The identification of runs of homozygosity give a focus on the genetic diversity and the adaptation of the "Charolais de Cuba" cattle
Rodríguez Valera, Yoel (Universidad de Granma. Facultad de Ciencias Agropecuarias)
Rocha, Dominique (Institut national de la recherche agronomique (França). Génétique Animale et Biologie Intégrative)
Naves, Michel (Institut National de la Recherche Agronomique (França))
Renand, Gilles (Institut national de la recherche agronomique (França). Génétique Animale et Biologie Intégrative)
Pérez-Pineda, Eliecer (Universidad de Granma. Facultad de Ciencias Agropecuarias)
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries)
Ramos-Onsins, Sebastian (Centre de Recerca en Agrigenòmica)

Date:	2020
Abstract:	Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5. 7%, 3. 4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43. 9%, 37. 0%, and 54. 2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
Grants:	European Commission 6655919 Ministerio de Economía y Competitividad SEV-2015-0533 Ministerio de Economía y Competitividad AGL2016-78709-R Ministerio de Economía y Competitividad AGL2013-41834-R
Note:	Altres ajuts: CERCA Programme/Generalitat de Catalunya.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Genomic inbreeding ; Effective population size ; Runs of homozygosity ; Candidate genes ; Tropical climate ; Adaptation
Published in:	Animals, Vol. 10, issue 12 (Dec. 2020) , art. 2233, ISSN 2076-2615

DOI: 10.3390/ani10122233
PMID: 33261195

16 p, 4.5 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
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