Genome‐wide association study identifies variants associated with hair length in Brangus cattle

Davila, Kaitlyn Sarlo; Howell, Alyssa; Nuñez, A. Esteve; Orelien, Arseia; Roe, Victoria; Rodríguez, Eduardo; Dikmen, Serdal; Mateescu, Raluca G.

doi:10.1111/age.12970

Cited by 8 publications

(3 citation statements)

References 24 publications

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“…In addition, these breeds can be kept on poor-quality pastures compared to other commercial breeds. Some of the genes identified in the ROH islands have been used for selection in different commercial cattle breeds to rear animals with shorter coats, improving thermotolerance in humid tropical climates [ 47 ]. Currently, studies should be conducted with native breeds, since cattle species face challenges every day, such as those associated with global climate changes that affect animal production.…”

Section: Discussionmentioning

confidence: 99%

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Toro-Ospina

Ríos

Schettini

et al. 2022

Genes

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The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4–8 Mb, 8–16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.

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Section: Discussionmentioning

confidence: 99%

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Toro-Ospina

Ríos

Schettini

et al. 2022

Genes

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“…In cattle, the PCCA gene has been associated with undercoat length and, as a result, with many aspects of thermoregulation adaptation. The regulation of fur length by the PCC gene is determined by its function in biotin transport and metabolism (Davila et al, 2020). Several reports have indicated that PCCA and PCCB gene activity is regulated by different diets and that the PCC enzyme is critical for propionate metabolism -a major substrate for gluconeogenesis in ruminants (Graber et al, 2010).…”

Section: Roh Hotspots and Their Gene Contentmentioning

confidence: 99%

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Szmatoła,

Gurgul,

Jasielczuk

et al. 2024

Annals of Animal Science

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This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding.

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“…Animal heat tolerance is a quantitative trait (Gaughan et al 2010;Li et al 2011;Chang et al 2012), and recent advancements in molecular genetic methodologies have facilitated the identification of the correlation between genetic variation at specific loci and their associated traits. Among these adaptive responses, the coat characteristics play a pivotal role in influencing the heat tolerance of animals under high ambient temperature and humidity conditions (Sarlo Davila et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Geographic Distribution of a Missense Mutation in theKRT38Gene and Its Association with Heat Tolerance in Chinese Indigenous Cattle Breeds

Chen,

Liu,

Liu

et al. 2023

Preprint

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Context: China has a vast area across many temperature zones and a variety of cattle breeds. These cattle resources are ideal models to research their adaptability to the environment. The KRT38 gene is an acidic protein, and its coding product can be used as a component of hair production. Aims. The objective of this study was to investigate the diversity of the KRT38 gene in Chinese local cattle and the association of different genotypes with mean temperature (T), relative humidity (RH) and temperature humidity index (THI). Methods. A missense mutation g.41650738 A > G in the KRT38 gene was screened from the database of bovine genomic variation (BGVD), was genotyped in a total of 246 samples from 15 local cattle breeds in China by PCR amplification and sequencing. Finally, the correlation between the locus and the three climatic factors was analysed. Key results. We successfully obtained the frequency of this SNP in three groups of cattle in northern, central and southern China. The frequency of allele A gradually declined from north to south, while the frequency of allele G showed the opposite trend with a clear geographic distribution. Conclusions. Our results indicate that KRT38 variation in Chinese indigenous cattle might be linked to heat tolerance. Implications. Our analysis may support in finding out its importance as a genetic signal for heat tolerance in cattle reproduction and genetics.

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Genome‐wide association study identifies variants associated with hair length in Brangus cattle

Cited by 8 publications

References 24 publications

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Geographic Distribution of a Missense Mutation in theKRT38Gene and Its Association with Heat Tolerance in Chinese Indigenous Cattle Breeds

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