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


RESULTS
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 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.


CONCLUSIONS
Our 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.
National Institute of Agronomic Research of Tunisia, Laboratoire des Productions Animales et Fourragères, Rue Hédi Karray, 2049, Ariana, Tunisia. benjemaaslim@yahoo.fr.
Slim
S
Ben Jemaa
INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352, Jouy-en-Josas, France. mekki.boussaha@jouy.inra.fr.|AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352, Jouy-en-Josas, France. mekki.boussaha@jouy.inra.fr.
Mekki
M
Boussaha
Livestock and Pasture Office, 1002, Tunis Belvedere, Tunisia. mondherbenmehdi@yahoo.fr.
Mondher
M
Ben Mehdi
Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, 305-764, South Korea. junheon@cnu.ac.kr.
Jun Heon
JH
Lee
Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, 305-764, South Korea. slee46@korea.kr.|Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, 232-952, South Korea. slee46@korea.kr.
Seung-Hwan
SH
Lee
D000818:Animals; D002417:Cattle / Q000235:genetics*; D016000:Cluster Analysis; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D016013:Likelihood Functions; D008957:Models, Genetic; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis