Identification of candidate SNPs associated with embryo mortality and fertility traits in lactating Holstein cows

Abstract

Introduction: Targeted single nucleotide polymorphisms (SNPs) have been used in genomic prediction methodologies to enhance the accuracy of associated genetic transmitting abilities in Holstein cows. The objective of this study was to identify and validate SNPs associated with fertility traits impacting early embryo mortality. Methods: The mRNA sequencing data from day 16 normal (n = 9) and embryo mortality (n = 6) conceptuses from lactating multiparous Holstein cows were used to detect SNPs. The selection of specific genes with SNPs as preliminary candidates was based on associations with reproductive and fertility traits. Validation of candidate SNPs and genotype-to-phenotype analyses were conducted in a separate cohort of lactating primiparous Holstein cows (n = 500). After genotyping, candidate SNPs were filtered using a quality control pipeline via PLINK software. Continuous numeric and binary models from reproductive traits were evaluated using the mixed procedure for a generalized linear model-one way ANOVA or logistic regression, respectively. Results: Sixty-nine candidate SNPs were initially identified, but only 23 passed quality control procedures. Ultimately, the study incorporated 466 observations for statistical analysis after excluding animals with missing genotypes or phenotypes. Significant (p <0.05) associations with fertility traits were identified in seven of the 23 SNPs: DSC2 (cows with the A allele were older at first calving); SREBF1 and UBD (cows with the T or G alleles took longer to conceive); DECR1 and FASN (cows with the C allele were less likely to become pregnant at first artificial insemination); SREBF1 and BOLA-DMB (cows with the T allele were less likely to be pregnant at 150 days in milk). It was also determined that two candidate SNPs within the DSC2 gene were tag SNPs. Only DSC2 SNPs had an important allele substitution effect in cows with the G allele, which had a decreased age at first calving by 10 days. Discussion: Candidate SNPs found in this study could be used to develop genetic selection tools to improve fertility traits in dairy production systems.

Keywords: Holstein cows; cattle; early embryo mortality; health traits; linkage disequilibrium; pregnancy; single-nucleotide polymorphisms.

FIGURE 1

Flowchart of methods used to identify candidate SNPs used in association analysis with reproduction traits in Holstein cows. EM, embryo mortality or N, normal pregnancy: cow’s pregnancy status; IPA, ingenuity pathway analysis.

FIGURE 2

Candidate single-nucleotide polymorphisms (SNPs) and published SNPs associated with quantitative trait loci (QTL, orange lines) within fertility for each chromosome (Chr) in Holstein cows. CR, conception rate; D2C, days to conception; P1AI1, pregnant at first artificial insemination. Orange lines represent published SNPs associated with quantitative trait loci; purple lines represent candidate SNPs. Created with Biorender.com.

FIGURE 3

Seven potential functional single-nucleotide polymorphisms (SNPs) within exons (E) and nucleotide (nt) position in each gene: (A) uridine monophosphate synthetase (UMPS), (B) 2,4-dienoyl-CoA reductase 1 (DECR1), (C) sterol regulatory element-binding transcription factor 1 (SREBF1), (D) fatty acid synthetase (FASN), (E) major histocompatibility complex, class II, DM beta (BOLA-DMB), (F) ubiquitin d (UBD), and (G) desmocollin-2 (DSC2) in their designated chromosome (Chr) for Holstein cows. Created with Biorender.com.