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. 2021 Jan 4;53(1):3.
doi: 10.1186/s12711-020-00597-9.

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

Lino C Ramírez-Ayala  1 , Dominique Rocha  2 , Sebas E Ramos-Onsins  1 , Jordi Leno-Colorado  1 , Mathieu Charles  2   3 , Olivier Bouchez  4 , Yoel Rodríguez-Valera  5 , Miguel Pérez-Enciso  1   6 , Yuliaxis Ramayo-Caldas  7   8
Affiliations

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

Lino C Ramírez-Ayala et al. Genet Sel Evol. .

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 conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with.

Results: In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome 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 adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression 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 identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals.

Conclusions: Whole-genome data confirm 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 differences observed between CHCU and CHFR cattle.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Population structure. (a) Principal component analysis using all samples. Individuals are grouped into Bos taurus, Bos indicus and Hybrid clusters. Black: Brangus, red: Brahman, blue: Canadian Charolais, cyan: Cuban Charolais, green: French Charolais, magenta: Limousin, purple: Texas Longhorn (b) Principal component analysis using all samples. Red: Brahman, cyan: Cuban Charolais, green: French Charolais (c) FST between CHCU and the other breeds. (d) Results of admixture analyses with two ancestral populations (K = 2) Red: Brahman (Bos indicus) and green: French and Canadian Charolais (Bos taurus)
Fig. 2
Fig. 2
Frequency of indicus component per CHCU sample and chromosome inferred from analysis with the ELAI software
Fig. 3
Fig. 3
Extended haplotype homozygosity (EHH) intervals per chromosome. The x-axis represents the chromosome positions and the y-axis the chromosome number
Fig. 4
Fig. 4
Percentage of BRM in windows containing putative selection events vs. the other windows, inferred from analysis with the ELAI software
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