Mutations in the MTHFR gene and their associations with milk production traits in dairy goats

An, Xiaopeng; Song, Yuxuan; Hou, Jinxing; Han, Peng; Peng, Jian; Zhang, Lei; Wang, Jiangang; Cao, Binyun

doi:10.1016/j.smallrumres.2015.06.008

Cited by 8 publications

(6 citation statements)

References 22 publications

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“…Despite only a few papers reporting GWAS studies in dairy goats, candidate genes related to milk traits have been widely studied. Some polymorphisms associated with milk production in goats include the LALBA gene (chromosome 5) which is linked to milk yield, lactose content and milk coagulation properties [46], the MTHFR gene (chromosome 6) involved in milk protein synthesis [47], the β-lactoglobulin gene (chromosome 11) [48,49] associated with milk yield and daily fat and protein yield, the TLR2 gene (chromosome 17) which is important in the recognition of the innate immune system of mastitis causing bacteria [50] and the PRLR gene (chromosome 20) [51] and the STAT5A gene (chromosome 19) [42], both which are associated with milk yield. But none of the significant SNPs in the current study were located in the regions of these genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

Scholtens

Jiang

Smith

et al. 2020

J Animal Sci Biotechnol

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Background: Identifying associations between genetic markers and traits of economic importance will provide practical benefits for the dairy goat industry, enabling genomic prediction of the breeding value of individuals, and facilitating discovery of the underlying genes and mutations. Genome-wide association studies were implemented to detect genetic regions that are significantly associated with effects on lactation yields of milk (MY), fat (FY), protein (PY) and somatic cell score (SCS) in New Zealand dairy goats. Methods: A total of 4,840 goats were genotyped with the Caprine 50 K SNP chip (Illumina Inc., San Diego, CA). After quality filtering, 3,732 animals and 41,989 SNPs were analysed assuming an additive linear model. Four GWAS models were performed, a single-SNP additive linear model and three multi-SNP BayesC models. For the single-SNP GWAS, SNPs were fitted individually as fixed covariates, while the BayesC models fit all SNPs simultaneously as random effects. A cluster of significant SNPs were used to define a haplotype block whose alleles were fitted as covariates in a Bayesian model. The corresponding diplotypes of the haplotype block were then fit as class variables in another Bayesian model. Results: Across all four traits, a total of 43 genome-wide significant SNPs were detected from the SNP GWAS. At a genome-wide significance level, the single-SNP analysis identified a cluster of variants on chromosome 19 associated with MY, FY, PY, and another cluster on chromosome 29 associated with SCS. Significant SNPs mapped in introns of candidate genes (45%), in intergenic regions (36%), were 0-5 kb upstream or downstream of the closest gene (14%) or were synonymous substitutions (5%). The most significant genomic window was located on chromosome 19 explaining up to 9.6% of the phenotypic variation for MY, 8.1% for FY, 9.1% for PY and 1% for SCS. Conclusions: The quantitative trait loci for yield traits on chromosome 19 confirms reported findings in other dairy goat populations. There is benefit to be gained from using these results for genomic selection to improve milk production in New Zealand dairy goats.

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Section: Discussionmentioning

confidence: 99%

Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

Scholtens

Jiang

Smith

et al. 2020

J Animal Sci Biotechnol

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“…The association between haplotypic sequences in the caprine chromosome 6 and milk yield, fat, and protein content has been addressed by many authors as reported by Mucha et al [ 51 ]. For instance, caprine autosome 6 hosts a genomic window (6:86,050,148–6:86,990,478) that explains 1% of the genomic variance in milk yield [ 43 ] and comprises the MTHFR gene, which accounts for a known relationship with milk protein synthesis [ 52 ]. However, associations with other important economical traits, such as lactose [ 53 ] or somatic cell counts, or parameters describing the shape of the curve for either milk yield or composition are scarce in goats.…”

Section: Discussionmentioning

confidence: 99%

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

Inostroza

González

Landi

et al. 2020

Animals

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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.

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“…In total, 2 SNP associated with milk yield were found at the genome level, and a further 5 were significant at the chromosome level. Review of the available literature provides evidence for associations in dairy goats between milk yield and polymorphisms within POU1F1 [Capra hircus autosome (CHI)7], a gene that is a positive regulator for growth hormone and prolactin (Lan et al, 2007); β-lactoglobulin gene (CHI11; Dettori et al, 2015;El Hanafy et al, 2015); LALBA (CHI5; Dettori et al, 2015); MTHFR (CHI6), a gene with known links to milk protein synthesis (An et al, 2015); STAT5A (CHI19; An et al, 2013); and PRLR (CHI20; Hou et al, 2013). However, these were not confirmed in the current study.…”

Section: Milk Yieldmentioning

confidence: 99%

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Mucha

Mrode

Coffey

et al. 2018

Journal of Dairy Science

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Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

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Mutations in the MTHFR gene and their associations with milk production traits in dairy goats

Cited by 8 publications

References 22 publications

Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

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

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

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