Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data

2015 ◽  
Vol 17 (1) ◽  
pp. 77-89 ◽  
Author(s):  
Karim Karimi ◽  
Ali Esmailizadeh Koshkoiyeh ◽  
Masood Asadi Fozi ◽  
Laercio R. Porto-Neto ◽  
Cedric Gondro
Keyword(s):  
Cattle Breeds ◽  
Snp Data ◽  
Genome Wide ◽  
Native Cattle

scholarly journals On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore Mastrangelo ◽  
Paolo Ajmone-Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Indices ◽  
Melting Pot ◽  
Cattle Breeds ◽  
Snp Data ◽  
Early Migration ◽  
Genome Wide ◽  
European Colonization ◽  
Approximate Bayesian ◽  
European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

scholarly journals Genomic relatedness and diversity of Swedish native cattle breeds

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Maulik Upadhyay ◽  
Susanne Eriksson ◽  
Sofia Mikko ◽  
Erling Strandberg ◽  
Hans Stålhammar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Demographic History ◽  
Genomic Diversity ◽  
Founder Population ◽  
Southern Sweden ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Native Cattle

Abstract Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

scholarly journals Into the origin and diversification of Podolian cattle breeds by testing Neolithic scenarios of European colonization using genome-wide SNP data

2020 ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore MASTRANGELO ◽  
Paolo Ajmone Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Cattle Breeds ◽  
Snp Data ◽  
Genome Wide ◽  
European Colonization

scholarly journals Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 932 ◽  
Author(s):  
Gabriele Senczuk ◽  
Lorenzo Guerra ◽  
Salvatore Mastrangelo ◽  
Claudia Campobasso ◽  
Kaouadji Zoubeyda ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Snp Array ◽  
Complex Nature ◽  
Cattle Breeds ◽  
Snp Data ◽  
Genome Wide ◽  
Almost All ◽  
Pleiotropic Functions ◽  
Fst Outlier

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.

scholarly journals Erratum to: A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Aditi Sharma ◽  
Seung-Hwan Lee ◽  
Dajeong Lim ◽  
Han-Ha Chai ◽  
Bong-Hwan Choi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Cattle Breeds ◽  
Genome Wide ◽  
A Genome ◽  
Native Cattle

scholarly journals Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

2021 ◽  
Vol 12 ◽  
Author(s):  
Lucas Lima Verardo ◽  
Fabyano Fonseca e Silva ◽  
Marco Antonio Machado ◽  
João Cláudio do Carmo Panetto ◽  
Daniele Ribeiro de Lima Reis Faza ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Population History ◽  
Breeding Systems ◽  
Genome Wide Association Studies ◽  
Effective Population ◽  
Cattle Breeds ◽  
Snp Data ◽  
Genome Wide ◽  
Production Behavior

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

scholarly journals A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

BMC Genetics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Aditi Sharma ◽  
Seung-Hwan Lee ◽  
Dajeong Lim ◽  
Han-Ha Chai ◽  
Bong-Hwan Choi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Cattle Breeds ◽  
Genome Wide ◽  
A Genome ◽  
Native Cattle

scholarly journals PSXII-21 Genome-wide search for genomic regions under putative selection in two Russian native cattle breeds using high-density SNP Bead Chip

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 242-243
Author(s):  
Arsen V Dotsev ◽  
Natalia A Zinovieva ◽  
Tatiana Evgenievna Deniskova ◽  
Alexandra Abdelmanova ◽  
Johann Sölkner ◽  
...  
Keyword(s):  
Production Systems ◽  
High Density ◽  
Dna Arrays ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Genome Wide Search ◽  
Native Cattle ◽  
Signatures Of Selection ◽  
Comparison Of The Results ◽  
Genomic Regions

Abstract National livestock genetic resources are the valuable source of genetic variability, which are necessary to ensure the sustainability of the local animal production systems. The aim of our work was to characterize the genomic architecture and to detect signatures of selection in two oldest Russian native cattle breeds, using high-density DNA arrays. Fifty-six animals of Yaroslavl (n = 31) and Kholmogor (n = 25) were selected for the study. The Illumina Bovine HD BeadChip (777,962 SNPs) was used for genotyping. High-density SNP genotypes for Holsteins (n = 25) were used as the reference. Three methods (Fst, hapFLK, and ROH) were implemented to detect the genomic regions to be under putative selection. The results of the PCA-plot, Neighbor-Net analysis and Admixture clustering showed clear genetic differences between Yaroslavl and Kholmogor breeds as well as between them and Holsteins. Comparison of the results produced by different methods showed presence of twelve regions in genome of Yaroslavl breed and nine regions in genome of Kholmogor breeds, which were identified at least by two methods. We have confirmed nine regions under putative selection in genome of Yaroslavl cattle and six regions in genome of Kholmogor cattle, which were described previously based on medium-density SNP genotypes, herewith the flanking positions of the most of these regions were expanded. Additionally, we detected three new putative genomic regions affected by selection in each studied breed, which were localized on chromosomes 4, 15 and 17 in Yaroslavl breed and on chromosomes 12, 15 and 18 in Kholmogor breed. The functional annotation of genes localized within identified regions was carried out. Our research results can be useful for genetic improvement of the studied cattle breeds and for developing the programs for their conservation. The study was supported by RSF within project No. 19-76-20012.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

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