Reverter A, Porto-Neto L R, Fortes M R S, Kasarapu P, de Cara M A R, Burrow H M, Lehnert S A
J Anim Sci. 2017 Sep;95(9):3809-3821. doi: 10.2527/jas2017.1643.
Inbreeding has the potential to negatively impact animal performance. Strategies to monitor and mitigate inbreeding depression require that it can be accurately estimated. Here, we used genomewide SNP data to explore 3 alternative measures of genomic inbreeding: the diagonal elements of the genomic relationship matrix (FGRM), the proportion of homozygous SNP (FHOM), and the proportion of the genome covered by runs of homozygosity (FROH). We used 2,111 Brahman (BR) and 2,550 Tropical Composite (TC) cattle with phenotypes recorded for 10 traits of relevance to tropical adaptation. We further explored 3 marker densities ranging from a high-density chip (729,068 SNP), a medium-density chip (71,726 SNP) specifically designed for cattle, and a low-density chip (18,860 SNP) associated with the measures of inbreeding. Measures of FGRM were highly correlated across the 3 SNP densities and negatively correlated with FHOM and FROH in the BR population. In both populations, there was a strong positive correlation for each measure of inbreeding across the 3 SNP panels. We found significant ( < 0.01) inbreeding depression for various traits, particularly when using the highest-density SNP chip in the BR population, where inbreeding was negatively associated with coat color and coat type such that inbred animals presented shorter, slicker, and lighter coats. Based on FGRM using the medium-density chip, we found that a 1% increase in inbreeding in the BR and TC populations was associated with a decrease of 0.514 and 0.579 kg BW, respectively, in yearlings. In the TC population, a 1% increase in FHOM was associated with a decrease in BCS of -0.636% ( < 0.001). The low-density chip, comprising SNP associated with inbreeding, captured genes, and regions with pleiotropic effects ( < 0.001). However, it did not improve our ability to identify inbreeding depression, relative to the use of higher-density panels. We conclude that where heterogeneous populations are present, such as in tropical environments where composite animals abound, measures of inbreeding that do not depend on allele frequencies, such as FHOM and FROH, are preferable for estimating genomic inbreeding. Finally, the sustainable intensification of livestock systems in tropical regions will rely on genetic safeguards to ensure that productivity is improved while also adapting animals to cope with climate change. The results of this study are a step toward achieving that goal.
近亲繁殖有可能对动物性能产生负面影响。监测和减轻近亲繁殖衰退的策略要求能够准确估计近亲繁殖。在此，我们使用全基因组SNP数据来探索基因组近亲繁殖的3种替代度量方法：基因组关系矩阵的对角元素（FGRM）、纯合SNP的比例（FHOM）以及纯合子连续片段覆盖的基因组比例（FROH）。我们使用了2111头婆罗门牛（BR）和2550头热带杂交牛（TC），记录了与热带适应性相关的10个性状的表型。我们进一步探索了3种标记密度，从高密度芯片（729,068个SNP）、专门为牛设计的中密度芯片（71,726个SNP）以及与近亲繁殖度量相关的低密度芯片（18,860个SNP）。FGRM度量在3种SNP密度间高度相关，并且在BR群体中与FHOM和FROH呈负相关。在两个群体中，3个SNP面板的每种近亲繁殖度量都呈现出很强的正相关。我们发现各种性状存在显著的（<0.01）近亲繁殖衰退，特别是在BR群体中使用最高密度SNP芯片时，近亲繁殖与毛色和毛型呈负相关，使得近亲繁殖的动物表现出更短、更光滑且更浅的毛发。基于使用中密度芯片的FGRM，我们发现BR和TC群体中近亲繁殖增加1%，分别与一岁龄牛体重下降0.514千克和0.579千克相关。在TC群体中，FHOM增加1%与体况评分下降-0.636%相关（<0.001）。包含与近亲繁殖、捕获基因以及具有多效性效应区域相关的SNP的低密度芯片（<0.001）。然而，相对于使用更高密度的面板，它并没有提高我们识别近亲繁殖衰退的能力。我们得出结论，在存在异质群体的地方，例如在复合动物众多的热带环境中，不依赖等位基因频率的近亲繁殖度量方法，如FHOM和FROH，更适合用于估计基因组近亲繁殖。最后，热带地区畜牧系统的可持续集约化将依赖于遗传保障措施，以确保在提高生产力的同时，使动物也能适应气候变化。本研究结果是朝着实现这一目标迈出的一步。
