Genome-wide association study (GWAS) of rice (Oryza sativa L.) panicle compactness

The Green Revolution altered the rice panicle by increasing grain numbers per panicle. Here, we perform a genome-wide association study to understand the molecular mechanisms determining the number of grains in a panicle in rice. Panicle image analyses were performed on 158 genetically diverse rice accessions, and GWAS was run using the FarmCPU model with 34,072 single nucleotide polymorphisms to relate genotypic variation to the corresponding phenotypes. Flanking regions of candidate SNPs were separately defined for each chromosome based on LD decay distance to identify putative-associated genes. An RNA-seq data analysis was performed between stem and panicle to emphasize the role of candidate genes in panicle compactness. The results were further confirmed by a PPI network analysis using the putative candidate genes. In total 95 significant SNPs were identified; as close SNPs were considered a QTL that resulted in 56 QTLs across the 12 rice chromosomes. We identified novel candidate genes for panicle compactness traits, such as cytochrome P450 , polygalacturonase , glycosyltransferase , MADS-box, WRKY , YABBY , WUSCHEL-related homeobox, protein kinase , lipase, zinc finger transcription factor and protein phosphatase . Haplotype analysis identified haplogroups qNSSBB53 , qNSSBB102 , qNSSBU3 , qNSSBU21 , and qLS3 for three traits of NSSBB, NSSBU and LS. An analysis of epistatic interactions among candidate SNPs identified 91 significant SNP-SNP interactions. • GWAS analyses of rice panicle compactness (PC) identified 95 significant SNPs. • The significant SNPs correspond to 56 QTLs that provide insights into the genetic basis of PC. • Cytochrome P450, protein phosphatase, MADS-box proteins were associated with PC traits. • Epistasis and haplotype analysis play a crucial role in identifying SNP markers for inclusion in rice breeding programs.