Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat

Abstract

The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02–10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

“…The observed moderate to high values of broad-sense heritability and the consistency of trait records evidenced by the significant correlations between the crop seasons suggest that a considerable part of the variation is due to inherent genetic differences among the accessions. These results agree with similar findings in bread and durum wheat for GPC [ 19 , 25 , 27 , 40 ], and TKW [ 13 , 41 ]. Given that the panel contains historical and contemporary varieties released or collected between 1925 and 2010, it is possible that the recorded genetic variance—especially for TKW—is inflated.…”

Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz)

“…A study by [ 85 ] also revealed multiple MTAs on chromosome 18 for cassava starch pasting properties, indicating the high LD of markers on this chromosome. Multiple MTAs have also been detected for flowering traits in Indian mustard ( Brassica juncea ) [ 57 ] and grain yield and related traits in durum wheat ( Triticum turgidum ) [ 90 ]. Other traits had only one MTA on a chromosome, such as S15_11747301 on chromosome 15 (associated with branching, branch type, branching levels, and number of nodes).…”

Genomic regions involved in the control of 1,000-kernel weight in wild relative-derived populations of durum wheat

“…To meet the future demand for durum wheat grains despite the climatic changes ( Mulugeta et al., 2023 ), a significant increase in production is necessary ( Sakuma and Schnurbusch, 2020 ). The indirect selection of production-related traits under more stringent genetic control is a potential solution to favor rapid pyramiding of useful alleles ( Tadesse et al., 2019 ; Colasuonno et al., 2021 ).…”

“…The NAM population was genotyped using the 25K TraitGenetics array (GmbH, Gatersleben, Germany), which combines the most polymorphic markers from the Axiom Breeder Array and the Illumina Infinium 90K ( Mulugeta et al., 2023 ). High-fidelity polymorphic SNPs were defined as those having less than 1% missing data and a minor allele frequency superior to 10% as can be expected in a biparental population.…”