Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds

Genomic Regions and Candidate Genes Associated with Milk Production Traits in Holstein and Its Crossbred Cattle: A Review

Genome-wide association studies (GWAS) are a powerful tool for identifying genomic regions and causative genes associated with economically important traits in dairy cattle, particularly complex traits, such as milk production. This is possible due to advances in next-generation sequencing technology. This review summarized information on identified candidate genes and genomic regions associated with milk production traits in Holstein and its crossbreds from various regions of the world. Milk production traits are important in dairy cattle breeding programs because of their direct economic impact on the industry and their close relationship with nutritional requirements. GWAS has been used in a large number of studies to identify genomic regions and candidate genes associated with milk production traits in dairy cattle. Many genomic regions and candidate genes have already been identified in Holstein and its crossbreds. Genes and single nucleotide polymorphisms (SNPs) that significantly affect milk yield (MY) were found in all autosomal chromosomes except chromosomes 27 and 29. Half of the reported SNPs associated with fat yield and fat percentage were found on chromosome 14. However, a large number of significant SNPs for protein yield (PY) and protein percentage were found on chromosomes 1, 5, and 20. Approximately 155 SNPs with significant influence on multiple milk production traits have been identified. Several promising candidate genes, including diacylglycerol O-acyltransferase 1, plectin, Rho GTPase activating protein 39, protein phosphatase 1 regulatory subunit 16A, and sphingomyelin phosphodiesterase 5 were found to have pleiotropic effects on all five milk production traits. Thus, to improve milk production traits it is of practical relevance to focus on significant SNPs and pleiotropic genes frequently found to affect multiple milk production traits.

Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle

Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.

X-linked genes influence various complex traits in dairy cattle

BACKGROUND

The search for quantitative trait loci (QTL) affecting traits of interest in mammals is frequently limited to autosomes, with the X chromosome excluded because of its hemizygosity in males. This study aimed to assess the importance of the X chromosome in the genetic determinism of 11 complex traits related to milk production, milk composition, mastitis resistance, fertility, and stature in 236,496 cows from three major French dairy breeds (Holstein, Montbéliarde, and Normande) and three breeds of regional importance (Abondance, Tarentaise, and Vosgienne).

RESULTS

Estimates of the proportions of heritability due to autosomes and X chromosome (h²_X) were consistent among breeds. On average over the 11 traits, h²_X=0.008 and the X chromosome explained ~ 3.5% of total genetic variance. GWAS was performed within-breed at the sequence level (~ 200,000 genetic variants) and then combined in a meta-analysis. QTL were identified for most breeds and traits analyzed, with the exception of Tarentaise and Vosgienne and two fertility traits. Overall, 3, 74, 59, and 71 QTL were identified in Abondance, Montbéliarde, Normande, and Holstein, respectively, and most were associated with the most-heritable traits (milk traits and stature). The meta-analyses, which assessed a total of 157 QTL for the different traits, highlighted new QTL and refined the positions of some QTL found in the within-breed analyses. Altogether, our analyses identified a number of functional candidate genes, with the most notable being GPC3, MBNL3, HS6ST2, and DMD for dairy traits; TMEM164, ACSL4, ENOX2, HTR2C, AMOT, and IRAK1 for udder health; MAMLD1 and COL4A6 for fertility; and NRK, ESX1, GPR50, GPC3, and GPC4 for stature.

CONCLUSIONS

This study demonstrates the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and highlights new functional candidate genes and variants for these traits. These results could potentially be extended to other species as many X-linked genes are shared among mammals.

Genomic and Phenotypic Udder Evaluation for Dairy Cattle Selection: A Review

The traditional point of view regarding dairy cattle selection has been challenged by recent genomic studies indicating that livestock productivity prediction can be redefined based on the evaluation of genomic and phenotypic data. Several studies that included different genomic-derived traits only indicated that interactions among them or even with conventional phenotypic evaluation criteria require further elucidation. Unfortunately, certain genomic and phenotypic-derived traits have been shown to be secondary factors influencing dairy production. Thus, these factors, as well as evaluation criteria, need to be defined. Owing to the variety of genomic and phenotypic udder-derived traits which may affect the modern dairy cow functionality and conformation, a definition of currently important traits in the broad sense is indicated. This is essential for cattle productivity and dairy sustainability. The main objective of the present review is to elucidate the possible relationships among genomic and phenotypic udder evaluation characteristics to define the most relevant traits related to selection for function and conformation in dairy cattle. This review aims to examine the potential impact of various udder-related evaluation criteria on dairy cattle productivity and explore how to mitigate the adverse effects of compromised udder conformation and functionality. Specifically, we will consider the implications for udder health, welfare, longevity, and production-derived traits. Subsequently, we will address several concerns covering the application of genomic and phenotypic evaluation criteria with emphasis on udder-related traits in dairy cattle selection as well as its evolution from origins to the present and future prospects.

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits.