Gene editing in breeding

Estimation of genetic parameters and molecular markers for in-vivo embryo production traits in dairy cattle

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Abstract

The in-vivo embryo production (IVEP) is one of the main techniques for embryo production which has been widely used for improving reproductive efficiency. However, extreme variation exists in almost all populations around the world. Due to the lack of mature tools, it is difficult to fulfill early and precise selection for donors with better performance. To address these issues, this study conducted out a comprehensive investigation for IVEP traits in dairy cattle, including genetic parameters estimation, genome-wide association studies (GWAS) and transcriptome differential analysis. This study collected the IVEP phenotype, pedigrees and genotype from 1,800 Holstein cattle, and the IVEP phenotype included total number of oocytes (TNO), number of transferable embryos (NTE) and percentage of transferable embryos (PTE). The genetic parameters were estimated based on multi-trait animal model and joint relationship matrix constructed by pedigree and genotype. The EBV were estimated using the joint relationship matrix, and the relationship between phenotype and EBV was analyzed. The GWAS was conducted for TNO and NTE using the generalized linear model of rMVP package in R software. Using RNA-seq data from peripheral blood, the differentially expression analysis for TNO and NTE based on individuals with high and low phenotype. The estimated heritabilities for IVEP traits were 0.137 (TNO), 0.096 (NTE) and 0.059 (PTE), respectively. The genetic correlation of NTE with TNO (0.892) and PTE (0.524) were relatively high, while the very low genetic correlation (0.084) for TNO and PTE. The EBV and phenotype had positive correlation for all traits, ranging from 0.07 (NTE) to 0.20 (TNO). For example, donors with EBV in the upper quarter generally had better IVEP phenotype (16.99 ± 11.57 for TNO), while those in the lowest quarter had poorer performance (3.78 ± 4.90 for TNO). Among the top 10 significant SNPs associated with TNO and NTE, SNPs were distributed on chromosome 2, 3, 12, 15, 18, 20 and 25. A total of 38 candidate genes were screened and were enriched in DNA replication, Cellular senescence, cGMP-PKG signaling pathway and so on. By integrating genomic and transcriptomic analysis, 11 key genes associated with IVEP were identified. In conclusion, the IVEP traits are heritable in Holstein population, and genomic prediction is poised to be a feasible tool for the early selection of donors with better performance. This study provides the comprehensive evaluation of genetic architecture of IVEP traits in dairy cattle.

Keywords: 2026

How to Cite:

Huang, Y., Zhang, H., Sun, W., Liu, Z., Zhao, S., Zhu, H. & Wang, Y., (2026) “Estimation of genetic parameters and molecular markers for in-vivo embryo production traits in dairy cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286409. doi: https://doi.org/10.31274/wcgalp.23990

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