QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments

Abstract

Genetic control of grain yield and phenology was examined in the Excalibur/Kukri doubled haploid mapping population grown in 32 field experiments across the climatic zones of southern Australia, India and north-western Mexico where the wheat crop experiences drought and heat stress. A total of 128 QTL were identified for four traits: grain yield, thousand grain weight (TGW), days to heading and grain filling duration. These QTL included 24 QTL for yield and 27 for TGW, showing significant interactions with the environment (Q * E). We also identified 14 QTL with a significant, small main effects on yield across environments. The study focussed on a region of chromosome 1B where two main effect QTL were found for yield and TGW without the confounding effect of phenology. Excalibur was the source of favourable alleles: QYld.aww-1B.2 with a peak at 149.5–150.1 cM and QTgw.aww-1B at 168.5–171.4 cM. We developed near isogenic lines (NIL) for the interval including QYld.aww-1B.2 and QTgw.aww-1B and evaluated them under semi-controlled conditions. Significant differences in four pairs of NIL were observed for grain yield but not for TGW, confirming a positive effect of the Excalibur allele for QYld.aww-1B.2. The interval containing QYld.aww-1B.2 was narrowed down to 2.9 cM which corresponded to a 2.2 Mbp genomic region on the chromosome 1B genomic reference sequence of cv. Chinese Spring and contained 39 predicted genes.

Dissection of Quantitative Trait Loci (QTL), annotation of Single Nucleotide Polymorphism (SNP), and Identification of Candidate Genes for Grain Yield in Triticum turgidum L. var durum

“…We found among 9 QTLs related to grain yield, four were located on 2A chromosome, these QTLs were detected in diverse stressed environments: EP characterized by cold, INC and RF by drought, and RQ by heat. These results are in accordance with several studies on grain yield QTLs located on 2A chromosome [24,32,33].…”

“…For the QTLs detection in specific and stressed environments, 9 QTLs were detected, 4 of which were localized on 2A, due to its strong contribution to grain yield [32,33], the full DNA sequence of 2A chromosome were downloaded from URGI and the 4 DNA sequences corresponding to the 4 QTL were isolated based on markers flanking of these QTL regions [24,25,29] using the GeneStudio software. More informations about the environments, DNA sequences size, environmental conditions, QTL intervals and flanking markers are summarized in Table 1.…”

“…These sequences can be compared with the public databases [URGI (Unité de Recherche Génomique Info) Blast of the Institut National de la Recherche Agronomique (INRA, France) and NCBI (National Center for Biotechnology Information, the USA)] to identify the candidate genes involved in a QTL controlling a specific trait. Recently the markers (SNP and DArT) were used for QTLs regions detection and for the identification of the candidate genes involved in these QTLs of wheat [24][25][26][27][28][29]. The high and stable grain yield across diverse environments constitutes the principal aim for durum breeding programs.…”

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

“…The detection of QTL affecting yield, under drought, would be of great interest for the design of molecular tools for markerassisted selection and identification of target genes for edition, mainly when complemented by fine mapping studies (Tura et al, 2020). Despite a smaller number of QTLs identified under drought (10) compared to the irrigated condition (25), novel genomic regions were detected.…”

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

“…Unraveling the genetic basis of grain yield can be carried out through the identification of QTLs for yield-related traits under irrigated, hot and dry environments, fine mapping those QTLs and finding molecular markers tightly linked to the QTL/gene for molecular breeding [ 25 ]. In this sense, significant progress has been made in the development of DNA-based molecular markers like AFLP, SSR, DArT and SNP, which have been used in the construction of genetic maps and for conducting QTL analysis through different methods such as single-marker analysis, interval mapping and genome-wide association studies, among others.…”