Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height

Abstract

Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

“…The latter are certainly suitable for identifying highly effective loci and easily measurable traits, but they disregard most of the genetic changes associated with crop improvement (Morrell et al, 2012). Genome-wide analyses based on patterns of linkage disequilibrium (LD) decay, as well as investigations on the genetic differentiation between populations, have already led to the identification of different chromosomal regions under selection in durum wheat (N'Diaye et al, 2018;Maccaferri et al, 2019).…”

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

“…Given that a large number of molecular markers are necessary for higher resolution and precision in the genetic mapping of complex traits, hundreds of thousands of markers have been developed in wheat, including a wheat 90K SNP iSelect assay containing 81,587 SNP markers [ 26 ]. SNPs have been widely used to dissect the genetic basis of several economically important traits [ 15 , 17 , 18 , 20 ], and to develop a high-density durum wheat consensus map [ 27 ].…”

“…Thus, the genetic basis of GY has been investigated through the three main yield components which will be explored in this review: kernel weight, kernels number and kernels number per unit area [ 28 , 31 ]. A total of 665 QTLs (100 with a pleiotropic effect) were identified and associated with grain yield and its components ( Table S1 ) [ 7 , 14 , 15 , 17 , 18 , 30 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ]. Specifically, nine additional yield components were considered: kernel length (KL), kernel width (KW), thousand-kernel weight (TKW) associated with the kernel weight, kernels number per spike (KNS), kernels number per spikelet (KNSL), spikelets number per spike (SLNS) associated with the kernels number, grain yield (GY), kernels number per square meter (KNM) and spike number per square meter (SNM) related to the kernels number per unit area ( Figure 1 ).…”

The content of yellow pigments in durum wheat (Titicum durum Desf.) grains: biosynthesis, genetic control, marker selection

“…Селекционные линии, полученные с применением методов MAS на основе MACS 3125 и HI 8498, показали значительное увеличение YPC: 6.16-7.7 и 5.0-7.46 ppm соответственно. В настоящее время MAS используется в CIMMYT и в Канаде для отбора селекционных линий с низкой активностью липоксигеназы при помощи маркера LOXA, нацеленного на аллель Lpx-B1.1c (Randhawa et al, 2013;Dreisigacker et al, 2016;N'Diaye et al, 2017N'Diaye et al, , 2018. В России во всех лабораториях, осуществляющих селекцию на увеличение концентрации каротиноидов в зерне, индекса желтизны семолины и конечных продуктов, применяются методы традиционной селекции.…”