Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries’ breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms ‘response-to-auxin’ and ‘response-to-wounding.’ Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

中文翻译：

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作物属性、选择和重组对加拿大面包小麦分子变异的影响

栽培种质为研究作物农艺性状、主要基因的选择以及交叉率差异如何驱动等位基因变异模式提供了机会。确定这些因素如何与栽培面包小麦 ( Triticum aestivumL.)，我们使用来自 Illumina Wheat iSelect 90K SNP 阵列的过滤单核苷酸多态性 (SNP) 调用为过去 170 年间在加拿大种植的 388 个种质生成基因型。条目的育种计划、发布时代、谷物质地、籽粒颜色和生长习性促成了等位基因分化。一些已知影响面筋强度、生长习性和谷物颜色等性状的主要基因座侧翼的标记的等位基因多样性和连锁不平衡 (LD) 与选择性扫描一致。尽管如此，主要位点的一些侧翼标记具有低 LD 和高等位基因多样性。正选择可能作用于同源基因，这些基因对基因本体术语“对生长素的反应”和“对伤口的反应”具有显着的富集。LD 的长区域，约占整个染色体长度的三分之一，与许多着丝粒周围区域有关。这些地区还具有多样性低的特点。加强这些地区的重组可以产生新的等位基因组合，以加速加拿大小麦的改良。