Sarviaho Katri, Uimari Pekka, Martikainen Katja
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
J Anim Breed Genet. 2023 May;140(3):343-353. doi: 10.1111/jbg.12762. Epub 2023 Feb 21.
Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5 Mbp, and a slight increase in the proportion of segments over 10 Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.
在过去十年中，基因组选择已应用于奶牛育种。利用基因组信息可以加快遗传进展，因为出生后就能相当准确地预测育种值。然而，如果每代的近亲繁殖率增加且有效种群规模减小，遗传多样性可能会降低。例如，尽管芬兰艾尔夏牛具有许多优良特性，如平均蛋白质产量高和繁殖力强，但随着时间的推移，该品种已失去其作为芬兰最常见奶牛品种的地位。因此，维持该品种的遗传变异性变得更加重要。我们研究的目的是利用系谱和基因组数据估计基因组选择对近亲繁殖率和有效种群规模的影响。基因组数据包括来自75038个个体的46914个推算单核苷酸多态性（SNP）变体，系谱数据包括2770025个个体。数据中的所有动物均出生于2000年至2020年之间。基因组近亲繁殖系数估计为纯合子连续片段（ROH）中的SNP占SNP总数的比例。通过将平均基因组近亲繁殖系数对出生年份进行回归来估计近亲繁殖率。然后根据近亲繁殖率估计有效种群规模。此外，还利用系谱数据根据个体近亲繁殖的平均增加量来估计有效种群规模。假设基因组选择是逐步引入的；2012 - 2014年被视为从传统的基于表型的育种值估计向基于基因组的估计的过渡期。所识别的纯合片段的中位数长度为5.5兆碱基对，2010年后观察到长度超过10兆碱基对的片段比例略有增加。近亲繁殖率在2000年至2011年下降，随后略有上升。基于系谱和基因组的近亲繁殖率估计彼此相似。基于回归方法的有效种群规模估计对所考虑的年份数量非常敏感；因此，这些估计不是很可靠。根据个体近亲繁殖的平均增加量估计的有效种群规模在2011年达到最高值160，之后降至150。此外，实施基因组选择后，父系路径中的世代间隔已从5.5年降至3.5年。根据我们的结果，实施基因组选择后，长ROH片段的比例增加，父系路径中的世代间隔减小，近亲繁殖率增加，有效种群规模减小。然而，有效种群规模仍处于良好水平，这使得芬兰艾尔夏牛品种能够实施高效的选择方案。
