Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

There is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker-assisted selection (MAS) schemes for cultivar improvement. This study prototype using segregating single nucleotide polymorphisms (SNPs) panicle architecture grain shape traits identified by GWAS the Rice Diversity Panel-1 colocalized QTL regions revealed linkage mapping Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable reliable detection surrounding most significant SNPs GWAS. Once developed, validated three Japonica subspecies biparental populations, to improve resolution, employed select potential parents use MAS. All marker alleles segregated tropical japonica subpopulation.