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. 2018 Jul 20;8(1):11005.
doi: 10.1038/s41598-018-29453-z.

Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed

Yoel Rodriguez-Valera  1 , Gilles Renand  2 , Michel Naves  3 , Yidix Fonseca-Jiménez  1 , Teresa Inés Moreno-Probance  4 , Sebastian Ramos-Onsins  5 , Dominique Rocha  6 , Yuliaxis Ramayo-Caldas  7   8   9
Affiliations

Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed

Yoel Rodriguez-Valera et al. Sci Rep. .

Abstract

In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the 'Charolais de Cuba' (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Principal component analysis using all samples. Individuals are grouped in Bos taurus, Bos indicus and Hybrid. Samples were colored according to geographic origin of breed; black: Africa, green: Asia, red: Europe and blue: America. CHCU and CHA samples are indicated using blue and light blue circle color respectively.
Figure 2
Figure 2
(A) Ancestry models with 2 ancestral populations (K = 2) the color correspond to: Black (Bos taurus) and red (Bos indicus). (B) 3 ancestral populations (K = 3) the color correspond to: blue (Eurasian Bos taurus), green (Bos indicus), black (African Bos taurus) and K = 37 (C). Breed names correspond to ABO: Abondance, AN: Angus, AUB: Aubrac, BALI: Bali, BAO: Baoule, BEFM: Beefmaster, BOR: Boran, BORG: Borgou, BR: Brahman, BRVH: Braunvieh, BSW: Brown Swiss, CANC: Canchim, CHA: French Charolais, CHCU: Cuban Charolais, GAS: Gascon, GEL: Gelbvieh, GIR: Gir, GNS: Guernsey, HFD: Hereford, HO: Holstein, JER: Jersey, KUR: Kuri, LAG: Lagune, LM: Limousin, MAAN: Maine-Anjou, MONT: Montbeliard, NDAM: N’Dama, NEL: Nelore, NORM: Normande, NRC: Norwegian Red, ONG: Ongole Grade, PIED: Piedmontese, PRP: French Red Pied Lowland, RMG: Romagnola, SAL: Salers, SGT: Santa Gertrudis, SIM: Simmental, SOM: Somba, TXLH: Texas Longhorn, VOS: Vosgienne, ZBO: Zebu Bororo, ZEB: East African Shorthorn Zebu, ZFU: Zebu Fulani, ZMA: Zebu from Madagascar.
Figure 3
Figure 3
Distribution of the Fst after randomization of the dataset. The red vertical line represents the differentiation (Fst value) between CHCU and CHA.
Figure 4
Figure 4
Linkage disequilibrium (r2) decay in CHA and CHCU populations.
Figure 5
Figure 5
Graphical representation of the EHH pattern in the BTA5 chromosomal interval reported as associated with parasite resistance, yearling weight, body condition score, coat color and penile sheath score (Porto-Neto et al. 2014b). The x-axis represents the chromosomal position (Mb) and the y-axis the ratio of the ln(Rsb) CHA/CHCU.
Figure 6
Figure 6
Over-represented canonical pathways considering all the EHH intervals.
See this image and copyright information in PMC

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