Abstract
Durum wheat is an important crop for the human diet and its consumption is gaining popularity. In order to ensure that durum wheat production maintains the pace with the increase in demand, it is necessary to raise productivity by approximately 1.5% per year. To deliver this level of annual genetic gain the incorporation of molecular strategies has been proposed as a key solution. Here, four RILs populations were used to conduct QTL discovery for grain yield (GY) and 1,000 kernel weight (TKW). A total of 576 individuals were sown at three locations in Morocco and one in Lebanon. These individuals were genotyped by sequencing with 3,202 high-confidence polymorphic markers, to derive a consensus genetic map of 2,705.7 cM, which was used to impute any missing data. Six QTLs were found to be associated with GY and independent from flowering time on chromosomes 2B, 4A, 5B, 7A and 7B, explaining a phenotypic variation (PV) ranging from 4.3 to 13.4%. The same populations were used to train genomic prediction models incorporating the relationship matrix, the genotype by environment interaction, and marker by environment interaction, to reveal significant advantages for models incorporating the marker effect. Using training populations (TP) in full sibs relationships with the validation population (VP) was shown to be the only effective strategy, with accuracies reaching 0.35–0.47 for GY. Reducing the number of markers to 10% of the whole set, and the TP size to 20% resulted in non-significant changes in accuracies. The QTLs identified were also incorporated in the models as fixed effects, showing significant accuracy gain for all four populations. Our results confirm that the prediction accuracy depends considerably on the relatedness between TP and VP, but not on the number of markers and size of TP used. Furthermore, feeding the model with information on markers associated with QTLs increased the overall accuracy.
Highlights
Durum wheat (Triticum durum Desf., 2n = 4x = 28, AABB) is grown annually on over 17 million hectares worldwide, and it represents one of the bases of the Mediterranean diet
For grain yield (GY), Gidara 2 had a smaller value than the average GY, same for the parents Icamor and Younes
The results of this study provide a framework for better understanding and deploying molecular selection in durum wheat
Summary
Durum wheat (Triticum durum Desf., 2n = 4x = 28, AABB) is grown annually on over 17 million hectares worldwide, and it represents one of the bases of the Mediterranean diet This region is the largest consumer of durum wheat products and the most significant durum import market (Soriano et al, 2017). Genetic linkage map and QTL mapping are useful tools for discovering genomic regions associated with traits of interest (Zhang et al, 2018). The development of consensus maps has already been shown to bridge the information between populations, and to increase marker density, improve genome coverage, provide a validation of the marker ordering, and reduce markers gaps due to the absence of polymorphism between two parents (Marone et al, 2012; Maccaferri et al, 2014). Numerous recent studies have used this marker system to identify quantitative trait loci (QTL) associated with yield, agronomic traits, and physiologic traits in drought and heat-stressed environments (Acuña-Galindo et al, 2015; Sukumaran et al, 2016; Edae et al, 2017; Hussain et al, 2017; Mwadzingeni et al, 2017; Asif et al, 2018; Bhatta et al, 2018; Roselló et al, 2019), in order to pyramid these QTLs via markerassisted breeding (Edae et al, 2014)
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