&lt;b&gt;Genome-wide association study using the Bayes C method for important traits in dairy yield in Colombian Holstein Cattle

Florez, Juan Carlos Rincón; Herrera, Albeiro López; Zuluaga, José Julián Echeverri

doi:10.4025/actascianimsci.v40i1.39015

Cited by 5 publications

(3 citation statements)

References 29 publications

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“…The proteins of the LRP1B gene (within CNVR_59, common to all breeds), participate in a wide range of physiological processes, including the regulation of lipid metabolism, neurodevelopment, and transport of nutrients and vitamins [ 52 , 53 ], but also in cell proliferation process, making it a potential candidate gene for the supernumerary nipple phenotype [ 54 ]. The KHDRBS2 gene, within the CNVR_310 with the highest variance, has been associated with fertility and reproductive traits in cattle [ 55 ], goat [ 56 ], and sheep [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Gerlando

Mastrangelo

Tolone

et al. 2022

Animals

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Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.

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Section: Discussionmentioning

confidence: 99%

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Gerlando

Mastrangelo

Tolone

et al. 2022

Animals

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“…Furthermore, the results indicate the TMEM229A, POLE, XKR4 and CADPS genes were harboring significant SNPs correlated to the bone quality trait. In relation to the BovineHD0400024774-rs133088614 SNP, located close to the transmembrane protein 229A gene (TMEM229A), Juan Carlos [72] described the polymorphism of this gene as having a great effect on dairy yield per lactation in Colombian Holstein cattle. There are no further publications concerning this gene in cattle.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

Abdalla

Nazar

et al. 2021

Animals

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Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4 and CADPS. Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (p ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.

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“…This can be explained by the fact that apolipoprotein E acts as an LDL receptor, which promotes the recognition and catabolism of triglyceride-rich lipoproteins (Mahley et al, 1984). In a study with Holstein dairy cattle, LRP1B was reported as a candidate for fat deposition in milk (Flórez et al, 2018). In other species, such as birds, it was reported as involved in the composition of fatty acids and in fat deposition (Jin et al, 2018;.…”

Section: Candidate Genes For Rump Fat Thicknessmentioning

confidence: 99%

Genome‐wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture–based systems

Martins

Machado

Pinto

et al. 2020

J Animal Breeding Genetics

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Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file.Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development.The main genes identified for RFT were GSK3β, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.

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<b>Genome-wide association study using the Bayes C method for important traits in dairy yield in Colombian Holstein Cattle

Cited by 5 publications

References 29 publications

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

Genome‐wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture–based systems

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