Although human-imposed selection is known to have altered plant traits during crop domestication, the effect of selection on host susceptibility or resistance is not well understood. Moreover, the domestication of perennial tree fruit crops, unlike annual crops, was driven by hybridization, clonal propagation, and selection of desirable phenotypes, which could confound the accurate assessment of domestication-associated effects on host resistance or susceptibility genes. We studied the effects of domestication on disease-related nucleotide-binding leucine-rich repeat (NLR) genes by combining phylogenetic, haplotype, and selection signature analysis using sequence data from Golden Delicious double haploid (GDDH13 v.1.1) apple genome and 80 resequenced domesticated and wild Malus accessions. The NLR gene family in the GDDH13 v.1.1 apple genome constituted 546 genes that showed expansion mainly through proximal (39.1%) and dispersed (29.5%) duplications. The genome duplication (WGD) within Rosaceae, affecting the Malus lineage, is also evident in the NLR genes. The NLR genes are found in genomic regions associated with previously detected disease resistance-related quantitative trait loci (QTL) for apple scab, fire blight, powdery mildew, and blue mold. A genomic diversity analysis identified that the NLR genes in domesticated apples (Malus domestica) have more variation (average π_dom=4.01 × 10⁻³) than their main progenitor, wild M. sieversii (average π_sie=2.95 × 10⁻³) and M. sylvestris (average π_syl=2.11 × 10⁻³), which hybridized with M. domestica during the domestication process. These results suggest evidence of selection on disease-related genes associated with domestication of apple. An increased diversity across NLR genes in the domesticated germplasm may be attributed to their diverse geographical origins and distinct pedigrees, together with selection for disease resistance during domestication. The NLR genes under selection can provide opportunities to explore their role in disease resistance in apples.

尽管已知人为选择会在作物驯化过程中改变植物性状，但人们对选择对寄主易感性或抗性的影响还知之甚少。而且，与一年生作物不同，多年生树果作物的驯化是由杂交，克隆繁殖和理想表型的选择驱动的，这可能混淆了驯化相关对宿主抗性或易感基因的影响的准确评估。我们通过使用Golden Delicious double haploid（GDDH13 v.1.1）苹果基因组和80个重测序序列数据进行系统发育，单倍型和选择签名分析相结合的研究，研究了驯化对疾病相关核苷酸结合的富含亮氨酸的重复序列（NLR）基因的影响驯养和野生海棠加入。GDDH13 v.1.1苹果基因组中的NLR基因家族构成了546个基因，这些基因主要通过近端重复（39.1％）和分散重复（29.5％）的重复表达。基因组中的重复（WGD）内蔷薇科，影响海棠谱系，也是在明显NLR基因。的NLR基因在对苹果黑星病，火疫病，白粉病，和蓝色模具之前检测到的疾病抗性相关的数量性状基因座（QTL）相关的基因组区域中。基因组多样性分析表明，家养苹果（Malus domestica）中的NLR基因具有更大的变异性（平均_πdom = 4.01×10 ^-3）。）与其主要祖先野生的M. sieversii（平均_πsie = 2.95×10 ^-3）和S.sylvestris（平均_πsyl = 2.11×10 ^-3）在驯化过程中与家蝇（M. domestica）杂交。这些结果表明选择与苹果驯化有关的疾病相关基因的证据。驯化种质中NLR基因的多样性增加可能归因于其多样化的地理起源和独特的血统，以及在驯化过程中对疾病抗性的选择。该NLR 选择的基因可以提供机会探索它们在苹果抗病性中的作用。