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

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.

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

Conservation Genetics ◽

10.1007/s10592-015-0762-9 ◽

2015 ◽

Vol 17 (1) ◽

pp. 77-89 ◽

Cited By ~ 10

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

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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 ◽

10.3390/genes11080932 ◽

2020 ◽

Vol 11 (8) ◽

pp. 932 ◽

Cited By ~ 1

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.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.702822 ◽

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.

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Systematic pathway-analysis of kinesin protein family (KIF) using genome-wide SNP data in patients with myocardial infarction: Genetic variation in KIFC3 gene associates with myocardial infarction

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0029-1191643 ◽

2009 ◽

Vol 56 (S 01) ◽

Author(s):

S Eifert ◽

A Goetz ◽

P Linsel-Nitschke ◽

A Medack ◽

C Hengstenberg ◽

...

Keyword(s):

Myocardial Infarction ◽

Genetic Variation ◽

Pathway Analysis ◽

Protein Family ◽

Snp Data ◽

Genome Wide

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

Scientific Reports ◽

10.1038/s41598-021-90325-0 ◽

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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Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

Livestock Science ◽

10.1016/j.livsci.2021.104587 ◽

2021 ◽

pp. 104587

Author(s):

Arnav Mehrotra ◽

Bharat Bhushan ◽

Karthikeyan A ◽

Akansha Singh ◽

Snehasmita Panda ◽

...

Keyword(s):

Divergent Selection ◽

Snp Data ◽

Genome Wide

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Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people

Journal of Human Genetics ◽

10.1038/s10038-020-00898-3 ◽

2021 ◽

Author(s):

Timothy Jinam ◽

Yosuke Kawai ◽

Yoichiro Kamatani ◽

Shunro Sonoda ◽

Kanro Makisumi ◽

...

Keyword(s):

Phylogenetic Network ◽

Principal Component ◽

Human Populations ◽

Structure Model ◽

Rice Farming ◽

Asian Continent ◽

Dual Structure ◽

Snp Data ◽

Genome Wide ◽

Kagoshima Prefecture

AbstractThe “Dual Structure” model on the formation of the modern Japanese population assumes that the indigenous hunter-gathering population (symbolized as Jomon people) admixed with rice-farming population (symbolized as Yayoi people) who migrated from the Asian continent after the Yayoi period started. The Jomon component remained high both in Ainu and Okinawa people who mainly reside in northern and southern Japan, respectively, while the Yayoi component is higher in the mainland Japanese (Yamato people). The model has been well supported by genetic data, but the Yamato population was mostly represented by people from Tokyo area. We generated new genome-wide SNP data using Japonica Array for 45 individuals in Izumo City of Shimane Prefecture and for 72 individuals in Makurazaki City of Kagoshima Prefecture in Southern Kyushu, and compared these data with those of other human populations in East Asia, including BioBank Japan data. Using principal component analysis, phylogenetic network, and f4 tests, we found that Izumo, Makurazaki, and Tohoku populations are slightly differentiated from Kanto (including Tokyo), Tokai, and Kinki regions. These results suggest the substructure within Mainland Japanese maybe caused by multiple migration events from the Asian continent following the Jomon period, and we propose a modified version of “Dual Structure” model called the “Inner-Dual Structure” model.

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A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

Genetics Selection Evolution ◽

10.1186/s12711-020-00599-7 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Wim Gorssen ◽

Roel Meyermans ◽

Steven Janssens ◽

Nadine Buys

Keyword(s):

Association Studies ◽

Genome Wide Association Studies ◽

Single Nucleotide ◽

Future Studies ◽

Snp Data ◽

Animal Populations ◽

Genome Wide ◽

Starting Point ◽

Different Populations ◽

Signatures Of Selection

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

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