Abstract
The present study aimed to improve the accuracy of genomic prediction of 16 agronomic traits in a diverse bread wheat (Triticum aestivum L.) germplasm under terminal drought stress and well-watered conditions in semi-arid environments. An association panel including 87 bread wheat cultivars and 199 landraces from Iran bread wheat germplasm was planted under two irrigation systems in semi-arid climate zones. The whole association panel was genotyped with 9047 single nucleotide polymorphism markers using the genotyping-by-sequencing method. A number of 23 marker-trait associations were selected for traits under each condition, whereas 17 marker-trait associations were common between terminal drought stress and well-watered conditions. The identified marker-trait associations were mostly single nucleotide polymorphisms with minor allele effects. This study examined the effect of population structure, genomic selection method (ridge regression-best linear unbiased prediction, genomic best-linear unbiased predictions, and Bayesian ridge regression), training set size, and type of marker set on genomic prediction accuracy. The prediction accuracies were low (-0.32) to moderate (0.52). A marker set including 93 significant markers identified through genome-wide association studies with P values ≤ 0.001 increased the genomic prediction accuracy for all traits under both conditions. This study concluded that obtaining the highest genomic prediction accuracy depends on the extent of linkage disequilibrium, the genetic architecture of trait, genetic diversity of the population, and the genomic selection method. The results encouraged the integration of genome-wide association study and genomic selection to enhance genomic prediction accuracy in applied breeding programs.
Highlights
The world wheat production in 2020 is estimated at 762.7 million tons [1]
The estimated PCs for the whole association panel (WAP) showed that PCs 1, 2, and 3 could explain 12.39, 5.58, and 2.81% of genotypic variations, respectively (Fig 2)
Chromosome 4D had the lowest number of markers (82), while chromosomes 2B and 3B had the highest number of markers (743 and 732, respectively) (S3 Table in S4 File)
Summary
The world wheat production in 2020 is estimated at 762.7 million tons [1]. Bread wheat (T. aestivum) has approximately 10.67 grams of proteins and 47.54 grams of carbohydrates (per 100 grams of seeds), which is remarkably higher than other cereals and makes bread wheat one of the most strategic crops [2]. Wheat is a highly adapted plant species which can grow between the latitudes of 30 ̊ to 60 ̊N and 27 ̊ to 40 ̊S [4]. In the Middle East, drought stress normally occurs at the end of the growing season when the spike has already appeared. In the Persian plateau, where most of the climate zone is arid or semi-arid, farmers are very well-trained during the centuries to deposit rainwater throughout spring for irrigating farms at the end of the growing season when there is no rain during the seed development stage [8]. The Persian farmers irrigate their farms two to four more times with the stored water after spike appearance to avoid yield loss due to late-season drought stress [8]
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