Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)

Abstract

In the current study, we used a linkage mapping–Genome-Wide Association Study (GWAS) joint strategy to investigate quantitative trait loci (QTLs) governing rice grain shape and weight in a doubled haploid (DH) population, using Kompetitive Allele-Specific PCR (KASP) markers. Results revealed the co-detection of the QTLs, qGLE-12-1 and qGLE-12-2 (Chromosome 12), qGTE-3-1 (Chromosome 3), and qGWL-5-1 and qLWRL-5-1 (Chromosome 5), associated with grain length, width, and length–width ratio, by both linkage mapping and GWAS. In addition, qGLL-7-1 (logarithm of the odds (LOD): 18.0, late-transplanted rice) and qGLE-3-1 (LOD: 8.1, early-transplanted rice), and qLWRL-7-1 (LOD: 34.5), detected only by linkage mapping, recorded a high phenotypic variation explained (PVE) of 32.5%, 19.3%, and 37.7% for grain length, and grain length–width ratio, respectively, contributed by the allele from 93-11. Meanwhile, qGWL-5-1 (LOD: 17.2) recorded a high PVE (31.7%) for grain width, and the allele from Milyang352 contributed to the observed phenotypic variation. Furthermore, qGTL-5-1 (LOD: 21.9) had a high PVE (23.3%) for grain thickness. Similarly, qTGWE-5-1 (LOD: 8.6) showed a high contribution to the PVE for grain weight (23.4%). Moreover, QTLs, qGW-5-1, qGT-5-1, qLWR-5-1, and qTGW-5-1 coincided on chromosome 5, flanked with KJ05_17 and KJ05_13 markers. Therefore, these QTLs are suggested to govern rice grain shape and weight. Additionally, the identified candidate genes could play active roles in the regulation of rice grain shape and weight, regarding their predicted functions, and similarity with previously reported genes. Downstream breeding and functional studies are required to elucidate the roles of these candidate genes in the regulation of grain shape and weight in rice.