Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers1,2

Abstract

Zebu animals () are known to take longer to reach puberty compared with taurine animals (), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being -0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant ( < 0.05) terms associated with HP-"Munc18 Proteins," "Fucose," and "Hemoglobins"-and with NF-"Cathepsin B," "Receptors, Neuropeptide," and "Palmitic Acid." This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

“…Júnior et al [54] reported higher heritability estimates for AFP (0.49 ± 0.09) in Nellore cattle compared to our findings. Moderate to high positive genetic correlations between AMH and AFP were reported to range from 0.56 to 0.68 in Nellore cattle and 0.73 to 0.90 in Holstein animals [52,55].…”

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)

“…For instance, prevalence of infertility may reach 16% 2 and 15% 3 in humans and beef female calves, respectively. Similar to what has been observed in humans 4 , the genetic architecture of fertility in beef heifers is very complex 5,6,7,8,9,10,11,12 . In line with this complexity, female reproductive traits have low heritability.…”

“…The examination of the genetic components of fertility in beef heifers have yielded several genes potentially associated with fertility traits 5,6,7,8,9,10,11,12 , but the effect of these markers are minimal, and there is no clear redundancy in genetic markers identified across breeds. Beyond the genomic profiling, the analysis of multiple layers of an individual’s molecular blueprint is likely key for understanding the underlying biology of complex traits 29 .…”

Beef heifer fertility: importance of management practices and technological advancements

“…Dias and others identified three haplotypes significantly associated with heifer pregnancy, which contained the genes fatty acid binding protein 4 (FABP4) and protein phosphatase 3 catalytic subunit alpha (PPP3CA) [85]. Focusing on chromosomic regions, two studies identified chromosome regions that explained as much as 8.91% [86] and 12.73% [87] of the variance in sexual precocity to become pregnant by 16 months of age and heifer pregnancy, respectively. Of note, both studies identified windows on chromosomes 5, 14, and 18, with a potential overlap on chromosome 14 [86,87].…”

“…Focusing on chromosomic regions, two studies identified chromosome regions that explained as much as 8.91% [86] and 12.73% [87] of the variance in sexual precocity to become pregnant by 16 months of age and heifer pregnancy, respectively. Of note, both studies identified windows on chromosomes 5, 14, and 18, with a potential overlap on chromosome 14 [86,87]. Takada and others focused on haplotypes encompassing 125 candidate genes and identified nine haplotypes with significant association with early pregnancy.…”