traits using genome-wide association studies (GWAS), and to identify candidate genes controlling these traits. A diverse collection of 195 and 199 rice cultivars, landraces, and breeding lines grown at the Texas A&M AgriLife Research Center in Beaumont were evaluated in 2018 and 2019, respectively, using the S21 grain analyzer. GWAS for these three traits were carried out using 854,832 SNPs. Thirteen significant marker-trait associations (MTAs) were detected in chromosomes 1, 3, 6, 7, 8, 9, and 12 in the best linear unbiased prediction (BLUP) estimates of total milling yield, while two MTAs located in chromosomes 1 and 2 were found in the head rice percentage BLUP estimates. Analyses using individual year data showed that three MTAs in chromosomes 3 and 6 were identified in 2018, and that 203 MTAs , mostly located in chromosome 9 with some from chromosomes 3, 7, and 11, were detected in 2019. For head rice percentage, six MTAs were located in chromosomes 6, 7, 8, 9, and 11 in 2019. For chalky grain, five MTAs from chromosomes 2, 4, 6, and 8 were identified in 2018, and 10 MTAs from chromosomes 1, 2, 3, 4, 7, 8, 11, and 12 were detected in 2019. Some of the identified SNPs are within previously-reported quantitative trait loci for the three traits.