Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions
Author
Ramírez-Ayala, Lino C.
Rocha, Dominique
Ramos-Onsins, Sebas E.
Leno-Colorado, Jordi
Charles, Mathieu
Bouchez, Olivier
Rodríguez-Valera, Yoel
Pérez-Enciso, Miguel
Publication date
2021-01-04ISSN
0999-193X
Abstract
Background: In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These
animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical condi‑
tions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that
European taurine cattle have difculty coping with.
Results: In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 wholegenome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure
and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population,
the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype
homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adapta‑
tion of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of
Bos indicus, but they were not sufcient to explain adaptation of CHCU to tropical conditions by Bos indicus introgres‑
sion only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin
involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within
these genes, we identifed single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute
to some of the observed phenotypic diferences between CHCU and CHFR animals.
Conclusions: Whole-genome data confrm that CHCU cattle are closely related to Charolais from France (CHFR) and
Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent
adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of
the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and
explain some of the phenotypic diferences observed between CHCU and CHFR cattle.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
619 - Veterinary science
Pages
11
Publisher
BMC
Is part of
Genetics Selection Evolution
Citation
Ramírez-Ayala, Lino C., Dominique Rocha, Sebas E. Ramos-Onsins, Jordi Leno-Colorado, Mathieu Charles, Olivier Bouchez, Yoel Rodríguez-Valera, Miguel Pérez-Enciso, and Yuliaxis Ramayo-Caldas. 2021. "Whole-Genome Sequencing Reveals Insights Into The Adaptation Of French Charolais Cattle To Cuban Tropical Conditions". Genetics Selection Evolution 53 (1). doi:10.1186/s12711-020-00597-9.
Grant agreement number
MINECO/Programa Estatal de I+D+I orientada a los retos de la sociedad/AGL2016-78709-R/ES/UTILIZACION DE SECUENCIAS COMPLETAS PARA LA MEJORA DE ESPECIES DOMESTICAS/
MINECO/Programa Estatal de Fomento de la investigación científica y técnica de excelencia/BFU2016-77236-P/ES/FUNCION DEL RELOJ CIRCADIANO EN EL CONTROL DE LAS RESPUESTAS DE LA PLANTA A CAMBIOS MEDIOAMBIENTALES/
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
EC/H2020/665919/EU/Opening Sphere UAB-CEI to PostDoctoral Fellows/P-SPHERE
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2831]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/