A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

Abstract

Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

“…Several pathways were involved in GABA processes ( Figure 8 ; Supplementary Figures S4A–C ): GABA is actively involved in regulating leptin, the satiety hormone, which has an essential role in nutrient intake and feeding motivation ( Miller 2017 ). Some pathways also appear to be associated with processes such as morphogenesis of the epithelium (GO:0048791, GO:0007492, GO:0048332, GO:0001707 GO:0035987; mesoderm morphogenesis in Figure 8 ), which has a connection with body weight (increased paracellular permeability for the absorption of nutrients leads to augmented energy intake ( Vanvanhossou et al, 2020 ).…”

Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

“…The phenotypic correlation between the traits was calculated using the following equation [ 34 ]: where rP is phenotypic correlation between two traits. σu xy and σe xy are genetic and residual covariances between two traits x and y, respectively.…”

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

“…Knowledge of the genome sequence from large numbers of individuals in a population enables low density SNP genotype data to be used to estimate higher density genotypes by "imputation" [98]. The analysis of phenotype and genotype in genome-wide association studies enables genetic loci with a major effect on the phenotype to be identified (e.g., [99][100][101]). In some cases the genes and causative polymorphisms controlling variations in target traits have been identified (e.g., [102]).…”

“…A GWAS of cattle indigenous to Benin [99] identified several potential candidate genes associated with stress and immune response (PTAFR, PBMR1, ADAM, TS12), feed efficiency (MEGF11, SLC16A4, CCDC117), and conformation and growth (VEPH1, CNTNAP5, GYPC). The study of cold stress in Siberian cattle breeds identified two candidate genes (MSANTD4 and GRIA4) on chromosome 15, putatively involved in cold shock response and body thermoregulation [100].…”