Construction of genetic linkage map using genotyping-by-sequencing and identification of QTLs associated with leaf color in spinach

Abstract

Spinach (Spinacia oleracea L.) is widely cultivated as an important green leafy vegetable crop with great economic values. High-density genetic linkage maps are valuable resources in marker-assisted breeding and functional genomics; however, most of such maps available for spinach are not of high density. Genotyping by sequencing (GBS) is an efficient and cost-effective tool for single nucleotide polymorphism (SNP) discovery and map construction. Here, we constructed a new high-density genetic linkage map using the GBS strategy and performed the QTL mapping of leaf color (red/green) in spinach. GBS data were generated from an F2 population comprising 282 individuals and the two parents. A total of 5333 homozygous SNP markers were identified between the two parents, and 3831 bin markers were located onto the genetic linkage map. The map spanned 1539.96 cM with an average marker interval of 0.4 cM and consisted of 6 linkage groups, corresponding to 6 chromosomes in spinach. Based on this genetic linkage map, we identified one major QTL associated with leaf color, accounting for 69.3% of the phenotypic variation, and having a genetic distance of 1.44 cM. Three important candidate genes responsible for spinach leaf color were identified through gene annotation and qRT-PCR analysis. This study provides useful tools for molecular marker-assisted selection, QTL mapping and map-based cloning in spinach.