Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle)

Toro-Ospina, A.M.; Ríos, Ana Cristina Herrera; Santos, Wellington Bizarria dos; Schettini, Gustavo Pimenta; Aristizabal, Viviana H Vallejo; Gilberto, Tovar-Claros; Morea, Edna Gicela Ortiz

doi:10.3390/d14100828

Cited by 7 publications

(3 citation statements)

References 54 publications

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“…All the genes implicated are also consistent with the QTLs found which are linked to meat and production traits. The OAR9:64.41–66.10 ROH island highlighted the CSMD3 gene that appears to be important for fertility, growth, and also for local adaptation and disease resistance ( 90 ). The OAR15:56.49–58.70 hotspot, highlighting numerous QTLs related to fat composition (meat PUFA content and meat omega-6 fatty acid content), was not mentioned in previous literature.…”

Section: Discussionmentioning

confidence: 99%

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

et al. 2023

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Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

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Section: Discussionmentioning

confidence: 99%

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

et al. 2023

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“…There are only a few studies that aimed at detecting selection signatures in Creole cattle (e.g. Pitt et al, 2019;Toro-Ospina et al, 2022). A previous study provided a first insight into footprints of selection in GUA cattle using the the Illumina BovineSNP50 chip assay (Gautier & Naves 2011).…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Jemaa

Adam

Boussaha

et al. 2023

Preprint

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Admixture is an evolutionary process that enables short-term adaptation. The Creole cattle from Guadeloupe is a tropically adapted breed. Its three-way admixture and long-term isolation offer a unique opportunity for understanding the genetic determinants of adaptive admixture in livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA) and combined our data with sequenced genomes of 99 cattle from 25 breeds representative of European, African and indicine groups to provide the most detailed exploration, to date, of patterns of genetic variation and to detect selection signatures in this population. We detect 17 228 983 single nucleotide polymorphisms (SNPs) and we confirmed the higher level of African and indicine ancestries, compared to the European ancestry, in the GUA genome. We show that, unlike Criollo cattle, GUA population originates directly from West Africa with indicine ancestry inherited via West African ancestors. We relied on consistency of signals across various methods based on excess of haplotype homozygosity, differences in allele frequencies and excess ⁄ deficiency of local ancestry to identify five strong candidate regions showing an excess of indicine ancestry. These encompass immune-, heat-tolerance- and physical exercise-related genes. Moreover, we found that a previously identified horn-related gene, RXFP2 is under strong selective pressure in GUA genome likely owing to human-driven (socio-cultural) pressure. Our study highlights the role played by population admixture for driving rapid adaptive response to local environmental constraints.

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“…There are only a few studies that aimed at detecting selection signatures in Creole cattle 6,7,13 . The results from these studies point to candidate regions linked to various molecular processes underlying tropical adaptation including slick hair coat, DNA repair processes 6 , immune response and adaptation to warm conditions in male and female reproductive functions 7,13 .…”

mentioning

confidence: 99%

Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Ben-Jemaa,

Adam,

Boussaha

et al. 2023

Sci Rep

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The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.

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Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle)

Cited by 7 publications

References 54 publications

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

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