<p>Runs of homozygosity script.</p>

The infection by Haemonchus contortus is a significant challenge to sheep production in tropical regions, particularly in developing countries. Although several genomic studies have been conducted on this topic, there is still a lack of research combining evolutionary information on resistance and resilience to nematode infection. The aim of this study was to provide evidence of different types of selection and their effects on traits associated with infection levels and animal productivity, using pedigree, phenotypic, and genomic data. It was hypothesized that these patterns would reflect indirect artificial selection and relaxed natural selection. Phenotypic data were collected for Faecal Egg Count (FEC), Eye Color Chart (ECC), Packed Cell Volume (PCV), Total Plasma Protein (TPP), Body Weight (BW), and Body Condition Score (BCS) from 1,283 Santa Inês sheep. A total of 638 animals were genotyped using the Ovine SNP50 BeadChip. After estimating breeding values using the BLUPF90 software, statistical models were employed to assess differences in the intensities of natural and artificial selection and to identify the type of selection acting on each trait, in comparison with classic studies of sexual selection. Selection signatures were investigated using Wright’s fixation index, in addition to analyses of runs of homozygosity. The gene content of the identified regions and their associated pathways were examined using the Ensembl BioMart tool and the Panther Classification System, respectively, along with alignments of quantitative trait loci (QTL). BCS was found to be the best indirect trait correlated with parasitological traits, and selection intensity analysis showed that natural selection contributed 76%, compared to 24% from artificial selection. Traits such as BW, PCV, and TPP exhibited directional selection, while FEC and ECC varied according to the challenge level applied. A total of 15 selection signatures were identified (11 for natural selection and 4 for artificial selection), with 9 overlapping with islands of homozygosity, encompassing 131 genes and 49 QTL. A critical analysis revealed that both types of selection contribute to the phenomena of resistance and resilience. However, evidence of directional selection, hard sweeps, and functional enrichment of innate immunity was found for artificial selection, while natural selection exhibited evidence of stabilizing selection, soft sweeps, and functional enrichment of adaptive immunity.捻转血矛线虫（Haemonchus contortus）感染对热带地区，尤其是发展中国家的绵羊养殖产业构成了严峻挑战。尽管目前已针对该主题开展了多项基因组学研究，但仍缺乏结合线虫感染抗性与恢复力进化信息的相关研究。本研究旨在利用系谱、表型及基因组数据，阐明不同选择类型及其对感染水平相关性状与动物生产性能的影响。研究假设，上述选择模式将体现间接人工选择与松弛化自然选择的特征。本研究采集了1283只圣塔伊内斯（Santa Inês）绵羊的表型数据，涵盖粪便虫卵计数（Faecal Egg Count, FEC）、眼色评分（Eye Color Chart, ECC）、红细胞压积（Packed Cell Volume, PCV）、血浆总蛋白（Total Plasma Protein, TPP）、体重（Body Weight, BW）及体况评分（Body Condition Score, BCS）。研究使用绵羊50K SNP基因分型芯片（Ovine SNP50 BeadChip）对638只个体进行了基因分型。在使用BLUPF90软件估计育种值后，本研究采用统计模型评估自然选择与人工选择的强度差异，并结合经典性选择研究，鉴定各性状所受的选择类型。除纯合子片段（runs of homozygosity, ROH）分析外，本研究还利用赖特固定指数（Wright’s fixation index）开展了选择信号检测。研究分别使用Ensembl BioMart工具与Panther分类系统，对鉴定得到的基因组区域的基因构成及其相关通路进行了分析，并结合数量性状基因座（quantitative trait loci, QTL）的比对结果。研究发现体况评分（BCS）是与寄生虫学性状相关性最优的间接性状；选择强度分析显示，自然选择的贡献占比达76%，人工选择占比为24%。体重（BW）、红细胞压积（PCV）及血浆总蛋白（TPP）等性状表现为定向选择，而粪便虫卵计数（FEC）与眼色评分（ECC）则随感染攻毒水平的不同而呈现差异。本研究共鉴定得到15个选择信号区域（其中11个对应自然选择，4个对应人工选择），其中9个区域与纯合子岛（islands of homozygosity）存在重叠，共涵盖131个基因与49个数量性状基因座（QTL）。批判性分析表明，两类选择均对抗性与恢复力相关表型的形成具有贡献。不过，人工选择的相关证据显示其存在定向选择、硬选择性清除以及先天免疫功能富集现象；而自然选择则表现为稳定化选择、软选择性清除以及适应性免疫功能富集特征。