Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Moscarelli, Angelo; Sardina, Maria Teresa; Cassandro, Martino; Ciani, Elena; Pilla, Fabio; Senczuk, Gabriele; Portolano, Baldassare; Mastrangelo, Salvatore

doi:10.1111/age.13019

Cited by 21 publications

(24 citation statements)

References 60 publications

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“…In Colombia, Creole cattle [44] reported Ho of 0.66, and the Costeño con Cuernos breed had the lowest, 0.635, and Casareño the highest, 0.733. These Ho estimates are quite different from those reported by [45], who found an average of 0.35 ± 0.167 for Ho in populations related to Braunvieh.…”

Section: Population Genetic Structurecontrasting

confidence: 99%

“…This suggests that the Mexican Braunvieh population has increased its genetic versatility for the candidate genes studied, with a higher number of heterozygous individuals. Exposure to climates different from their native climate for over a century in the tropical systems of Mexico could have caused a change in Ho, with respect to original Braunvieh populations [13,45]. On the other hand, the non-significant differences between He and Ho for most of the traits (Table 6) is similar to the results obtained in other studies, where neither the breed nor the environment modified the non-rejection of the null hypothesis, He = Ho for Xi2 [13,44,46].…”

Section: Population Genetic Structurementioning

confidence: 99%

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Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Trujano-Chavez

Sánchez-Ramos

Pérez‐Rodríguez

et al. 2021

Veterinary Sciences

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Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.

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Section: Population Genetic Structurecontrasting

confidence: 99%

Section: Population Genetic Structurementioning

confidence: 99%

Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Trujano-Chavez

Sánchez-Ramos

Pérez‐Rodríguez

et al. 2021

Veterinary Sciences

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“…The next highest RAiSD μ statistic windows in Simmental are immediately upstream of MC1R, the gene responsible for red versus black coat color in cattle (Gutiérrez-Gil et al 2007). The most significant nSL signature with a clear candidate gene resided within TMEM132D, a gene that has been identified in numerous selective sweep analyses (Qanbari et al 2014;Mészáros et al 2019;Moradian et al 2020;Moscarelli et al 2020) and is pleiotropic across dairy and beef cattle breeds (Martins et al 2020).…”

Section: Sweep Mapping Identifies Known and Novel Selected Locimentioning

confidence: 99%

Uncovering the architecture of selection in two Bos taurus cattle breeds

Rowan

Schnabel

Decker

2021

Preprint

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Selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally-stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal’s generation and 11 million imputed SNPs. Using these datasets with high power and dense mapping resolution, GPSM detected a total of 294 unique loci actively under selection in two cattle breeds. We observed that GPSM has a high power to detect selection in the very recent past (< 10 years), even when allele frequency changes are small. Variants identified by GPSM reside in genomic regions associated with known breed characteristics, such as fertility and maternal ability in Red Angus and carcass merit and coat color in Simmental. Over 60% of the selected loci reside in or near (<50 kb) annotated genes. Additionally, 36% of selected loci overlap known epigenetic marks or putative functional genomic regions. Using RAiSD and nSL, we identify hundreds of putative selective sweeps; however, these sweeps have little overlap with polygenic selected loci. This makes GPSM a complementary approach to sweep detection methods when temporal genotype data are available. The selected loci that we identify across methods demonstrate the complex architecture of selection in domesticated cattle.

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“…Although less productive under intense production conditions, these local breeds may carry alleles that enabled them to adapt to local conditions. Moscarelli et al [3] reported the presence of several genomic regions that vary between original and modern Brown cattle populations, in line with their different breeding histories. Selection and genetic drift will both have contributed to the genetic differentiation between original and modern breeds.…”

Section: Introductionmentioning

confidence: 99%

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

Hulsegge

Oldenbroek

Bouwman

et al. 2022

Animals

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Over the last century, genetic diversity in many cattle breeds has been affected by the replacement of traditional local breeds with just a few milk-producing breeds. In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF). The objective of this study is to investigate genomewide genetic diversity between a group of historically and recently used DF bulls and a group of recently used HF bulls. Genetic material of 12 historic (hDF), 12 recent DF bulls (rDF), and 12 recent HF bulls (rHF) in the Netherlands was sequenced. Based on the genomic information, different parameters—e.g., allele frequencies, inbreeding coefficient, and runs of homozygosity (ROH)—were calculated. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has a unique genetic identity (12% of the single nucleotide polymorphisms were group-specific). The rDF is slightly more diverged from rHF than hDF. The inbreeding coefficient based on runs of homozygosity (Froh) was higher for rDF (0.24) than for hDF (0.17) or rHF (0.13). Our results also displayed the presence of several genomic regions that differentiated between the groups. In addition, thirteen, forty-five, and six ROH islands were identified in hDF, rDF, and rHF, respectively. The genetic diversity of the DF breed reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors was not increased.

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Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Abstract: Identification of genomic regions involved in the phenotypic differences between original and modern Brown populations

Cited by 21 publications

References 60 publications

Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Uncovering the architecture of selection in two Bos taurus cattle breeds

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

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