Identification of loci and molecular markers associated with Super Soft kernel texture in wheat

Abstract

The preferential application of wheat flour in various end-use products is primarily driven by kernel texture (softness/hardness). Herein, a population of 268 F6 recombinant inbred lines (RILs) was developed by crossing the wheat cultivar Alpowa (‘normal’ soft) (SKCS HI = 20.2) with a related ‘Super Soft’ line (BC2SS163) (HI = −1.2). A set of 19 polymorphic markers including 16 Kompetitive allele specific PCR (KASP) and three simple sequence repeat (SSR) markers were targeted to three genomic regions (4BS, 1BS and 5AL) and used to genotype the RILs and parents. Four QTLs were detected for kernel texture using composite interval mapping (CIM) including one major QTL on 4BS, and three minor QTLs [5AL (2) and 1BS (1)]. Eight significant markers were identified using single marker-trait association (SMA) analysis and explained 3.8–28.0% phenotypic variation (PV). Two markers from the combined analyses were selected with the highest PV (8.0% and 36.7%). These two marker loci were independent and additive. RILs possessing both favorable (soft) alleles had an average SKCS hardness of 4.9 vs. 15.7 for the alternate haplotype. We conclude that the Super Soft trait is polygenic and that we have identified one of two or more major loci conferring this phenotype.