Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Office of the Director for Scientific Affairs, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Genes (Basel). 2021 Mar 17;12(3):429. doi: 10.3390/genes12030429.
Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (F) and genomic inbreeding estimates was found for F (runs of homozygosity-based F coefficient) and F (F coefficient based on the correlation between uniting gametes). F correlation with F tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.
传统上，基于系谱的亲缘关系系数被用于管理群体内的近交和控制近交衰退。基因组数据在畜牧业中的广泛应用为开发和实施基于基因组水平管理群体的方法创造了机会。因此，可以更准确地估计两个个体共享的基因组比例，而不是使用系谱信息来估计共享等位基因的预期比例。为了利用这一改进，本研究评估了波兰保种冷血马群体的基因组近交度量，并将数据与传统的近交度量进行了比较。此外，还测试了 Admixture 软件的祖先分数/比例作为符合保护计划的马的血统（血统系数）的估计。基于系谱的（F）和基于基因组的近交估计的最高相关性是在 F（基于纯合子运行的 F 系数）和 F（基于联合配子之间相关性的 F 系数）中发现的。随着系谱中登记的世代数的增加，F 与 F 的相关性趋于增加。虽然 Admixture 软件的血统和基因贡献（Q）相关，但它们显示出较差的直接一致性；因此，不能推荐 Q 值作为基于系谱的血统的估计值。所有这些发现表明，在保守性繁殖中分析群体结构时，应考虑基因组学方法作为替代或支持，以帮助控制稀有马种群的近交。
