Wientjes Yvonne C J, Peeters Katrijn, Bijma Piter, Huisman Abe E, Calus Mario P L
Animal Breeding and Genomics, Wageningen University & Research, 6700 AH, Wageningen, The Netherlands.
Hendrix Genetics B.V., 5830AC, Boxmeer, The Netherlands.
Genet Sel Evol. 2024 Dec 17;56(1):76. doi: 10.1186/s12711-024-00941-3.
Genetic selection improves a population by increasing the frequency of favorable alleles. Understanding and monitoring allele frequency changes is, therefore, important to obtain more insight into the long-term effects of selection. This study aimed to investigate changes in allele frequencies and in results of genome-wide association studies (GWAS), and how those two are related to each other. This was studied in two maternal pig lines where selection was based on a broad selection index. Genotypes and phenotypes were available from 2015 to 2021.
Several large changes in allele frequencies over the years were observed in both lines. The largest allele frequency changes were not larger than expected under drift based on gene dropping simulations, but the average allele frequency change was larger with selection. Moreover, several significant regions were found in the GWAS for the traits under selection, but those regions did not overlap with regions with larger allele frequency changes. No significant GWAS regions were found for the selection index in both lines, which included multiple traits, indicating that the index is affected by many loci of small effect. Additionally, many significant regions showed pleiotropic, and often antagonistic, associations with other traits under selection. This reduces the selection pressure on those regions, which can explain why those regions are still segregating, although the traits have been under selection for several generations. Across the years, only small changes in Manhattan plots were found, indicating that the genetic architecture was reasonably constant.
No significant GWAS regions were found for any of the traits under selection among the regions with the largest changes in allele frequency, and the correlation between significance level of marker associations and changes in allele frequency over one generation was close to zero for all traits. Moreover, the largest changes in allele frequency could be explained by drift and were not necessarily a result of selection. This is probably because selection acted on a broad index for which no significant GWAS regions were found. Our results show that selecting on a broad index spreads the selection pressure across the genome, thereby limiting allele frequency changes.
遗传选择通过增加有利等位基因的频率来改良种群。因此，了解和监测等位基因频率的变化对于深入了解选择的长期影响至关重要。本研究旨在调查等位基因频率的变化以及全基因组关联研究（GWAS）的结果，以及这两者之间的相互关系。这在两个母系猪品系中进行了研究，其选择基于广泛的选择指数。2015年至2021年的基因型和表型数据可用。
在两个品系中均观察到多年来等位基因频率的几个大的变化。基于基因降序模拟，最大的等位基因频率变化不超过随机漂变预期的范围，但选择作用下的平均等位基因频率变化更大。此外，在针对所选性状的GWAS中发现了几个显著区域，但这些区域与等位基因频率变化较大的区域不重叠。在两个品系中，针对包含多个性状的选择指数均未发现显著的GWAS区域，这表明该指数受许多小效应位点的影响。此外，许多显著区域显示出与其他所选性状的多效性且通常是拮抗的关联。这降低了这些区域上的选择压力，这可以解释为什么尽管这些性状已经经过几代的选择，这些区域仍在分离。多年来，在曼哈顿图中仅发现了微小变化，表明遗传结构相当稳定。
在等位基因频率变化最大的区域中，未发现针对任何所选性状的显著GWAS区域，并且所有性状在一代中标记关联的显著水平与等位基因频率变化之间的相关性接近零。此外，最大的等位基因频率变化可以用随机漂变来解释，不一定是选择的结果。这可能是因为选择作用于一个未发现显著GWAS区域的广泛指数。我们的结果表明，基于广泛指数进行选择会将选择压力分散到整个基因组，从而限制等位基因频率的变化。
