Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example.
Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example.
复制标题
DOI：
10.1186/s12711-021-00683-6
复制
发表时间：
2021-11-27
期刊：
影响因子：
--
通讯作者：
Misztal I
中科院分区：
文献类型：
--
作者：
Abdollahi-Arpanahi R;Lourenco D;Legarra A;Misztal I
了解基因组选择是否对牲畜有效以及基因组选择的结果何时变得可见是我们在本文中解决的基本问题。使用三个标准来确定育种计划随时间的实践：(1) 基于谱系的最佳线性无偏预测 (BLUP) 与单步基因组 BLUP (ssGBLUP) 的估计遗传趋势的分歧点，(2) 基于 BLUP 和 ssGBLUP 的实现孟德尔采样 (RMS) 趋势的分歧点，以及 (3) 将遗传趋势划分为基因分型个体和非基因分型个体所贡献的趋势以及男性和女性。我们使用了来自商业猪母系的 282,035 头动物的数据，其中 32,856 头在质量控制后进行了 36,612 个单核苷酸多态性 (SNP) 的基因分型。表型数据分别包括 228,427、101,225 和 11,444 条出生体重、保育室平均日增重和采食量记录。使用 BLUP 和 ssGBLUP 在多性状框架中预测育种值。 BLUP和ssGBLUP估计的遗传趋势和RMS趋势的分歧点表明，基因组选择实际上从2019年开始。将整体遗传趋势分为基因分型个体和非基因分型个体发现，基因分型动物对整体遗传趋势的贡献从2016年的 ~ 74%迅速增加到2019年的90%。雌性途径对遗传趋势的贡献也迅速增加。自从在该猪群中实施基因组选择以来，这一数字有所增加，这反映了近年来基因分型策略的变化。我们的结果表明，对育种计划实践的评估可以基于 BLUP 和 ssGBLUP 之间遗传和 RMS 趋势的分歧点以及基于将遗传趋势划分为不同选择途径的贡献来进行。然而，应该指出的是，如果对优良动物进行追溯性基因分型，遗传趋势可能会在基因组选择开始之前出现分歧。以猪群体为例，结果表明基因组选择在该群体中是有效的。
Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females. We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control. Phenotypic data included 228,427, 101,225, and 11,444 records for birth weight, average daily gain in the nursery, and feed intake, respectively. Breeding values were predicted in a multiple-trait framework using BLUP and ssGBLUP. The points of divergence of the genetic and RMS trends estimated by BLUP and ssGBLUP indicated that genomic selection effectively started in 2019. Partitioning the overall genetic trends into that for genotyped and non-genotyped individuals revealed that the contribution of genotyped animals to the overall genetic trend increased rapidly from ~ 74% in 2016 to 90% in 2019. The contribution of the female pathway to the genetic trend also increased since genomic selection was implemented in this pig population, which reflects the changes in the genotyping strategy in recent years. Our results show that an assessment of breeding program practices can be done based on the point of divergence of genetic and RMS trends between BLUP and ssGBLUP and based on the partitioning of the genetic trend into contributions from different selection pathways. However, it should be noted that genetic trends can diverge before the onset of genomic selection if superior animals are genotyped retroactively. For the pig population example, the results showed that genomic selection was effective in this population.
登录
查看更多内容
影响因子：
3.5
作者：
Aguilar, I.;Misztal, I.;Lawlor, T. J.
通讯作者：
Lawlor, T. J.
影响因子：
2.6
作者：
Koivula, M.;Stranden, I.;Mantysaari, E. A.
通讯作者：
Mantysaari, E. A.
影响因子：
1.5
作者：
RENDEL, JM;ROBERTSON, A
通讯作者：
ROBERTSON, A
影响因子：
3.5
作者：
Tyriseva, A. -M.;Mantysaari, E. A.;Lidauer, M. H.
通讯作者：
Lidauer, M. H.
影响因子：
3.6
作者：
Garcia-Cortes, L. A.;Martinez-Avila, J. C.;Toro, M. A.
通讯作者：
Toro, M. A.