Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats

Abstract

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats.

Genetic Diversity in Casein Gene Cluster in a Dromedary Camel (C. dromedarius) Population from the United Arab Emirates

“…The identified variants have been associated with differential gene expression and rates of protein synthesis [ 14 , 15 ]. Moreover, the results of recent studies suggest that casein gene variants may be associated with milk yield and composition [ 16 ]. In camels, genetic variants have previously been reported for CSN1S1 [ 17 , 18 , 19 ], CSN2 [ 20 ], and CSN3 [ 21 ].…”

A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds

“…Environmental factors play an essential role in milk production and mastitis occurrence, so controlling environmental factors could permit or prevent animals from expressing their genetic potential [ 15 ]. In our analysis, we considered the following fixed effects: the combined effect of the herd-year (HY), month of milking, lactation order, and breed.…”

“…For example, the AGPAT6 gene was found to significantly influence both the fat and protein contents and milk yield [ 53 ]. Additionally, the variability of the haplotypic sequences at the loci of the casein complex was studied [ 15 ]. The authors point out that a complete definition of the haplotypes in the casein complex in goats is difficult given the high genetic variability.…”

“…The consideration of the αS1-casein genotype may improve the model’s efficiency, translating into more accurate genetic parameters and breeding values [ 14 ]. In another study, 48 SNPs in αS1, αS2, β, and κ casein genes were included in the evaluation of genetic parameters [ 15 ]. Including genetic effects and relationships among these heritable biomarkers may improve the model efficiency, genetic parameters, and breeding values for milk yield and composition; this inclusion could also help optimise selection practices and profitability for components where technological application may be especially relevant for the cheese-making dairy sector [ 15 ].…”

“…In another study, 48 SNPs in αS1, αS2, β, and κ casein genes were included in the evaluation of genetic parameters [ 15 ]. Including genetic effects and relationships among these heritable biomarkers may improve the model efficiency, genetic parameters, and breeding values for milk yield and composition; this inclusion could also help optimise selection practices and profitability for components where technological application may be especially relevant for the cheese-making dairy sector [ 15 ]. In addition to the study of candidate loci, the genomic approach in the genome-wide association study has also been applied for the detection of genetic regions of interest [ 16 ].…”