Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle

Sousa, Luis Paulo B.; Pinto, Luis Fernando B.; Cruz, Valdecy A.R.; Oliveira Jr., Gerson A.; Rojas de Oliveira, Hinayah; Chud, Tatiane S.; Pedrosa, Victor B.; Miglior, Filippo; Schenkel, Flávio S.; Brito, Luiz F.

doi:10.3168/jds.2023-23806

Cited by 3 publications

(1 citation statement)

References 130 publications

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“…The expression of RDM1 is correlated with the degree of immune infiltration of immune cells, including macrophages and neutrophils, in a variety of cancer types ( Qui et al, 2021 ). A SNP located within 100 Kb of the RDM1 gene was associated with interdigital hyperplasia, and another was associated with sole hemorrhage in Holsteins ( Sousa Junior et al, 2023 ). Finally, RDM1 was found to be significantly downregulated in less feed-efficient beef cattle ( Chen et al, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

The genetic architecture of complete blood counts in lactating Holstein dairy cows

Siberski-Cooper,

Mayes,

Gorden

et al. 2024

Front. Genet.

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Complete blood counts (CBCs) measure the abundance of individual immune cells, red blood cells, and related measures such as platelets in circulating blood. These measures can indicate the health status of an animal; thus, baseline circulating levels in a healthy animal may be related to the productive life, resilience, and production efficiency of cattle. The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained more than 1% of the genetic variance for at least one CBC trait, with 10 windows explaining more than 1% of the genetic variance for two or more traits. Multiple genes in the identified regions have functions related to immune response, cell differentiation, anemia, and disease. Positional candidate genes include RAD52 motif-containing protein 1 (RDM1), which is correlated with the degree of immune infiltration of immune cells, and C-X-C motif chemokine ligand 12 (CXCL12), which is critically involved in neutrophil bone marrow storage and release regulation and enhances neutrophil migration. Since animal health directly impacts feed intake, understanding the genetics of CBCs may be useful in identifying more disease-resilient and feed-efficient dairy cattle. Identification of genes responsible for variation in CBCs will also help identify the variability in how dairy cattle defend against illness and injury.

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Section: Discussionmentioning

confidence: 99%

The genetic architecture of complete blood counts in lactating Holstein dairy cows

Siberski-Cooper,

Mayes,

Gorden

et al. 2024

Front. Genet.

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An overview of recent technological developments in bovine genomics

Ghavi Hossein-Zadeh

2024

Veterinary and Animal Science

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An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows

Zhang,

Liu,

Jiang

et al. 2024

Microbiome

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Background Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows. Results The results indicated that the proportions of highly heritable subsets ( h 2 ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn 2+ transport) ( P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp. , Prevotella_sp._E15-22 , Prevotella_sp._E13-27 , which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) ( P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 ( P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp . , which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942). Conclusion Our comprehensive study revealed the distinct heritability patterns of rumen micr...

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Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle

Cited by 3 publications

References 130 publications

The genetic architecture of complete blood counts in lactating Holstein dairy cows

The genetic architecture of complete blood counts in lactating Holstein dairy cows

An overview of recent technological developments in bovine genomics

An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows

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