ArticleFrontiers in genetics2022
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.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 19 citations in OpenAlex.
- Integrating multi-layer perceptron and random forest in an ensemble framework for improved genomic prediction accuracy and SHAP-derived interpretability of residual feed intake in cattle.Journal of animal science and biotechnology · 2026Article
- Unravelling Heterozygosity-Rich Regions in the Holstein Genome.Animals : an open access journal from MDPI · 2025Article
- Effect of genomic regions harboring putative lethal haplotypes on reproductive performance in closed experimental selection lines of Nellore cattle.Scientific reports · 2025Article
- Genetic parameters and genome-wide association studies including the X chromosome for various reproduction and semen quality traits in Nellore cattle.BMC genomics · 2025Article
- Applying the algorithm for Proven and young in GWAS Reveals high polygenicity for key traits in Nellore cattle.Frontiers in genetics · 2025Article
- Applying traditional and machine learning-based GWAS approaches for marker-trait identification in wheat.Frontiers in plant science · 2025Article
- Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle.BMC genomics · 2024Article
- Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle.Journal of animal science · 2024Article
- Genome-wide association studies for milk production traits and persistency of first calving Holstein cattle in Türkiye.Frontiers in veterinary science · 2024Article
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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