Superior haplotypes to enhance grain filling in rice (Oryza sativa L.) identified through GWAS

Abstract Background Key traits for determining rice grain yield include the total number of spikelets per panicle (STOT), the total number of grains per panicle (GTOT), and the percentage of grain filling per panicle (GFTOT). Molecular genetic basis of grain yield is complex and regulates several interconnected genes. Identification of candidate genes and their favourable haplotypes associated with the spikelets, grains and grain filling would accelerate rice grain yield enhancement projects. The interface between genetic and environmental factors often influences the grain filling, affecting overall grain yield. Therefore, we executed a Genome-Wide Association Study (GWAS) to investigate the candidate genes associated with grain-filling traits and to explore genotype × environment (G × E) interactions influencing grain filling traits in rice—STOT, GTOT and GFTOT in the subset of Rice Diversity Panel 1 (RDP1). Methods and results A set of 188 RDP1 accessions were evaluated across two environments (wet seasons—2021 and 2022) following the standard package of practices to raise healthy crop. Phenotyping analysis identified promising genotypes for three traits of study—STOT and GTOT (Priano Guaira and Tainan-Iku No. 512) and GFTOT (IR8 and Biser-1). GWAS was carried out using 5.2 M SNP dataset in the Parallel Identification of QTL’s using EMMAX (PIQUE) pipeline. Five QTLs, one for STOT (qSTOT6.6), one for GTOT (qGTOT4.2) and three for GFTOT (qGFTOT3.4, qGFTOT3.5 and qGFTOT12.1), were detected. Further, superior haplotypes for eight candidate genes (LOC_Os6g38850 and LOC_OS6g39050 for STOT; LOC_OS4g11040 for GTOT; LOC_OS3g62720, LOC_OS3g62750, LOC_OS3g62820, LOC_OS12g03450 and LOC_OS12g03470 for GFTOT) were identified. Conclusions Our results provide key genetic information for the enhancement of grain filling traits in rice. The identified candidate genes and superior haplotypes can possibly be utilized in marker-assisted selection to improve rice grain yield through gene-pyramid breeding/haplotype-assisted breeding.