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

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

Cloning of Vgt3, a major QTL for flowering time in maize

Flowering time is a complex trait important for crop adaptation to local environments and an essential breeding target to face the challenge of global climate change. A major quantitative trait locus (QTL) for flowering time and number of nodes (ND), qVgt3.05 (Vgt3), was previously identified on chromosome 3, bin 3.05, in a maize introgression library (IL) derived from the cross B73 x Gasp\ue9 Flint (recipient and donor genotypes, respectively. Salvi et al. 2011). In order to clone Vgt3, B73 was crossed with its early isogenic line 39-1-2-33 which carries a 17-cM Gasp\ue9 Flint introgression on bin 3.05. Using this cross, Vgt3 showed an addictive effect of 1.4 nodes, explained 56.6% of the phenotypic variance and was mapped within 0.3 cM. For positional cloning, a total of 7,500 F2 plants were phenotyped and genotyped with SNPs and SSR markers flanking the QTL interval. One-hundred recombinants lines were derived and the QTL was further narrowed the target genomic region to a 380-kb interval. A MADS-box gene with no coding sequence variation between the two alleles was found in the physical interval. However, the MADS-box gene RNA expression profile and transgenics testing confirmed its effect on flowering time. We are currently searching for the Vgt3 causative regulatory region by studying chromosome structural variation between the B73 and Gasp\ue9 Flint alleles