Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat

Abstract

A high-resolution chromosome arm-specific mapping population was used in an attempt to locate/detect gene(s)/QTL for different root traits on the short arm of rye chromosome 1 (1RS) in bread wheat. This population consisted of induced homoeologous recombinants of 1RS with 1BS, each originating from a different crossover event and distinct from all other recombinants in the proportions of rye and wheat chromatin present. It provides a simple and powerful approach to detect even small QTL effects using fewer progeny. A promising empirical Bayes method was applied to estimate additive and epistatic effects for all possible marker pairs simultaneously in a single model. This method has an advantage for QTL analysis in minimizing the error variance and detecting interaction effects between loci with no main effect. A total of 15 QTL effects, 6 additive and 9 epistatic, were detected for different traits of root length and root weight in 1RS wheat. Epistatic interactions were further partitioned into inter-genomic (wheat and rye alleles) and intra-genomic (rye-rye or wheat-wheat alleles) interactions affecting various root traits. Four common regions were identified involving all the QTL for root traits. Two regions carried QTL for almost all the root traits and were responsible for all the epistatic interactions. Evidence for inter-genomic interactions is provided. Comparison of mean values supported the QTL detection.

Fig. 1

Three-dimensional graphic representation of QTL effects for six different root traits of the 1RS-1BS recombinant bread wheat population. a Number of roots greater than 30 cm (NR > 30), b longest root length (LRL), c total root length of roots greater than 30 cm (TRL > 30), d shallow root weight (SRW), e deep root weight (DRW), and f dry root biomass (TRW). The main (additive) effects are on the diagonals and the epistatic effects are on the left triangle of the 3D plots (the graphical scales for LOD scores in individual graphs are different, as generated by the software program)

Fig. 2

Diagrammatic representations of QTL for root traits on the consensus genetic map of 1RS-1BS recombinant lines. a Values on the left side of the 1RS-1BS map are genetic distances and right side of the map show different markers. Values in the parentheses are the number of markers used in this study as reference starting at 1 from the proximal side of the 1RS-1BS map to 15 at the distal end. I, II, III, and IV are the main regions comprising most of the QTL effects for root traits, b location of different QTL effects on 1RS-1BS map, yellow rectangles are the additive effects, green rectangles are intra-genomic epistatic effects (between rye–rye or wheat–wheat loci), and c location of inter-genomic epistatic interaction (between rye and wheat loci), red rectangles connected by curved dashed line. Boxes with borders show different root traits, NR number of roots greater than 30 cm, LRL longest root length, TRL total root length of roots greater than 30 cm, SRW shallow root weight, DRW deep root weight, TRW total root weight