Structural organization of the group-1 chromosomes of two bread wheat sister lines

Variation in crossover rates across a 3-Mb contig of bread wheat (Triticum aestivum) reveals the presence of a meiotic recombination hotspot

In bread wheat (Triticum aestivum L.), initial studies using deletion lines indicated that crossover (CO) events occur mainly in the telomeric regions of the chromosomes with a possible correlation with the presence of genes. However, little is known about the distribution of COs at the sequence level. To investigate this, we studied in detail the pattern of COs along a contig of 3.110 Mb using two F2 segregating populations (Chinese Spring × Renan (F2-CsRe) and Chinese Spring × Courtot (F2-CsCt)) each containing ~2,000 individuals. The availability of the sequence of the contig from Cs enabled the development of 318 markers among which 23 co-dominant polymorphic markers (11 SSRs and 12 SNPs) were selected for CO distribution analyses. The distribution of CO events was not homogeneous throughout the contig, ranging from 0.05 to 2.77 cM/Mb, but was conserved between the two populations despite very different contig recombination rate averages (0.82 cM/Mb in F2-CsRe vs 0.35 cM/Mb in F2-CsCt). The CO frequency was correlated with the percentage of coding sequence in Cs and with the polymorphism rate between Cs and Re or Ct in both populations, indicating an impact of these two factors on CO distribution. At a finer scale, COs were found in a region covering 2.38 kb, spanning a gene coding for a glycosyl transferase (Hga3), suggesting the presence of a CO hotspot. A non-crossover event covering at least 453 bp was also identified in the same interval. From these results, we can conclude that gene content could be one of the factors driving recombination in bread wheat.

Mixed-model QTL mapping for kernel hardness and dough strength in bread wheat

Plant breeding data comprise unbalanced phenotypic data for inbreds with complex pedigrees. As traditional methods to map quantitative trait loci (QTL) cannot exploit plant breeding data, an alternative approach is QTL mapping via a mixed-model procedure. Our objective was to validate mixed-model QTL mapping for self-pollinated crops by detecting QTL for kernel hardness and dough strength from data in a bread wheat (Triticum aestivum L.) breeding program. We studied 80 parental and 373 experimental inbreds genotyped for 65 simple sequence repeat (SSR) markers and three candidate loci. The methodology involved three steps: variance component estimation, single-marker analyses, and a final multiple-marker analysis with marker effects treated as fixed effects. Two QTLs for kernel hardness were detected on chromosomes 1A (close to candidate locus GluA3) and 5D (close to candidate locus Ha). Four QTLs were detected for dough strength on chromosomes 1A, 1B, 1D, and 5B. Candidate gene GluA1, which was associated with dough strength, was the only candidate locus found significant. Results were consistent with previously reported markers and QTLs associated with kernel hardness and dough strength. Unlike previous studies that have assumed QTL effects as random, the assumption of fixed marker effects identified the favorable marker alleles to select for. We conclude that the detection of previously mapped QTL validates the usefulness of mixed-model QTL mapping in the context of a plant-breeding program.