A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle

Abstract

This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores within the tree ensemble non-linear structure. Data from Nellore cattle were used, including records of animals born between 1984 and 2015 and raised in commercial herds located in different regions of Brazil. The estimated breeding values (EBV) were computed and used as the response variable in the genomic analyses. After quality control, the remaining number of animals and SNPs considered were 3,174 and 360,130, respectively. Five independent RF analyses were carried out, considering different initialization seeds. The importance score of each SNP was averaged across the independent RF analyses to rank the markers according to their predictive relevance. A total of 117 SNPs associated with AFC were identified, which spanned 10 autosomes (2, 3, 5, 10, 11, 17, 18, 21, 24, and 25). In total, 23 non-overlapping genomic regions embedded 262 candidate genes for AFC. Enrichment analysis and previous evidence in the literature revealed that many candidate genes annotated close to the lead SNPs have key roles in fertility, including embryo pre-implantation and development, embryonic viability, male germinal cell maturation, and pheromone recognition. Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening candidate regions associated with complex traits. Complementary analyses revealed that many SNPs top-ranked in the RF-based GWAS did not present a strong marginal linear effect but are potentially involved in epistatic hotspots between genomic regions in different autosomes, remarkably in the BTAs 3, 5, 11, and 21. The reported results are expected to enhance the understanding of genetic mechanisms involved in the biological regulation of AFC in this cattle breed.

Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle

“…The FUT8 gene on BTA10 encodes an enzyme that transfers fucose from GDP-fucose to glycoconjugates such as glycoproteins [ 47 ]. This gene was also associated with AFC [ 48 ] and sire conception rate [ 49 ]. Deletion of this gene in mice induced severe growth retardation and death during postnatal development [ 50 ].…”

Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle

“…The ATPase phospholipid transporting 10A, putative ( ATP10A ) has been associated with calving ease ( Frischknecht et al, 2017 ) and milking speed ( Marete et al, 2018 ). UBE3A and SNRPN ( small nuclear ribonucleoprotein polypeptide N ) have been associated with cattle temperament by Costilla et al (2020) and, together with the SNURF ( SNRPN upstream open reading frame ) gene, with the age at first calving ( Alves et al, 2022 ). As Suzuki et al (2009) pointed out, the SNRPN and SNURF constituted a bicistronic gene ( SNRPN-SNURF ), which has been extensively studied in mice and humans and has been associated with neurodevelopmental disorders.…”