Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil.
Department of Animal Science, University of Nebraska, Lincoln, NE, USA.
Sci Rep. 2018 Jun 11;8(1):8851. doi: 10.1038/s41598-018-27259-7.
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r and |D'| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r for |D'| across all chromosomes. The average r between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
为了使基因组选择取得成功，标记与因果突变之间必须存在足够的连锁不平衡。本研究的目的是评估使用 Santa Inês 品种的连锁不平衡程度，并推断达到合理预测精度所需的最小标记数量。总共使用了 38168 个 SNPs 和 395 个样本。用 r 和 |D'| 测量的相邻标记对之间的平均 LD 分别为 0.166 和 0.617。相邻标记对之间的 LD 值在所有染色体上的 r 为 0.135 至 0.194，|D'| 为 0.568 至 0.650。每个染色体上所有 SNP 之间的平均 r 为 0.018。间隔 0.10 到 0.20 Mb 的 SNP 之间的 r 估计平均为 0.1033。确定的单倍型块由 2 到 21 个标记组成。此外，估计的平均近交系数和有效种群大小分别为 0.04 和 96。本研究中估计的 LD 低于其他物种报告的 LD，其特征是短的单倍型块。我们的研究结果表明，建议在 Santa Inês 品种中使用更高密度的 SNP 面板来实施基因组选择。
