Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Abstract

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up-and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.

Whole‐genome resequencing reveals candidate genes associated with milk production trait in Guanzhong dairy goats

“…In our study, we identified an SNP (g.44250104T>G) in PRKG1 and found that mutated allele G at position 44 250 104 of the gene is more frequent in the high milk yield group than in the low milk yield group. Interestingly, we found that apart from ADAMTS3 , other genes such as ADRA1A , EPHX2 , ANPEP and PRKG1 were not found in the GWAS of Saanen dairy goats (Massender et al., 2023). This suggests that these genes may only be candidate genes for milk production traits in Guanzhong dairy goats.…”

“…With the development of high‐throughput sequencing technology, whole‐genome resequencing has enabled the identification of the genomic variants generated during the selection process for domestic animals including SNPs. Based on genome‐wide association studies (GWAS), many genes and SNPs associated with milk production traits in dairy goats have been discovered (Jiang et al., 2022; Massender et al., 2023; Scholtens et al., 2020).…”

“…In a previous study, it was suggested to be associated with milk and protein yields in dairy cattle (Jiang et al., 2019). A recent study found that ADAMTS3 is associated with protein percentage of Saanen dairy goats in first lactation and the fat percentage of Alpine dairy goats in later lactations by GWAS (Massender et al., 2023). Based on the origin of Guanzhong dairy goats, this may indicate a potential association between ADAMTS3 and milk production traits.…”

Single and longitudinal genome‐wide association studies for dairy traits available in goats with three recorded lactations

“…Milk yield and composition are traits of economic importance in dairy goats because cheese manufacturing is the main economic activity associated with the breeding of this species. The performance of genome‐wide association studies (GWAS) has been helpful to identify genomic regions associated with milk traits in several caprine breeds including New Zealand goats (Jiang et al., 2022; Scholtens et al., 2020), French Alpine and Saanen (Martin et al., 2017, 2018; Massender et al., 2023; Talouarn et al., 2020), and a composite breed of Saanen, Toggenburg, and Alpine goats (Mucha et al., 2018). Several genomic regions have emerged as consistently associated with dairy traits.…”

“…Such a finding is probably explained by the major role of the casein α S1 ( CSN1S1 ) gene polymorphism on modulating milk casein α S1 , protein and fat contents as well as the technological and organoleptic properties of cheese (Martin et al., 2002). Another important locus is the chromosome 14 region containing the diacylglycerol O‐acyltransferase 1 ( DGAT1 ) gene, which has been associated with milk fat content (Martin et al., 2017; Massender et al., 2023). The DGAT1 gene contains two causal missense R251L and R396W mutations that decrease milk fat content and explain 46% and 6% of the genetic variance of this trait, respectively (Martin et al., 2017).…”