QTL mapping for Zinc accumulation in a barley doubled haploid population: R/qtl vs common software packages

Abstract Zinc deficiency is one of the important malnutrition globally. For identification of the genomic regions associated with seed Zn concentration in barley, 149 doubled haploid lines derived from a cross between Clipper and Sahara 3771 were characterized for the shoot and seed Zn concentration and content, as well as single plant grain yield under greenhouse conditions. The linkage map consisted of 246 SSRs, and EST-SSRs, 238 RFLPs, and 33 IRAP and REMAP markers spanned 1502.40 cM of the barley genome with an average distance of 2.9 cM between two adjacent markers. A total of 36, 32, and 39 QTLs for the six traits under study were detected using the composite interval mapping method implemented in QTL IciMapping, QGene, and QTL Cartograph, respectively. The custom-made R-script revealed the most powerful ability to find QTL, which mapped 39 QTLs underlying the six traits on all barley chromosomes. Out of 89 QTLs identified, 30 QTLs were commonly detected at least by two packages. The majority of the common QTLs were major QTLs, explaining more than 15% of the trait’s phenotypic variation. The most of QTLs mapped by R-script for the studied traits except single plant grain yield were confirmed by other programs.