scholarly journals Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours

2021 ◽  
Author(s):  
Francesca Bertolini ◽  
Giulia Moscatelli ◽  
Giuseppina Schiavo ◽  
Samuele Bovo ◽  
Anisa Ribani ◽  
...  
Keyword(s):  
Cattle Breeds ◽  
The North ◽  
Signatures Of Selection

scholarly journals Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

2019 ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe

2016 ◽  
Vol 47 (6) ◽  
pp. 647-657 ◽  
Author(s):  
T. Iso-Touru ◽  
M. Tapio ◽  
J. Vilkki ◽  
T. Kiseleva ◽  
I. Ammosov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Northern Europe ◽  
Cattle Breeds ◽  
Genomic Signatures ◽  
Signatures Of Selection

Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds

2018 ◽  
Vol 216 ◽  
pp. 100-108 ◽  
Author(s):  
L. Xu ◽  
W.G. Zhang ◽  
H.X. Shen ◽  
Y. Zhang ◽  
Y.M. Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Signatures Of Selection

scholarly journals Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Christin Schmidtmann ◽  
Anna Schönherz ◽  
Bernt Guldbrandtsen ◽  
Jovana Marjanovic ◽  
Mario Calus ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Northern Europe ◽  
Genetic Constitution ◽  
Breeding Strategies ◽  
Dual Purpose ◽  
Cattle Breeds ◽  
Genomic Signatures ◽  
Comprehensive Knowledge ◽  
Shared Ancestry ◽  
Signatures Of Selection

Abstract Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. Conclusions This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

scholarly journals Evaluating signatures of selection through variation in linkage disequilibrium among different cattle breeds

2016 ◽  
Vol 19 (Special issue) ◽  
pp. 105-110
Author(s):  
Veronika Kukučková ◽  
Nina Moravčíková ◽  
Radovan Kasarda
Keyword(s):  
Linkage Disequilibrium ◽  
Cattle Breeds ◽  
Signatures Of Selection

scholarly journals Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Pedro H. F. Freitas ◽  
Yachun Wang ◽  
Ping Yan ◽  
Hinayah R. Oliveira ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Thermal Tolerance ◽  
Climatic Conditions ◽  
Biological Processes ◽  
Biological Mechanisms ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Selection For ◽  
Genomic Regions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

scholarly journals Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

2019 ◽  
Vol 23 (5) ◽  
pp. 559-568
Author(s):  
N. S. Yudin ◽  
D. M. Larkin
Keyword(s):  
Russian Federation ◽  
Association Studies ◽  
Coat Colour ◽  
Whole Genome ◽  
Cattle Breeds ◽  
Genome Association ◽  
Whole Genome Association ◽  
The Russian Federation ◽  
Signatures Of Selection ◽  
Cattle Domestication

Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.

scholarly journals Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel

2014 ◽  
Vol 41 (2) ◽  
pp. 957-965 ◽  
Author(s):  
Giordano Mancini ◽  
Maria Gargani ◽  
Giovanni Chillemi ◽  
Ezequiel Luis Nicolazzi ◽  
Paolo Ajmone Marsan ◽  
...  
Keyword(s):  
Cattle Breeds ◽  
Snp Panel ◽  
Signatures Of Selection

scholarly journals Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

Abstract Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6  × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

scholarly journals Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Susanne Eriksson ◽  
Anna M. Johansson ◽  
Majid Khansefid ◽  
Sima Moghaddaszadeh-Ahrabi ◽  
...  
Keyword(s):  
Cold Acclimation ◽  
Candidate Genes ◽  
Economic Traits ◽  
Cattle Breeds ◽  
Signatures Of Selection
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