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

Rodríguez-Valera, Yoel; Renand, Gilles; Naves, Michel; Fonseca-Jiménez, Yidix; Moreno-Probance, Teresa Inés; Ramos-Onsins, Sebastián E.; Rocha, Dominique; Ramayo-Caldas, Yuliaxis

doi:10.1038/s41598-018-29453-z

Cited by 9 publications

(14 citation statements)

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“…In previous work based on the Illumina 50 k SNP Chip genotype data, we reported a putative introgression of B. indicus into CHCU and although it was small [6], it could explain why CHCU and CHFR are clearly separated, in spite of the short period since the original importation of Charolais from France. Here, we confirm this introgression with a better resolution using whole-genome data.…”

Section: Population Structure and Impact Of B Indicus Introgression mentioning

confidence: 83%

“…In this short period of time, several clear phenotypic differences between the original French Charolais (CHFR) and its Cuban counterpart have appeared. CHCU cattle are smaller than CHFR, with weights of 34 vs. 46 kg at birth and 290 vs. 493 kg for heifer's weight at 18 months, respectively [6,7]. Also, CHCU cattle are hairless and their carcasses have a lower grade and higher fat content than CHFR [7].…”

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confidence: 99%

“…Although the CHCU cattle are thought to form a closed population with no records of interbreeding, Ribas [8] reported the presence of a specific B. indicus blood group allele (U' 1 ), at a very low frequency. More recently, Rodriguez-Valera et al [6] used the Illumina Bovine 50 k single nucleotide polymorphism (SNP) BeadChip to investigate the genetic structure and putative ancestral origin of this population and showed that CHCU clusters with the taurine breeds. Nevertheless, in spite of the short period of time since the importation of Charolais animals from France, a marked differentiation (fixation index (F ST ) = 0.049) is observed between CHFR and CHCU cattle.…”

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confidence: 99%

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

et al. 2021

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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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Section: Population Structure and Impact Of B Indicus Introgression mentioning

confidence: 83%

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confidence: 99%

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

et al. 2021

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“…River buffalo have been selected for many similar traits as other domesticated species, for example size, coat colour and production phenotypes [11][12][13] . Consequently, understanding how selection for these traits has affected a particular species' genome will likely not only provide insights into its phenotypic adaptation, but also that of other domesticated species.…”

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Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

et al. 2020

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More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

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“…The identification of genomic regions impacted both by human selection and climate adaptation will help understand how changes at the genome level modulate changes in phenotype, which holds high promises to improve animal breeding processes for production, health, and welfare [4]. Previous analyses using single nucleotide polymorphism (SNP) arrays [5][6][7][8][9][10][11][12][13] and whole-genome sequences [14,15] have identified candidate regions and potential genes under selection in various cattle breeds. However, compared to other domestic species for which selection is known to impact mostly conserved elements, transcription start sites or regulatory regions [16][17][18], to our knowledge, there has been no effort to understand the impact of selection at the functional-genomic level in cattle.…”

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confidence: 99%

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

et al. 2020

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Background: Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results: We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N'Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions: Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultraviolet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

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

Cited by 9 publications

References 51 publications

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

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

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

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