Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.

中文翻译：

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利用全基因组关联研究表征伊朗和巴基斯坦小麦地方品种局部适应的遗传基础

对地方品种适应的基因组区域进行表征可以揭示当地小麦 ( Triticum aestivum L.) 适应性的数量遗传学框架。使用通过基因分型测序产生的全基因组单核苷酸多态性标记对来自伊朗和巴基斯坦新月沃地东部边缘的 512 个小麦地方品种进行了基因分型。巴基斯坦小麦地方品种（MAF = 0.19，H = 0.008）的次要等位基因频率（MAF）和杂合度（H ） 略高于伊朗小麦地方品种（MAF = 0.17，H = 0.005），表明巴基斯坦地方品种的遗传多样性略高。种群结构分析清楚地将巴基斯坦地方品种与伊朗地方品种区分开来，这表明两条独立的适应性轨迹。相关系数显示，伊朗和巴基斯坦的七个变量的大规模农业气候数据差异很大。全基因组关联研究使用农业气候数据确定了 91 个和 58 个位点，这可能分别支持了来自伊朗和巴基斯坦的小麦地方品种的当地适应性。选择性扫描分析确定了染色体 4A、4B、6B、7B、2D 和 6D 上的显着命中，这些命中与与局部适应性相关的基因座以及与开花时间和谷物大小相关的一些已知基因共定位。