Maddahi Narges, Sadeghi Mostafa, Miraee Ashtiani Seyed Reza, Kholghi Muna, Jalil Sarghale Ali
Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
BMC Genomics. 2025 Jul 11;26(1):656. doi: 10.1186/s12864-025-11744-1.
The reproduction process in domestic animals is one of the most important challenges of animal husbandry. Fertility is an important trait that contributes to herd profitability and can be improved by genomic information. One of the best ways to investigate the association between single nucleotide polymorphisms (SNPs) and phenotypic performance is the genome-wide association study (GWAS). The aim of our study was to identify the genomic regions affecting reproductive traits, interval between first and last insemination (IFL), days open (DO), days from calving to first service (DFS), number of services per conception (NSPC), age at first calving (AFC) and age at first insemination (AFI) using SNP chip data in Iranian Holstein cows.
GWAS analysis for all reproductive traits based on the significant-association threshold P < 1 × 10, led to the identification of 55 single nucleotide polymorphisms (SNPs) for IFL (n = 3), DFS (n = 0), DO (n = 5), NSPC (n = 5), AFI (n = 33), and AFC (n = 9) traits. Based on the results of gene ontology analysis, 54 different candidate genes for reproductive traits were identified in this study. For IFL, NSPCC, DO, AFC, and AFI traits 4, 8, 11, 10, and 21 candidate genes were identified in the vicinity of significant SNPs, respectively. Key genes with biologically important positions for heifers (ATG7, PTPN5, STAC, GAD2, PLXDC2, KARS1, PRIM2, and ZNF597) and cows (LPL, SERP2, BIRC6, CENPU, PIK3C3, and MYLK3) can be mentioned.
Our results identified 55 marker-trait associations (MTAs) and 54 different candidate genes associated with reproductive traits. As a result, the SNPs and candidate genes discovered in this study can be used in genomic experiments to improve the reproductive performance of Iranian Holstein dairy cows and provide new information about the genetic architecture of these traits.
家畜的繁殖过程是畜牧业面临的最重要挑战之一。繁殖力是影响畜群盈利能力的重要性状，可通过基因组信息加以改善。全基因组关联研究（GWAS）是探究单核苷酸多态性（SNP）与表型表现之间关联的最佳方法之一。我们研究的目的是利用伊朗荷斯坦奶牛的SNP芯片数据，确定影响繁殖性状的基因组区域，即首次与末次授精间隔（IFL）、空怀天数（DO）、产犊至首次配种天数（DFS）、每次受孕的配种次数（NSPC）、首次产犊年龄（AFC）和首次授精年龄（AFI）。
基于显著关联阈值P < 1×10对所有繁殖性状进行GWAS分析，共鉴定出与IFL（n = 3）、DFS（n = 0）、DO（n = 5）、NSPC（n = 5）、AFI（n = 33）和AFC（n = 9）性状相关的55个单核苷酸多态性（SNP）。基于基因本体分析结果，本研究鉴定出54个与繁殖性状不同的候选基因。对于IFL、NSPCC、DO、AFC和AFI性状，分别在显著SNP附近鉴定出4、8、11、10和21个候选基因。可提及在小母牛（ATG7、PTPN5、STAC、GAD2、PLXDC2、KARS1、PRIM2和ZNF597）和母牛（LPL、SERP2、BIRC6、CENPU、PIK3C3和MYLK3）中具有生物学重要位置的关键基因。
我们的结果鉴定出55个标记-性状关联（MTA）和54个与繁殖性状相关的不同候选基因。因此，本研究中发现的SNP和候选基因可用于基因组实验，以提高伊朗荷斯坦奶牛的繁殖性能，并为这些性状的遗传结构提供新信息。
