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

BMC Genomics
Slim Ben JemaaSeung-Hwan Lee

Abstract

Tunisian 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. Our 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...Continue Reading

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Citations

Feb 6, 2017·Genomics & Informatics·Aditi SharmaYongmin Cho
Aug 3, 2018·PloS One·Amanda Marchi MaioranoJosineudson Augusto Ii de Vasconcelos Silva
Jan 14, 2017·Scientific Reports·Neo Christopher ChungUNKNOWN 1000 Bull Genomes Project
Jul 31, 2018·Asian-Australasian Journal of Animal Sciences·Seungchang KimChang-Yeon Cho
Jul 28, 2020·Animal Genetics·K ZhangJ Liu
Mar 10, 2018·Frontiers in Genetics·Sam BrowettDavid E MacHugh
Jun 27, 2018·Genetics, Selection, Evolution : GSE·Salvatore MastrangeloFabio Pilla
Feb 19, 2019·Genetics and Molecular Biology·Slim Ben JemaaMekki Boussaha
Jul 16, 2020·Genetics, Selection, Evolution : GSE·Gabriele SenczukMartino Cassandro
Oct 2, 2021·Tropical Animal Health and Production·Ricardo José Ocampo GallegoDiego Hernán Bejarano Garavito

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Methods Mentioned

BETA
genotyping
chips
PCA
chip

Software Mentioned

adegenet R package
phyclust R package
package
Admixture
PLINK
Distruct
package StAMMP
R package StAMPP
Treemix
Genepop

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