Hereford genotypes for South Africa, Ireland, New Zealand, and Uruguay

This study aimed to develop a better understanding of the local adaptation and selection of South African, Irish, Uruguayan, and New Zealand Hereford populations in their respective environments. Before analyses, a total of 1 693 individual genotypes were received where 1 538 individuals for the four populations remained after quality control for further downstream data analyses. All individuals were genotyped using seven different arrays, as listed in Table1. Descriptive genomic diversity parameters were estimated as HE, HO, FIS, MAF, and LD using PLINK v 1.9. All populations showed a moderate level of heterozygosity with HE values ranging from 0.359 to 0.391, and HO values ranging from 0.352 to 0.388. FIS values were -0.00475 to 0.0189 with MAF values ranging from 0.24 to 0.29 and LD ranging from 0.41 to 0.70. Population structure was visualised through principal component analysis. Each population showed to have a distinct cluster with some overlap between clusters. Intra-population genomic relatedness was determined through ROH. The detectRUNS package was used in R and a consecutive runs method was applied. The Irish and New Zealand populations showed to have the lowest degree of intra-population relatedness. A high level of genetic differentiation was observed in all populations. Selection signatures and candidate genes were identified using ROH for an intra-population approach and Pairwise Wright’s FST for an inter-population approach. Most notably, intra-population candidate genes related to traits of adaptation where the KDR and KIT genes were identified. Inter-population comparisons revealed 60 candidate genes related to traits of adaptation, production, and quality. The most common trait identified was that of bovine respiratory disease susceptibility. Five candidate genes, namely ARL6, ENOPH1, PPARGC1A, SCD5, and SNCA, were found to overlap between four of the six inter-population comparisons. Production and quality-related traits aligned with the breeding objectives of each population. The candidate genes related to adaptability traits showed that each population is adapted to its environment. Overall, each population showed to be genomically diverse and adapted to its geographically separated production region.

本研究旨在深入解析南非、爱尔兰、乌拉圭及新西兰赫里福德牛（Hereford）种群在各自生存环境中的本地适应与选育机制。分析前共收集到1693份个体基因型样本，经质量控制后保留4个种群的1538份个体样本用于后续下游数据分析。所有个体均通过7种不同的基因分型阵列完成基因分型，具体信息如表1所列。本研究利用PLINK v1.9软件估算了期望杂合度（Expected Heterozygosity, HE）、观测杂合度（Observed Heterozygosity, HO）、近交系数（Fixation Index, FIS）、次要等位基因频率（Minor Allele Frequency, MAF）以及连锁不平衡（Linkage Disequilibrium, LD）等基因组多样性描述参数。结果显示，所有种群均表现出中等水平的杂合性：HE值介于0.359至0.391之间，HO值介于0.352至0.388之间；FIS值范围为-0.00475至0.0189，MAF值介于0.24至0.29之间，LD值介于0.41至0.70之间。通过主成分分析（Principal Component Analysis, PCA）对种群遗传结构进行可视化，结果表明各种群均形成独立聚类簇，仅簇间存在少量重叠。本研究利用纯合子片段（Runs of Homozygosity, ROH）评估种群内基因组亲缘关系：采用R语言的detectRUNS包，通过连续片段检测方法完成分析，结果显示爱尔兰与新西兰种群的种群内亲缘关系程度最低。所有种群均呈现出较高水平的遗传分化。本研究分别采用种群内ROH分析策略，以及种群间成对赖特F统计量（Pairwise Wright’s FST）分析策略，鉴定选择信号与候选基因。其中，种群内分析中最值得关注的是鉴定出与适应性性状相关的候选基因，包括KDR与KIT基因。种群间比较共鉴定出60个与适应性、生产性能及品质性状相关的候选基因，其中最常见的性状为牛呼吸道疾病易感性。在6组种群间比较中的4组里，均检测到ARL6、ENOPH1、PPARGC1A、SCD5及SNCA这5个重叠的候选基因。与生产性能和品质相关的候选基因与各群体的育种目标高度契合。与适应性性状相关的候选基因分析结果表明，各种群均已适应其所处的地理环境。总体而言，各种群均具有丰富的基因组多样性，并已适配其地理分隔的生产区域。