A statistical framework for QTL hotspot detection

A consensus map for quality traits in durum wheat based on genome-wide association studies and detection of ortho-meta QTL across cereal species

The present work focused on the identification of durum wheat QTL hotspots from a collection of genome-wide association studies, for quality traits, such as grain protein content and composition, yellow color, fiber, grain microelement content (iron, magnesium, potassium, selenium, sulfur, calcium, cadmium), kernel vitreousness, semolina, and dough quality test. For the first time a total of 10 GWAS studies, comprising 395 marker-trait associations (MTA) on 57 quality traits, with more than 1,500 genotypes from 9 association panels, were used to investigate consensus QTL hotspots representative of a wide durum wheat genetic variation. MTA were found distributed on all the A and B genomes chromosomes with minimum number of MTA observed on chromosome 5B (15) and a maximum of 45 on chromosome 7A, with an average of 28 MTA per chromosome. The MTA were equally distributed on A (48%) and B (52%) genomes and allowed the identification of 94 QTL hotspots. Synteny maps for QTL were also performed in Zea mays, Brachypodium, and Oryza sativa, and candidate gene identification allowed the association of genes involved in biological processes playing a major role in the control of quality traits.

Identification and Validation of a Chromosome 4D Quantitative Trait Locus Hotspot Conferring Heat Tolerance in Common Wheat (Triticum aestivum L.)

Understanding of the genetic mechanism of heat tolerance (HT) can accelerate and improve wheat breeding in dealing with a warming climate. This study identified and validated quantitative trait loci (QTL) responsible for HT in common wheat. The International Triticeae Mapping Initiative (ITMI) population, recombinant inbreed lines (RILs) derived from a cross between Synthetic W7984 and Opata M85, was phenotyped for shoot length, root length, whole plant length under heat stress and corresponding damage indices (DIs) to compare HT performances of individuals. Wide variations among the RILs were shown for all the traits. A total of 13 QTL including 9 major QTL and 4 minor QTL were identified, distributed on 6 wheat chromosomes. The six major QTL with the highest R² were associated with different traits under heat stress. They were all from Opata M85 background and located within a 2.2 cm interval on chromosome 4D, making up a QTL hotspot conferring HT in common wheat. The QTL hotspot was validated by genotyping-phenotyping association analysis using single-nucleotide-polymorphism (SNP) assays. The QTL, especially the 4D QTL hotspot identified and validated in this study, are valuable for the further fine mapping and identification of key genes and exploring genetic mechanism of HT in wheat.