Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

Autor: Sandra Afonso, Rute R. da Fonseca, Irene Ureña, Lounès Chikhi, Catarina Ginja, Ana Elisabete Pires, Emil Jørsboe
Přispěvatelé: Repositório da Universidade de Lisboa, Uppsala University, Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), Universidade do Porto, Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
Male
Animal breeding
Population genetics
ved/biology.organism_classification_rank.species
Native breeds
Breeding
Sex chromosome diversity
Genome
01 natural sciences
Gene flow
Nucleotide diversity
Y Chromosome
ComputingMilieux_MISCELLANEOUS
Phylogeny
2. Zero hunger
0303 health sciences
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Genomics
Breed
Europe
Female
Research Article
Biotechnology
lcsh:QH426-470
Genotype
lcsh:Biotechnology
Biology
Genetic differentiation
010603 evolutionary biology
DNA
Mitochondrial
03 medical and health sciences
lcsh:TP248.13-248.65
Microsatellite repeats
Genetics
Animals
Genetic variation
Domestication
030304 developmental biology
Autosome
Genomic diversity
ved/biology
Taurine cattle
Haplotype
population structure
Chromosomes
Mammalian
lcsh:Genetics
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
Genetics
Population
Haplotypes
Evolutionary biology
Cattle
Iberia
Cattle genomes
010606 plant biology & botany
Zdroj: Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
da Fonseca, R R, Urena, I, Afonso, S, Pires, A E, Jørsboe, E, Chikhi, L & Ginja, C 2019, ' Consequences of breed formation on patterns of genomic diversity and differentiation : the case of highly diverse peripheral Iberian cattle ', BMC Genomics, vol. 20, 334, pp. 1-13 . https://doi.org/10.1186/s12864-019-5685-2
BMC Genomics
BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-5685-2⟩
BMC Genomics, Vol 20, Iss 1, Pp 1-13 (2019)
ISSN: 1471-2164
DOI: 10.1186/s12864-019-5685-2
Popis: BackgroundIberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.ResultsWe sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y‐chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male‐biased gene flow.ConclusionsOur results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
Databáze: OpenAIRE
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