Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

Abstract Identification of superior alleles controlling grain appearance quality is the prerequisite for improving rice grain quality. Here, we conducted genome-wide association studies (GWASs) at the SNP level (SNP-GWAS) and bin level (bin-GWAS) for five traits controlling appearance quality using a 4-way MAGIC population. A total of 16 and 20 QTLs were identified for these traits by SNP-GWAS and bin-GWAS, respectively. Both methods commonly identified the major QTLs, but bin-GWAS detected a larger number of minor QTLs. One novel minor chalkiness QTL, qPGWC8.2/qDEC8, was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior and inferior parental alleles for five known genes namely GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were identified for the four parents by multiple comparisons. The high-quality parents Cypress and Yuejingsimiao (YJSM) carried superior alleles in most cases, while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles. Hence, the pyramiding of these superior alleles could be useful for the genetic improvement of rice appearance quality.