Davenport Kimberly M, Lockhart Kelsey, Stoecklein Katy, Schnabel Robert D, Spencer Thomas E, Ortega M Sofia
Division of Animal Sciences, University of Missouri, Columbia, MO 65211; Department of Animal Sciences, Washington State University, Pullman, WA 99164.
Division of Animal Sciences, University of Missouri, Columbia, MO 65211.
J Dairy Sci. 2025 Jul;108(7):7775-7789. doi: 10.3168/jds.2025-26496. Epub 2025 Apr 28.
Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole-genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.
繁殖成功是盈利且可持续的奶牛养殖运营的重要组成部分。尽管对产奶量等生产性状的选择导致了奶牛繁殖力的下降，但包括体外受精和胚胎移植等辅助生殖技术以及针对繁殖性状的基因组选择等策略正在实施，以帮助减轻这种损失。先前的研究已经确定了与繁殖性状相关的遗传标记，如女儿怀孕率、受孕率和首次受孕间隔时间。然而，与体外胚胎发育相关的遗传标记尚未得到探索。因此，本研究旨在确定与体外胚胎分裂率和囊胚率相关的遗传标记，未来目标是创建一个指数，以选择具有卓越体外胚胎生产能力的公牛。严格的体外受精试验确定了荷斯坦公牛在体外产生成功分裂并发育成囊胚的胚胎的能力存在差异。总共对40头具有胚胎分裂和囊胚率表型的公牛进行了全基因组测序。测序在Illumina平台上进行，采用PE150读长，随后进行清洗、映射到ARS-UCD1.2、使用GATK HaplotypeCaller进行变异调用，并按照1000公牛基因组计划的最佳实践进行质量控制。全基因组关联分析分别确定了819个和442个与胚胎分裂率和囊胚率相关的单核苷酸多态性（SNP）。15号、18号、21号、22号和23号染色体上的显著区域与先前与牛繁殖性状相关的数量性状位点（QTL）处于连锁不平衡状态。此外，28号染色体上与分裂率相关的最显著变异所在区域在EGLN1中包含几个同义变异，EGLN1是缺氧诱导途径的关键组成部分。18号染色体上另一个与分裂率相关的区域在SMG9中包含一个错义变异，SMG9是参与无义介导的mRNA降解途径的基因。21号染色体上与囊胚率相关的区域在AEN下游的调控区域也包含变异，AEN是p53依赖的凋亡途径中有效DNA片段化所需的基因。总之，本研究确定了与体外胚胎分裂率和囊胚率相关的基因组区域的初步集合，这些区域包含与牛繁殖性状相关的相关基因和其他QTL。这些区域经过验证后，可有助于建立一个选择指数，用于识别具有遗传倾向在体外产生更多胚胎以供辅助生殖技术使用的公牛。
