The knowledge about linkage disequilibrium (LD) and effective population size (N_e) is essential to determine the optimal marker density required for performing genomic studies. In this study, the aim was to estimate the LD and N_e of a Saanen goat population using a panel of 62,557 single nucleotide polymorphisms (SNPs), Axiom_OviCap (Caprine), customized by Affimetrix. Twenty-four males and 916 females were genotyped from herds from the Dairy Goats Breeding Program (from Portuguese Programa de Melhoramento Genético de Caprinos Leiteiros - Capragene®). The decay of the LD was analysed using quadratic correlation coefficient (r²) for all pairs of markers on each chromosome. To estimate N_e the values of r² combined with the distance between the markers was used, based on the physical map used for the LD analysis. The mean value of r² between adjacent markers (∼52 kb) was 0.04 ± 0.06. Among chromosomes, the range of values varied from 0.03 ± 0.06 to 0.05 ± 0.08. The LD fell rapidly from the first to the second distance range. In later intervals, the average of r² decreased more gradually. Moderate levels of r² (> 0.20), on a scale of 0–1, were observed only in the genetic distance classes up to 20 kb. The estimate of N_e decreased over time, ranging from 42 animals, 19 past generations, to 15 animals in the current generation. The observed results have practical applications for performing genomic studies, and indicate the need to use a denser marker panel (∼ 300k), since the LD level was relatively small even at short distances, and it is essential to expand the size of the reference population.

有关连锁不平衡 (LD) 和有效种群大小 (N _e ) 的知识对于确定执行基因组研究所需的最佳标记密度至关重要。在本研究中，目的是使用 Affimetrix 定制的一组 62,557 个单核苷酸多态性 (SNP) Axiom_OviCap (Caprine)来估计Saanen 山羊种群的 LD 和 N _e。从来自奶山羊育种计划（来自葡萄牙 Programa de Melhoramento Genético de Caprinos Leiteiros - Capragene®）的群中对 24 只雄性和 916 只雌性进行了基因分型。对于每个染色体上的所有标记对，使用二次相关系数 (r ² )分析 LD 的衰减。估计 N _e r ²的值基于用于 LD 分析的物理图，结合使用标记之间的距离。相邻标记之间r ²的平均值(~52 kb) 为 0.04 ± 0.06。在染色体中，值的范围从 0.03 ± 0.06 到 0.05 ± 0.08 不等。LD从第一到第二距离范围迅速下降。在以后的间隔中，r ²的平均值逐渐下降。仅在高达 20 kb 的遗传距离类别中观察到中等水平的 r ² (> 0.20)，范围为 0–1。N _e的估计随着时间的推移，数量从 42 只动物（过去的 19 代）到当代的 15 只。观察到的结果对进行基因组研究具有实际应用，并表明需要使用更密集的标记面板（~ 300k），因为即使在短距离内 LD 水平也相对较小，并且必须扩大参考群体的规模.