Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip

Abstract

BackgroundTunisian local cattle populations are at risk of extinction as they were massively crossed with imported breeds. Preservation of indigenous livestock populations is important because each of them comprises a unique set of genes resulting from a local environment-driven selection that occurred over hundreds of years. The diversity and genetic structure of Tunisian local cattle populations are poorly understood. However, such information is crucial to the conservation and sustainable use of genetic resources.In addition, comparing the genomic structure of population sets from different parts of the world could help yield insight into their origin and history.In the present study, we provide a detailed assessment of the population structure of the three Tunisian local cattle populations using various methods, and we highlight their origin and history by investigating approximately ~38,000 SNPs in a broad panel of 878 individuals from 37 worldwide cattle breeds representative of African, European and indicine populations.ResultsOur study revealed a low level of divergence and high genetic diversity in Tunisian local cattle reflecting low levels of genetic drift. A Comparison with the worldwide cattle panel pinpointed the admixed origin of the genome of the three Tunisian populations with the two main European and African ancestries. Our results were in agreement with previous historical and archaeological reports about the past gene flow that existed between North African and South European breeds, in particular with Iberian cattle. We also detected a low-level indicine introgression in the three Tunisian populations and we inferred that indicine ancestry was inherited via African ancestors.ConclusionsOur results represent the first study providing genetic evidence about the origin and history of Tunisian local cattle. The information provided by the fine-scale genetic characterization of our study will enhance the establishment of a national conservation strategy for these populations. These results may enable the identification of genetic variants involved in adaptation to harsh environmental conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1638-6) contains supplementary material, which is available to authorized users.

Population Structure Analysis of Bull Genomes of European and Western Ancestry

“…However, these methods may be sensitive to early divergence events or unable to capture hierarchical relationships7. Analysis of regional breeds often needs to include other published cattle genomes in order to estimate introgression or admixture589. This poses a significant challenge in population genomics.…”

“…The 1000 Bull Genomes Consortium has successfully collaborated with institutions from more than 20 countries to collect 1577 whole genome sequences (as of version 5). Although the structural complexity of cattle has previously been studied based on array-based genome profiles or selected genetic markers, focusing on regions and breeds456789, a population genomic study involving whole genome sequences related to European and Western ancestry has not been performed.…”

“…Recent studies using unsupervised classification, admixture models, and other techniques demonstrate greater structural complexity128, but direct estimation and utilization of population structure with relaxed assumptions have been challenging. Logistic factor analysis (LFA) uses recently developed probabilistic models of individual allele frequencies underlying genotypes that are appropriate for a wide range of population structures (e.g., discrete, continuous, or admixture)10.…”

Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

“…The availability of powerful and cheap tools for genotyping large numbers of single nucleotide polymorphisms (SNPs) has provided conservation biologists and animal geneticists with the opportunity to characterise genomic variation and estimate population genetic parameters at very high resolution in threatened or endangered livestock breeds (Pertoldi et al, 2014; Ben Jemaa et al, 2015; Beynon et al, 2015; Meszaros et al, 2015; Burren et al, 2016; Decker et al, 2016; Iso-Touru et al, 2016; Manunza et al, 2016; Mastrangelo et al, 2016; Visser et al, 2016; Williams et al, 2016; Francois et al, 2017). These studies are already providing important baseline data for genetic conservation and will underpin programmes for managed breeding and biobanking of these populations (Groeneveld et al, 2016).…”

Population Structure Analysis of Globally Diverse Bull Genomes

“…This international collection of diverse genomes can be regarded as representative of genetic diversity within bulls and thus enables systematic analysis of population genomics. Although the structural complexity of cattle has previously been studied based on limited genome profiles or genetic markers, focusing on regions and breeds [4][5][6][7] , a population genetic study involving a large and diverse collection of whole genome sequences has not been performed.…”