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Rajawat D, Panigrahi M, Nayak SS, Ghildiyal K, Sharma A, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Dutt T. Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection. Anim Biotechnol 2023; 34:3920-3933. [PMID: 37493405 DOI: 10.1080/10495398.2023.2240387] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Pharmacology and Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Animal Biotechnology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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Ballan M, Bovo S, Bertolini F, Schiavo G, Schiavitto M, Negrini R, Fontanesi L. Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds. J Anim Breed Genet 2023; 140:663-678. [PMID: 37435689 DOI: 10.1111/jbg.12818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/13/2023]
Abstract
Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources.
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Affiliation(s)
- Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Michele Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Volturara Appula, Italy
| | | | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
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Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data. Genes (Basel) 2022; 13:genes13091601. [PMID: 36140768 PMCID: PMC9498432 DOI: 10.3390/genes13091601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% Fst approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions.
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