Martikainen K, Tyrisevä A M, Matilainen K, Pösö J, Uimari P
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
Natural Resources Institute Finland (Luke), Jokioinen, Finland.
J Anim Breed Genet. 2017 Oct;134(5):383-392. doi: 10.1111/jbg.12285. Epub 2017 Jul 27.
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F ), runs of homozygosity (F ) and pedigree (F ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F was 0.02, F 0.06 and F 0.63. A correlation of 0.71 was found between F and F , 0.66 between F and F and 0.94 between F and F . Pedigree-based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F or F was used as a covariate, significant inbreeding depression was observed; a 10% increase in F was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non-inbred cows.
单核苷酸多态性（SNP）数据有助于在基因组水平上估计近亲繁殖情况。在本研究中，我们对19,075头芬兰艾尔夏奶牛进行了低密度SNP芯片（8K）基因分型，以估计其近亲繁殖水平。将基因型推算至50K密度，经过质量控制后，剩余39,144个SNP用于分析。基于纯合SNP的百分比（F）、纯合子连续片段（F）和系谱（F）为每头动物估计近亲繁殖系数。13,712头动物有表型记录，包括后备母牛的返情率（NRR）、输精次数（AIS）以及首次至末次输精间隔（IFL），母牛则有多达三个胎次的记录，还有母牛的产犊至首次输精间隔（ICF）。平均F为0.02，F为0.06，F为0.63。F与F之间的相关性为0.71，F与F之间为0.66，F与F之间为0.94。基于系谱的近亲繁殖系数在任何性状中均未显示出近亲繁殖衰退。然而，当将F或F用作协变量时，观察到了显著的近亲繁殖衰退；与非近亲繁殖的母牛相比，F增加10%与IFL0和IFL1延长5天、IFL3延长2周以及ICF2延长3天相关。
