Department of Genetics, University of Cordoba, Córdoba, Spain.
Department of Agronomy, ETSIA, University of Seville, Seville, Spain.
J Anim Breed Genet. 2024 Jul;141(4):453-464. doi: 10.1111/jbg.12856. Epub 2024 Feb 1.
Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wg) and ssGREML (g) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (F) and ROH-based genomic (F) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when F was used. However, all traits were negatively affected by the increase in genomic inbreeding, and F was found to capture more inbreeding depression than F. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.
近亲繁殖衰退是一种与由于亲属间交配而导致适应性和表型性能丧失相关的遗传现象。历史上，近亲繁殖系数是根据系谱信息估算的。然而，基因组选择计划的开始提供了大量使用 SNP 阵列进行基因分型的个体数据集，这使得使用基因组数据更精确地评估个体的基因组水平近亲繁殖。受近亲繁殖增加影响最大的特征之一是繁殖。这在马中尤为重要，因为其繁殖力与其他家畜物种相比仅中等水平。为了进一步探讨这个问题，我们评估了近亲繁殖对西班牙纯种马五个繁殖特征（首次产驹年龄（AFF）、产驹间隔平均时间（AIF）、总产驹数（NF）、繁殖寿命（PL）和繁殖效率（RE））的影响，使用基因组数据。通过在 29847 头 PRE 母马的繁殖数据中，使用 REML（wg）和 ssGREML（g）方法对这些特征进行清洗，获得了剩余预测表型。然后，我们使用来自 1018 头动物的基于系谱（F）和基于 ROH 的基因组（F）近亲繁殖系数，这些动物使用 61271 个 SNP 进行基因分型，以估计近亲繁殖衰退（线性回归）。我们的结果表明，所有繁殖特征都存在显著水平的近亲繁殖衰退，除了使用 F 时的 AIF 特征。然而，所有特征都受到基因组近亲繁殖增加的负面影响，并且 F 比 F 捕获更多的近亲繁殖衰退。同样，使用基因组数据的 REML 模型（ssGREML）用于估计预测剩余表型的结果表明，与不使用基因组的模型相比，模型解释的方差更高。最后，进行了分段回归分析以评估近亲繁殖衰退的影响，结果表明，亲缘和基因组同型性的水平在繁殖特征中并不均匀表现。相反，随着同型性的增加，近亲繁殖衰退的水平从低到高不等。该分析还表明，繁殖特征对近亲繁殖衰退非常敏感，即使同型性水平相对较低。
