Genomic characterization of Peruvian Creole goats: Insights into Population Structure and Runs of Homozygosity

AbstractPeruvian Creole goats (PCGs) represent a unique genetic resource shaped by adaptation to diverse environments and traditional breeding practices. In this study, we performed a genomic analysis of six regional populations (Ancash, Ica, Lambayeque, Lima, Piura, and Tumbes) using high-density SNP genotype data. Principal component analysis revealed a moderate genetic structure, with the Ica population showing clear separation and northern populations exhibiting overlap. Runs of homozygosity were predominantly short, and specific regions on chromosome 6 were shared across populations. Inbreeding coefficients were generally low, with Ancash showing the highest values. Linkage disequilibrium decayed rapidly over genetic distance, especially in Piura, indicating higher genetic diversity. Estimates of effective population size revealed decreasing trends across populations, with Piura maintaining the largest recent population size. These findings offer valuable insights into the population structure of Peruvian Creole goats, providing guidance for conservation and sustainable breeding efforts.摘要：秘鲁克里奥尔山羊（Peruvian Creole goats，以下简称PCGs）是一类独特的遗传资源，其演化形成受多样环境适应与传统育种实践的共同塑造。本研究利用高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因型数据，对安卡什、伊卡、兰巴耶克、利马、皮乌拉及通贝斯共6个地理类群开展基因组分析。主成分分析（Principal Component Analysis, PCA）结果显示类群间存在中等程度的遗传结构：伊卡类群呈现显著的遗传分化，北部类群则表现出遗传重叠现象。纯合性片段（Runs of Homozygosity, ROH）整体长度偏短，且6号染色体上的特定区域在所有类群中均存在共享片段。近交系数整体处于较低水平，其中安卡什类群的近交系数最高。连锁不平衡（Linkage Disequilibrium, LD）随遗传距离增加快速衰减，尤以皮乌拉类群最为显著，暗示其遗传多样性更高。有效种群大小（Effective Population Size, Ne）的估算结果显示，所有类群的有效种群规模均呈下降趋势，皮乌拉类群的近期有效种群规模最大。本研究结果为秘鲁克里奥尔山羊的类群遗传结构解析提供了重要见解，同时为其保护与可持续育种工作提供了科学指导。