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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Farahvashi MA, Mousavi SF, Banabazi MH, Asadi Fozi M. High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep. Trop Anim Health Prod 2024; 56:150. [PMID: 38691202 DOI: 10.1007/s11250-024-04002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Mohammad Ali Farahvashi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran
| | - Seyedeh Fatemeh Mousavi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI) Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
- Department of Animal Biosciences (HBIO), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
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Baazaoui I, Bedhiaf-Romdhani S, Mastrangelo S, Lenstra JA, Da Silva A, Benjelloun B, Ciani E. Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data. Front Vet Sci 2024; 11:1339321. [PMID: 38487707 PMCID: PMC10938946 DOI: 10.3389/fvets.2024.1339321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. Methods In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. Results and discussion We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.
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Affiliation(s)
- Imen Baazaoui
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Sonia Bedhiaf-Romdhani
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Da Silva
- Faculté des Sciences et Techniques de Limoges, E2LIM, Limoges, France
| | - Badr Benjelloun
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, Beni Mellal, Morocco
| | - Elena Ciani
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, University of Bari Aldo Moro, Bari, Italy
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Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023; 54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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5
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [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: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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Cinar MU, Arslan K, Sohel MMH, Bayram D, Piel LMW, White SN, Daldaban F, Aksel EG, Akyüz B. Genome-wide association study of early liveweight traits in fat-tailed Akkaraman lambs. PLoS One 2023; 18:e0291805. [PMID: 37988399 PMCID: PMC10662757 DOI: 10.1371/journal.pone.0291805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/06/2023] [Indexed: 11/23/2023] Open
Abstract
Small ruminants, especially sheep, are essential for sustainable agricultural production systems, future food/nutrition security, and poverty reduction in developing countries. Within developed countries, the ability of sheep to survive on low-quality forage intake could act as buffer against climate change. Besides sheep's importance in sustainable agricultural production, there has been less ongoing work in terms of sheep genetics in Near East, Middle East and in Africa. For lamb meat production, body weight and average daily gain (ADG) until weaning are critical economic traits that affects the profitability of the industry. The current study aims to identify single nucleotide polymorphisms (SNPs) that are significantly associated with pre-weaning growth traits in fat tail Akkaraman lambs using a genome-wide association study (GWAS). A total of 196 Akkaraman lambs were selected for analysis. After quality control, a total of 31,936 SNPs and 146 lambs were used for subsequent analyses. PLINK 1.9 beta software was used for the analyses. Based on Bonferroni-adjusted p-values, one SNP (rs427117280) on chromosome 2 (OAR2) had significant associations with weaning weight at day 90 and ADG from day 0 to day 90, which jointly explains a 0.8% and 0.9% of total genetic variation respectively. The Ovis aries natriuretic peptide C (NPPC) could be considered as a candidate gene for the defined significant associations. The results of the current study will help to increase understanding of the variation in weaning weight and ADG until weaning of Akkaraman lambs and help enhance selection for lambs with improved weaning weight and ADG. However, further investigations are required for the identification of causal variants within the identified genomic regions.
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Affiliation(s)
- Mehmet Ulas Cinar
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri, Turkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Korhan Arslan
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Md Mahmodul Hasan Sohel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Dhaka, Bangladesh
| | - Davut Bayram
- Faculty of Veterinary Medicine, Department of Animal Science, Erciyes University, Kayseri, Turkiye
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Res. 3003 ADBF, WSU Pullman, Pullman, Washington, United States of America
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Fadime Daldaban
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Esma Gamze Aksel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Bilal Akyüz
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
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Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
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Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
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8
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Ben Jemaa S, Tolone M, Sardina MT, Di Gerlando R, Chessari G, Criscione A, Persichilli C, Portolano B, Mastrangelo S. A genome-wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection. J Anim Breed Genet 2023; 140:558-567. [PMID: 37226373 DOI: 10.1111/jbg.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of four genomic regions on two chromosomes were jointly identified by at least two statistical approaches. Several candidate genes for milk production were identified, corroborating the polygenic nature of this trait and which may provide clues to potential new selection targets. We also found candidate genes for growth and reproductive traits. Overall, the identified genes may explain the effect of selection to improve the performances related to milk production traits in the breed. Further studies using high-density array data, would be particularly relevant to refine and validate these results.
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Affiliation(s)
- Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Christian Persichilli
- Dipartimento di Agraria, Ambientale e Scienze dell'alimentazione, University of Molise, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Hu R, Jiang X, Yang H, Liu G. Selection signature analysis reveals RDH5 performed key function in vision during sheep domestication process. Arch Anim Breed 2023. [DOI: 10.5194/aab-66-81-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Abstract. As one of the most successful domesticated animals in the Neolithic age,
sheep gradually migrated all over the world with human activities. During the
domestication process, remarkable changes have taken place in morphology,
physiology, and behavior, resulting in different breeds with different
characters via artificial and natural selection. However, the genetic
background responsible for these phenotypic variations remains largely
unclear. Here, we used whole genome resequencing technology to compare and
analyze the genome differences between Asiatic mouflon wild sheep (Ovis orientalis) and Hu
sheep (Ovis aries). A total of 755 genes were positively selected in the process of
domestication and selection, and the genes related to sensory perception had
directional evolution in the autosomal region, such as OPRL1, LEF1, TAS1R3, ATF6, VSX2, MYO1A, RDH5, and some novel
genes. A missense mutation of c.T722C/p.M241T in exon 4 of RDH5 existing in sheep
were found, and the T allele was completely fixed in Hu sheep. In addition, the
mutation with the C allele reduced the retinol dehydrogenase activity encoding
by RDH5, which can impair retinoic acid metabolism and further influenced the visual
cycle. Overall, our results showed significant enrichment for positively
selected genes involved in sensory perception development during sheep
domestication; RDH5 and its variants may be related to the retinal degeneration
in sheep. We infer that the wild sheep ancestors with weaker visual sensitivity
were weeded out by humans, and the mutation was selective, swept by the dual
pressures of natural and artificial selection.
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Seasonal Adaptation: Geographic Photoperiod-Temperature Patterns Explain Genetic Variation in the Common Vole Tsh Receptor. Genes (Basel) 2023; 14:genes14020292. [PMID: 36833219 PMCID: PMC9957289 DOI: 10.3390/genes14020292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in the mammalian seasonal reproduction pathway. Its abundance and function can tune sensitivity to the photoperiod. To investigate seasonal adaptation in mammals, the hinge region and the first part of the transmembrane domain of the Tshr gene were sequenced for 278 common vole (Microtus arvalis) specimens from 15 localities in Western Europe and 28 localities in Eastern Europe. Forty-nine single nucleotide polymorphisms (SNPs; twenty-two intronic and twenty-seven exonic) were found, with a weak or lack of correlation with pairwise geographical distance, latitude, longitude, and altitude. By applying a temperature threshold to the local photoperiod-temperature ellipsoid, we obtained a predicted critical photoperiod (pCPP) as a proxy for the spring onset of local primary food production (grass). The obtained pCPP explains the distribution of the genetic variation in Tshr in Western Europe through highly significant correlations with five intronic and seven exonic SNPs. The relationship between pCPP and SNPs was lacking in Eastern Europe. Thus, Tshr, which plays a pivotal role in the sensitivity of the mammalian photoperiodic neuroendocrine system, was targeted by natural selection in Western European vole populations, resulting in the optimized timing of seasonal reproduction.
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Dzomba EF, Van Der Nest MA, Mthembu JNT, Soma P, Snyman MA, Chimonyo M, Muchadeyi FC. Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders. Front Genet 2023; 13:932272. [PMID: 36685923 PMCID: PMC9847500 DOI: 10.3389/fgene.2022.932272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/22/2022] [Indexed: 01/05/2023] Open
Abstract
Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7 Mb and MAP2K4 on OAR 11:28.6-31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.
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Affiliation(s)
- E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa,*Correspondence: E. F. Dzomba,
| | - M. A. Van Der Nest
- Agricultural Research Council Biotechnology Platform, Private Bag X5 Onderstepoort, Pretoria, South Africa
| | - J. N. T. Mthembu
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - P Soma
- Agricultural Research Council, Animal Production and Improvement, Pretoria, South Africa
| | - M. A. Snyman
- Grootfontein Agricultural Development Institute, Middelburg, South Africa
| | - M. Chimonyo
- Discipline of Animal and Poultry Science, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - F. C. Muchadeyi
- Agricultural Research Council Biotechnology Platform, Private Bag X5 Onderstepoort, Pretoria, South Africa
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Guo Y, Bai F, Wang J, Fu S, Zhang Y, Liu X, Zhang Z, Shao J, Li R, Wang F, Zhang L, Zheng H, Wang X, Liu Y, Jiang Y. Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep. J Anim Sci 2023; 101:skac383. [PMID: 36402741 PMCID: PMC9833038 DOI: 10.1093/jas/skac383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
The efficiency of molecular breeding largely depends on inexpensive genotyping arrays. In this study, we aimed to develop an ovine high-resolution multiple-single-nucleotide polymorphism (SNP) capture array, based on genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology. All the markers were from 40K captured regions, including genes located within selective sweep regions, breed-specific regions, quantitative trait loci (QTL), and the potential functional SNPs on the sheep genome. The results showed that a total of 210K high-quality SNPs were identified in the 40K regions, indicating a high average capture ratio (99.7%) for the target genomic regions. Using genotyped data (n = 317) from liquid chip technology, we further performed genome-wide association studies (GWAS) to detect the genetic loci affecting sheep hair types and teat number. A single significant association signal for hair types was identified on 6.7-7.1 Mb of chromosome 25. The IRF2BP2 gene (chr25: 7,067,974-7,071,785), which is located within this genomic region, has been previously known to be involved in hair/wool traits in sheep. The results further showed a new candidate region around 26.4 Mb of chromosome 13, between the ARHGAP21 and KIAA1217 genes, that was significantly related to teat number in sheep. The haplotype patterns of this region also showed differences in animals with 2, 3, or 4 teats. Advances in using the high-accuracy and low-cost liquid chip are expected to accelerate sheep genomic and breeding studies in the coming years.
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Affiliation(s)
- Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fengting Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jintao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shaoyin Fu
- Institute of Animal Science, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoyi Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huiling Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010070, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Chessari G, Criscione A, Tolone M, Bordonaro S, Rizzuto I, Riggio S, Macaluso V, Moscarelli A, Portolano B, Sardina MT, Mastrangelo S. High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context. Front Vet Sci 2023; 10:1127354. [PMID: 37205231 PMCID: PMC10185747 DOI: 10.3389/fvets.2023.1127354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
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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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Bordonaro
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Vito Macaluso
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
- *Correspondence: Salvatore Mastrangelo,
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McManus CM, Lucci CM, Maranhão AQ, Pimentel D, Pimentel F, Rezende Paiva S. Response to heat stress for small ruminants: Physiological and genetic aspects. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Kizilaslan M, Arzik Y, White SN, Piel LMW, Cinar MU. Genetic Parameters and Genomic Regions Underlying Growth and Linear Type Traits in Akkaraman Sheep. Genes (Basel) 2022; 13:genes13081414. [PMID: 36011330 PMCID: PMC9407525 DOI: 10.3390/genes13081414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 02/07/2023] Open
Abstract
In the current study, the genetic architecture of growth and linear type traits were investigated in Akkaraman sheep. Estimations of genomic heritability, genetic correlations, and phenotypic correlations were implemented for 17 growth and linear type traits of 473 Akkaraman lambs by the univariate and multivariate analysis of animal mixed models. Correspondingly, moderate heritability estimates, as well as high and positive genetic/phenotypic correlations were found between growth and type traits. On the other hand, 2 genome-wide and 19 chromosome-wide significant single nucleotide polymorphisms were found to be associated with the traits as a result of animal mixed model-based genome-wide association analyses. Accordingly, we propose several genes located on different chromosomes (e.g., PRDM2, PTGDR, PTPRG, KCND2, ZNF260, CPE, GRID2, SCD5, SPIDR, ZNF407, HCN3, TMEM50A, FKBP1A, TLE4, SP1, SLC44A1, and MYOM3) as putative quantitative trait loci for the 22 growth and linear type traits studied. In our study, specific genes (e.g., TLE4, PTGDR, and SCD5) were found common between the traits studied, suggesting an interplay between the genetic backgrounds of these traits. The fact that four of the proposed genes (TLE4, MYOM3, SLC44A1, and TMEM50A) are located on sheep chromosome 2 confirms the importance of these genomic regions for growth and morphological structure in sheep. The results of our study are therefore of great importance for the development of efficient selection indices and marker-assisted selection programs, as well as for the understanding of the genetic architecture of growth and linear traits in sheep.
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Affiliation(s)
- Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research, Washington State University Pullman, Pullman, WA 991646630, USA
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
- Correspondence: ; Tel.: +90-352-2076666-38601
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16
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Tijjani A, Salim B, da Silva MVB, Eltahir HA, Musa TH, Marshall K, Hanotte O, Musa HH. Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle. Genomics 2022; 114:110423. [PMID: 35803449 PMCID: PMC9388378 DOI: 10.1016/j.ygeno.2022.110423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022]
Abstract
Background Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. Results We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Conclusions Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle. Sudanese cattle thrive in the harshest environments of the African drylands. Bos indicus shared selected genes are involved in immune response, conformation, and heat stress response. Sudanese zebu-specific sweep includes genes involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Environmental adaptation in zebu cattle may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control.
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Affiliation(s)
- Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Bashir Salim
- Faculty of Veterinary Medicine, University of Khartoum, Sudan
| | | | | | - Taha H Musa
- Biomedical Research Institute, Darfur College, Sudan
| | - Karen Marshall
- International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100, Kenya; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi 00100, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Hassan H Musa
- Institute of Molecular Biology, University of Nyala, Sudan; Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan.
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Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection. Animals (Basel) 2022; 12:ani12111423. [PMID: 35681887 PMCID: PMC9179914 DOI: 10.3390/ani12111423] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Fatness-related traits are economically very important in sheep production and are associated with serious diseases in humans. Using a denser set of SNP markers and a variety of statistical approaches, our results were able to refine the regions associated with fat deposition and to suggest new insights into molecular aspects of fat tail selection. These results may provide a strong foundation for studying the regulation of fat deposition in sheep and do offer hope that the causal mutations and the mode of inheritance of this trait will soon be discovered by further investigation. Abstract The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.
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Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
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Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
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Malatji DP. Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance. Vet World 2022; 15:1031-1043. [PMID: 35698514 PMCID: PMC9178589 DOI: 10.14202/vetworld.2022.1031-1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/11/2022] [Indexed: 11/30/2022] Open
Abstract
Trypanosomiasis is a disease caused by unicellular protozoan parasites. Small ruminants succumb to trypanosomiasis in areas of high tsetse fly challenge, resulting in serious economic loss often to farmers in low-input smallholder systems. At present, trypanosomiasis is treated with trypanocidal drugs, but access to these can be limited, and increasing parasite resistance raises questions about their efficacy. The development of trypanotolerance in small ruminant flocks through targeted breeding strategies is considered a sustainable and economical option for controlling African trypanosomiasis. Recently, quantitative trait loci (QTLs) associated with trypanotolerance traits in sheep have been reported. The results of these studies form the basis for more studies to identify QTLs associated with trypanosomiasis resistance, particularly in African livestock species. For example, signatures of positive selection for trypanotolerance have been identified using genome-wide single-nucleotide polymorphism data. However, there are several challenges in performing genetic analyses using data from low-input smallholder systems, including a lack of recorded pedigree and production records and the need for large sample sizes when flock sizes are often fewer than 50 animals. Breeding strategies to improve trypanotolerance should also preserve existing genetic diversity as well as minimize excessive genetic introgression by trypanosusceptible breeds. This review discusses the possibilities of breeding for trypanosome tolerance/resistance in low-input/low-output small ruminant production systems. Potential challenges are outlined, and potential available genetic resources are described as a foundation for future work.
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Affiliation(s)
- Dikeledi P. Malatji
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, Gauteng Province, South Africa
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Paim TDP, Alves dos Santos C, Faria DAD, Paiva SR, McManus C. Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Rajawat D, Panigrahi M, Kumar H, Nayak SS, Parida S, Bhushan B, Gaur GK, Dutt T, Mishra BP. Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds. Gene 2022; 816:146165. [PMID: 35026292 DOI: 10.1016/j.gene.2021.146165] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022]
Abstract
In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, FST, FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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22
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Maiorano AM, Cardoso DF, Carvalheiro R, Júnior GAF, de Albuquerque LG, de Oliveira HN. Signatures of selection in Nelore cattle revealed by whole-genome sequencing data. Genomics 2022; 114:110304. [DOI: 10.1016/j.ygeno.2022.110304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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23
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Signer-Hasler H, Henkel J, Bangerter E, Bulut Z, Drögemüller C, Leeb T, Flury C. Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection. Genet Sel Evol 2022; 54:6. [PMID: 35073837 PMCID: PMC8785455 DOI: 10.1186/s12711-022-00695-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00695-w.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland.
| | - Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association SZZV, Schützenstrasse 10, 3052, Zollikofen, Switzerland
| | - Zafer Bulut
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland
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24
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Ouhrouch A, Boitard S, Boyer F, Servin B, Da Silva A, Pompanon F, Haddioui A, Benjelloun B. Genomic Uniqueness of Local Sheep Breeds From Morocco. Front Genet 2021; 12:723599. [PMID: 34925440 PMCID: PMC8675355 DOI: 10.3389/fgene.2021.723599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.
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Affiliation(s)
- Abdessamad Ouhrouch
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco.,Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Anne Da Silva
- PEREINE/E2LIM, Faculty of Science and Technics, Limoges, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Abdelmajid Haddioui
- Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
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25
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Serranito B, Cavalazzi M, Vidal P, Taurisson-Mouret D, Ciani E, Bal M, Rouvellac E, Servin B, Moreno-Romieux C, Tosser-Klopp G, Hall SJG, Lenstra JA, Pompanon F, Benjelloun B, Da Silva A. Local adaptations of Mediterranean sheep and goats through an integrative approach. Sci Rep 2021; 11:21363. [PMID: 34725398 PMCID: PMC8560853 DOI: 10.1038/s41598-021-00682-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.
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Affiliation(s)
- Bruno Serranito
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France
- CRESCO, Museum National d'Histoire Naturelle (MNHN), 35800, Dinard, France
| | | | - Pablo Vidal
- Universidad Catolica de Valencia, Valencia, Spain
| | - Dominique Taurisson-Mouret
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
- CNRS, UMR 5815, Dynamiques du droit, Université de Montpellier, Montpellier, France
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Marie Bal
- GEOLAB, UMR 6042, Univ. Limoges, Limoges, France
| | | | - Bertrand Servin
- GenPhySE, INRAE, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | | | - Stephen J G Hall
- Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000, Grenoble, France
- National Institute of Agronomic Research (INRA), Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Anne Da Silva
- INRA, EA7500, USC1061 GAMAA, Univ. Limoges, 87000, Limoges, France.
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26
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Hall SJG, Arney DR, Bunce RGH, Vollmer E. Video recording and vegetation classification elucidate sheep foraging ecology in species-rich grassland. Ecol Evol 2021; 11:14873-14887. [PMID: 34765147 PMCID: PMC8571568 DOI: 10.1002/ece3.8172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Factors influencing grazing behavior in species-rich grasslands have been little studied. Methodologies have mostly had a primary focus on grasslands with lower floristic diversity.We test the hypothesis that grazing behavior is influenced by both animal and plant factors and investigate the relative importance of these factors, using a novel combination of video technology and vegetation classification to analyze bite and step rates.In a semi-natural, partially wooded grassland in northern Estonia, images of the vegetation being grazed and records of steps and bites were obtained from four video cameras, each mounted on the sternum of a sheep, during 41 animal-hours of observation over five days. Plant species lists for the immediate field of view were compiled. Images were partnered by direct observation of the nearest-neighbor relationships of the sheep. TWINSPAN, a standard vegetation classification technique allocating species lists to objectively defined classes by a principal components procedure, was applied to the species lists and 25 vegetation classes (15 open pasture and 10 woodland) were identified from the images.Taking bite and step rates as dependent variables, relative importance of animal factors (sheep identity), relative importance of day, and relative importance of plant factors (vegetation class) were investigated. The strongest effect on bite rates was of vegetation class. Sheep identity was less influential. When the data from woodland were excluded, sheep identity was more important than vegetation class as a source of variability in bite rate on open pasture.The original hypothesis is therefore supported, and we further propose that, at least with sheep in species-rich open pastures, animal factors will be more important in determining grazing behavior than plant factors. We predict quantifiable within-breed and between-breed differences, which could be exploited to optimize conservation grazing practices and contribute to the sustainability of extensive grazing systems.
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Affiliation(s)
| | | | | | - Elis Vollmer
- Estonian University of Life SciencesTartuEstonia
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27
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Kominakis A, Tarsani E, Hager-Theodorides AL, Mastranestasis I, Gkelia D, Hadjigeorgiou I. Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PLoS One 2021; 16:e0257461. [PMID: 34529728 PMCID: PMC8445479 DOI: 10.1371/journal.pone.0257461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of 'mainland-island' populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.
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Affiliation(s)
- Antonios Kominakis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Eirini Tarsani
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | | | | | - Dimitra Gkelia
- Association of Pastoral Farmers of Epirus, Ioannina, Greece
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28
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Gurgul A, Jasielczuk I, Miksza-Cybulska A, Kawęcka A, Szmatoła T, Krupiński J. Evaluation of genetic differentiation and genome-wide selection signatures in Polish local sheep breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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30
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Bakoev S, Getmantseva L, Kostyunina O, Bakoev N, Prytkov Y, Usatov A, Tatarinova TV. Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia. PeerJ 2021; 9:e11595. [PMID: 34249494 PMCID: PMC8256806 DOI: 10.7717/peerj.11595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
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Affiliation(s)
- Siroj Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia
| | - Lyubov Getmantseva
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Olga Kostyunina
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Nekruz Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Yuri Prytkov
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, United States of America.,Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia.,Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute for General Genetics, Moscow, Russia
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31
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Sweet-Jones J, Lenis VP, Yurchenko AA, Yudin NS, Swain M, Larkin DM. Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits. Front Genet 2021; 12:612492. [PMID: 34220925 PMCID: PMC8253514 DOI: 10.3389/fgene.2021.612492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
Background Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches. Results Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R). Conclusion We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.
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Affiliation(s)
- James Sweet-Jones
- Royal Veterinary College, University of London, London, United Kingdom
| | - Vasileios Panagiotis Lenis
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom.,School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
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32
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Rodríguez-Ramilo S, Reverter A, Legarra A. Islands of runs of homozygosity indicate selection signatures in Ovis aries 6 (OAR6) of French dairy sheep. JDS COMMUNICATIONS 2021; 2:132-136. [PMID: 36339500 PMCID: PMC9623631 DOI: 10.3168/jdsc.2020-0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/05/2021] [Indexed: 11/21/2022]
Abstract
The presence of runs of homozygosity is not randomly distributed across the genome. Islands of runs of homozygosity may be the result of selection pressure. Concordance existed between islands of runs of homozygosity and selection signatures on OAR6. Candidate genes NCAPG and LCORL on OAR6 have agricultural and adaptive importance.
Runs of homozygosity (ROH) are contiguous homozygous segments of the genome where the haplotypes inherited from each parent are identical. The occurrence of ROH is not randomly distributed across the genome, and ROH islands across many animals may be the result of selective pressure. The objective of this study was to demonstrate that the presence of ROH islands may be indicative of selection signatures in French dairy sheep breeds and subpopulations. The data set available included animals (artificial insemination males) from various breeds and subpopulations: Basco-Béarnaise breed (321 individuals), Manech Tête Noire breed (329 individuals), Manech Tête Rousse breed (1,906 individuals), Lacaune Confederation subpopulation (3,030 individuals), and Lacaune Ovitest subpopulation (3,114 individuals). Animals were genotyped with the Illumina OvineSNP50 BeadChip. After applying filtering criteria, the genomic data included 38,287 autosomal SNP distributed across 26 chromosomes and 8,700 individuals. One island of ROH was detected on OAR6 in the same genomic position across animals (between 30 and 40 Mb). Global Wright's differentiation coefficients for 2 SNP within this ROH island were high (0.67–0.68). The linkage disequilibrium between both SNP was also elevated (0.98). The divergence in allele frequencies in those SNP grouped Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse breeds in one cluster and Lacaune Confederation and Lacaune Ovitest subpopulations in another cluster. The closest candidate genes are NCAPG and LCORL, which have been reported to be under positive selection and suggested to control weight and height in sheep. The preliminary identification of ROH suggests the presence of selection. However, for the identification of potential candidate genes, ROH detection should be combined with other approaches to improve mapping accuracy.
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Affiliation(s)
- S.T. Rodríguez-Ramilo
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
- Corresponding author
| | - A. Reverter
- CSIRO Agriculture & Food, Brisbane, QLD 4067, Australia
| | - A. Legarra
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
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Karimi K, Farid AH, Myles S, Miar Y. Detection of selection signatures for response to Aleutian mink disease virus infection in American mink. Sci Rep 2021; 11:2944. [PMID: 33536540 PMCID: PMC7859209 DOI: 10.1038/s41598-021-82522-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Aleutian disease (AD) is the most significant health issue for farmed American mink. The objective of this study was to identify the genomic regions subjected to selection for response to infection with Aleutian mink disease virus (AMDV) in American mink using genotyping by sequencing (GBS) data. A total of 225 black mink were inoculated with AMDV and genotyped using a GBS assay based on the sequencing of ApeKI-digested libraries. Five AD-characterized phenotypes were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (FST) and nucleotide diversity (θπ), that were validated by haplotype-based (hap-FLK) test. The total of 99 putatively selected regions harbouring 63 genes were detected in different groups. The gene ontology revealed numerous genes related to immune response (e.g. TRAF3IP2, WDR7, SWAP70, CBFB, and GPR65), liver development (e.g. SULF2, SRSF5) and reproduction process (e.g. FBXO5, CatSperβ, CATSPER4, and IGF2R). The hapFLK test supported two strongly selected regions that contained five candidate genes related to immune response, virus–host interaction, reproduction and liver regeneration. This study provided the first map of putative selection signals of response to AMDV infection in American mink, bringing new insights into genomic regions controlling the AD phenotypes.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep. Animals (Basel) 2021; 11:ani11010157. [PMID: 33445473 PMCID: PMC7827510 DOI: 10.3390/ani11010157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. There is large variation in the reproductive abilities of Bamei mutton sheep. After recent artificial selection, the average lambing rate of the Bamei mutton nucleus group was over 150%. We used the FST (Fixation Index) and XP-EHH (The Cross-Population Extended Haplotype Homozygosity) statistical approach to detect the selective sweeps between high- and low-fecundity Bamei mutton sheep groups. JUN (JUN proto-oncogene, AP-1 transcription factor subunit), ITPR3 (inositol 1,4,5-trisphosphate receptor type 3, PLCB2 (phospholipase C beta 2), HERC5 (HECT and RLD domain containing E3 ubiquitin protein ligase 5), and KDM4B (lysine demethylase 4B) were detected that are potential responsible for litter size. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. Abstract Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent artificial selection to improve the efficiency of mutton production. We selected five high- and five low-fecundity Bamei mutton sheep for whole-genome resequencing to identify candidate genes for sheep prolificacy. We used the FST and XP-EHH statistical approach to detect the selective sweeps between these two groups. Combining the two selective sweep methods, the reproduction-related genes JUN, ITPR3, PLCB2, HERC5, and KDM4B were detected. JUN, ITPR3, and PLCB2 play vital roles in GnRH (gonadotropin-releasing hormone), oxytocin, and estrogen signaling pathway. Moreover, KDM4B, which had the highest FST value, exhibits demethylase activity. It can affect reproduction by binding the promoters of estrogen-regulated genes, such as FOXA1 (forkhead box A1) and ESR1 (estrogen receptor 1). Notably, one nonsynonymous mutation (p.S936A) specific to the high-prolificacy group was identified at the TUDOR domain of KDM4B. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. The identified genomic regions that are responsible for litter size can in turn be used for further selection.
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Saravanan K, Panigrahi M, Kumar H, Bhushan B, Dutt T, Mishra B. Genome-wide analysis of genetic diversity and selection signatures in three Indian sheep breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2020.104367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Hou H, Wang X, Zhang C, Tu Y, Lv W, Cai X, Xu Z, Yao J, Yang C. Genomic analysis of GBS data reveals genes associated with facial pigmentation in Xinyang blue-shelled layers. Arch Anim Breed 2020; 63:483-491. [PMID: 33473373 PMCID: PMC7810225 DOI: 10.5194/aab-63-483-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
Facial pigmentation is an important economic trait of chickens, especially for laying hens, which will affect the carcass appearance of eliminated layers. Therefore, identifying the genomic regions and exploring the function of this region that contributes to understanding the variation of skin color traits is significant for breeding. In the study, 291 pure-line Xinyang blue-shelled laying hens were selected, of which 75 were dark-faced chickens and 216 were white-faced chickens. The population was sequenced and typed by GBS genotyping technology. The obtained high-quality SNPs and pigmentation phenotypes were analyzed by a genome-wide association study (GWAS) and a F ST scan. Based on the two analytical methods, we identified a same genomic region (10.70-11.60 Mb) on chromosome 20 with 68 significant SNPs ( - log 10 ( P ) > 6 ), mapped to 10 known genes, including NPEPL1, EDN3, GNAS, C20orf85, VAPB, BMP7, TUBB1, ELMO2, DDX27, and NCOA5, which are associated with dermal hyperpigmentation.
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Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.,National Poultry Engineer Research Center, Shanghai 201106, China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.,National Poultry Engineer Research Center, Shanghai 201106, China
| | - Caiyun Zhang
- National Poultry Engineer Research Center, Shanghai 201106, China
| | - Yingying Tu
- National Poultry Engineer Research Center, Shanghai 201106, China
| | - Wenwei Lv
- National Poultry Engineer Research Center, Shanghai 201106, China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.,National Poultry Engineer Research Center, Shanghai 201106, China
| | - Zhigang Xu
- Shanghai Poultry Breeding Co., Ltd., Shanghai 201100, China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.,National Poultry Engineer Research Center, Shanghai 201106, China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.,National Poultry Engineer Research Center, Shanghai 201106, China
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Association of TMEM8B and SPAG8 with Mature Weight in Sheep. Animals (Basel) 2020; 10:ani10122391. [PMID: 33333720 PMCID: PMC7765121 DOI: 10.3390/ani10122391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Domestication and the subsequent selection of animals for either economic or morphological features can impact the legacy genome of a population in myriad ways. In sheep, the rs426272889 single nucleotide polymorphism (SNP) was identified as the peak of a signature of selection. We examined phenotypic data and identified associations for the Transmembrane protein 8B (TMEM8B) rs426272889 SNP and its genetically linked Sperm-associated antigen 8 (SPAG8) rs160159557 SNP with ewe mature weight in four sheep breeds. These data provided the first production-relevant phenotypes, as well as the first organism-level (as opposed to cellular or tumor-derived) phenotypes, associated with TMEM8B, and in so doing, improved the annotation of this gene and genomic region by adding body weight implications. Once validated, these data can be applied in genetic or genomic selection aiming to achieve desired mature body weight. Abstract Signature of selection studies have identified many genomic regions with known functional importance and some without verified functional roles. Multiple studies have identified Transmembrane protein 8B (TMEM8B)rs426272889 as having been recently under extreme selection pressure in domesticated sheep, but no study has provided sheep phenotypic data clarifying a reason for extreme selection. We tested rs426272889 for production trait association in 770 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. TMEM8Brs426272889 was associated with mature weight at 3 and 4 years (p < 0.05). This suggested selection for sheep growth and body size might explain the historical extreme selection pressure in this genomic region. We also tested Sperm-associated antigen 8 (SPAG8) rs160159557 encoding a G493C substitution. While this variant was associated with mature weights at ages 3 and 4, it was not as strongly associated as TMEM8Brs426272889. Transmembrane protein 8B has little functional information except as an inhibitor of cancer cell proliferation. To our knowledge, this is the first study linking TMEM8B to whole organism growth and body size under standard conditions. Additional work will be necessary to identify the underlying functional variant(s). Once identified, such variants could be used to improve sheep production through selective breeding.
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40
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Paris JM, Letko A, Häfliger IM, Ammann P, Drögemüller C. Ear type in sheep is associated with the MSRB3 locus. Anim Genet 2020; 51:968-972. [PMID: 32805068 DOI: 10.1111/age.12994] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2020] [Indexed: 12/01/2022]
Abstract
Ear morphology is an important determinant of sheep breeds. It includes different variable traits such as ear size and erectness, suggesting a polygenic architecture. Here, we performed a comprehensive genome-wide analysis to identify regions under selection for ear morphology in 515 sheep from 17 breeds fixed for diverse ear phenotypes using 34k SNP genotyping data. GWASs for two ear type traits, size and erectness, revealed a single genome-wide significant association on ovine chromosome 3. The derived marker alleles were enriched in sheep with large and/or floppy ears. The GWAS signal harboured the MSRB3 gene encoding methionine sulphoxide reductase B3, which has already been found to be associated with different ear types in other species. We attempted whole-genome resequencing to identify causal variant(s) within a 1 Mb interval around MSRB3. This experiment excluded major copy number variants in the interval, but failed to identify a compelling candidate causal variant. Fine-mapping suggested that the causal variant for large floppy ears most likely resides in a 175 kb interval downstream of the MSRB3 coding region.
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Affiliation(s)
- J M Paris
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - A Letko
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - I M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - P Ammann
- ProSpecieRara, Basel, 4052, Switzerland
| | - C Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, 3001, Switzerland
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Gaire R, Ohm H, Brown-Guedira G, Mohammadi M. Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population. THE PLANT GENOME 2020; 13:e20031. [PMID: 33016613 DOI: 10.1002/tpg2.20031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 05/28/2023]
Abstract
Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome-wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LD with slow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for selection signatures using FST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.
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Affiliation(s)
- Rupesh Gaire
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Herbert Ohm
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
- US Department of Agriculture, Agricultural Research Services, Southeast Area, Plant Science Research, Raleigh, NC, 27695, USA
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
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Abstract
Wild sheep and many primitive domesticated breeds have two coats: coarse hairs covering shorter, finer fibres. Both are shed annually. Exploitation of wool for apparel in the Bronze Age encouraged breeding for denser fleeces and continuously growing white fibres. The Merino is regarded as the culmination of this process. Archaeological discoveries, ancient images and parchment records portray this as an evolutionary progression, spanning millennia. However, examination of the fleeces from feral, two-coated and woolled sheep has revealed a ready facility of the follicle population to change from shedding to continuous growth and to revert from domesticated to primitive states. Modifications to coat structure, colour and composition have occurred in timeframes and to sheep population sizes that exclude the likelihood of variations arising from mutations and natural selection. The features are characteristic of the domestication phenotype: an assemblage of developmental, physiological, skeletal and hormonal modifications common to a wide variety of species under human control. The phenotypic similarities appeared to result from an accumulation of cryptic genetic changes early during vertebrate evolution. Because they did not affect fitness in the wild, the mutations were protected from adverse selection, becoming apparent only after exposure to a domestic environment. The neural crest, a transient embryonic cell population unique to vertebrates, has been implicated in the manifestations of the domesticated phenotype. This hypothesis is discussed with reference to the development of the wool follicle population and the particular roles of Notch pathway genes, culminating in the specific cell interactions that typify follicle initiation.
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Abied A, Bagadi A, Bordbar F, Pu Y, Augustino SM, Xue X, Xing F, Gebreselassie G, Han JL, Mwacharo JM, Ma Y, Zhao Q. Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments. Genes (Basel) 2020; 11:genes11050494. [PMID: 32365888 PMCID: PMC7290715 DOI: 10.3390/genes11050494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/30/2022] Open
Abstract
Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (FST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by FST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.
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Affiliation(s)
- Adam Abied
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Alnoor Bagadi
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Wad Madani 511, Sudan;
| | - Farhad Bordbar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Yabin Pu
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Serafino M.A. Augustino
- College of Animal Science and Technology, China Agricultural University (CAU), Beijing 100193, China;
| | - Xianglan Xue
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Feng Xing
- College of Animal Science, Talimu University (TU), Xinjiang, Alar 843300, China;
| | - Gebremedhin Gebreselassie
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Joram M. Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa 1108-2010, Ethiopia;
| | - Yuehui Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
| | - Qianjun Zhao
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (A.A.); (F.B.); (Y.P.); (X.X.); (G.G.); (Y.M.)
- Correspondence:
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Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types. Animals (Basel) 2020; 10:ani10050773. [PMID: 32365604 PMCID: PMC7278473 DOI: 10.3390/ani10050773] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023] Open
Abstract
Simple Summary According to the tail types, sheep can be briefly classified into three groups (fat-tailed, fat-rumped, and thin-tailed sheep). In this study, we used these three typical breeds from Chinese indigenous sheep breeds to perform a genome scan for selective sweeps using Ovine Infinium HD SNP BeadChip genotype data. Results showed that 25 genomic regions exhibited selection signals and harbored 73 positional candidate genes. These genes were documented not only to be associated with tail fat formation, but also be related to reproduction, body conformation, and appearance. Our findings contributed to understanding genetic basis of fat deposition in sheep tail and provide a reference for developing new sheep breeds with an ideal tail type. Abstract It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.
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Naval-Sanchez M, McWilliam S, Evans B, Yáñez JM, Houston RD, Kijas JW. Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Front Genet 2020; 11:264. [PMID: 32318091 PMCID: PMC7147387 DOI: 10.3389/fgene.2020.00264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to versican, a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include arcvf, sema6, errb4, id2-like, and 6n1-like genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.
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Affiliation(s)
| | | | - Bradley Evans
- Salmon Enterprises of Tasmania Pty. Limited, Wayatinah, TAS, Australia
| | - José M Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - James W Kijas
- CSIRO Agriculture and Food, Brisbane, QLD, Australia
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Mastrangelo S, Ben Jemaa S, Ciani E, Sottile G, Moscarelli A, Boussaha M, Montedoro M, Pilla F, Cassandro M. Genome-wide detection of signatures of selection in three Valdostana cattle populations. J Anim Breed Genet 2020; 137:609-621. [PMID: 32219904 DOI: 10.1111/jbg.12476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/15/2022]
Abstract
The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST ) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, GABI, Université Paris Saclay, Jouy-en-Josas, France
| | - Marina Montedoro
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
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Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino. Animals (Basel) 2020; 10:ani10030524. [PMID: 32245132 PMCID: PMC7143548 DOI: 10.3390/ani10030524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Runs of homozygosity (ROH) are commonly used to estimate inbreeding coefficients and identify selection signatures in livestock population. The present study determined ROH patterns, estimated the inbreeding levels, and identified the genome regions with high ROH frequency (ROH hotspots) in Chinese Merino. Our results showed that the genome of Chinese Merino harbored lower ROH abundance. Moreover, the inbreeding levels were relatively low. Thirteen ROH hotspots consisting of 190 genes were identified. The ROH hotspots overlapped the selective signatures might be associated with body size, horn traits, immune traits and environment adaption. These findings could contribute to an optimum breeding program by identifying the candidate genes related to economically traits in Chinese Merino. Abstract In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.
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Álvarez I, Fernández I, Traoré A, Pérez-Pardal L, Menéndez-Arias NA, Goyache F. Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Rep 2020; 10:2824. [PMID: 32071365 PMCID: PMC7028950 DOI: 10.1038/s41598-020-59839-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
The Djallonké (West African Dwarf) sheep is a small-sized haired sheep resulting from a costly evolutionary process of natural adaptation to the harsh environment of West Africa including trypanosome challenge. However, genomic studies carried out in this sheep are scant. In this research, genomic data of 184 Djallonké sheep (and 12 Burkina-Sahel sheep as an outgroup) generated using medium-density SNP Chips were analyzed. Three different statistics (iHS, XP-EHH and nSL) were applied to identify candidate selection sweep regions spanning genes putatively associated with adaptation of sheep to the West African environment. A total of 207 candidate selection sweep regions were defined. Gene-annotation enrichment and functional annotation analyses allowed to identify three statistically significant functional clusters involving 12 candidate genes. Genes included in Functional Clusters associated to selection signatures were mainly related to metabolic response to stress, including regulation of oxidative and metabolic stress and thermotolerance. The bovine chromosomal areas carrying QTLs for cattle trypanotolerance were compared with the regions on which the orthologous functional candidate cattle genes were located. The importance of cattle BTA4 for trypanotolerant response might have been conserved between species. The current research provides new insights on the genomic basis for adaptation and highlights the importance of obtaining information from non-cosmopolite livestock populations managed in harsh environments.
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Affiliation(s)
- Isabel Álvarez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Iván Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou, 04 BP 8645, Burkina Faso
| | | | | | - Félix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain.
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Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed. PLoS One 2020; 15:e0227212. [PMID: 32049967 PMCID: PMC7015314 DOI: 10.1371/journal.pone.0227212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022] Open
Abstract
Thoroughbred horse racing is a global sport with major hubs in Europe, North America, Australasia and Japan. Regional preferences for certain traits have resulted in phenotypic variation that may result from adaptation to the local racing ecosystem. Here, we test the hypothesis that genes selected for regional phenotypic variation may be identified by analysis of selection signatures in pan-genomic SNP genotype data. Comparing Australian to non-Australian Thoroughbred horses (n = 99), the most highly differentiated loci in a composite selection signals (CSS) analysis were on ECA6 (34.75–34.85 Mb), ECA14 (33.2–33.52 Mb and 35.52–36.94 Mb) and ECA16 (24.28–26.52 Mb) in regions containing candidate genes for exercise adaptations including cardiac function (ARHGAP26, HBEGF, SRA1), synapse development and locomotion (APBB3, ATXN7, CLSTN3), stress response (NR3C1) and the skeletal muscle response to exercise (ARHGAP26, NDUFA2). In a genome-wide association study for field-measured speed in two-year-olds (n = 179) SNPs contained within the single association peak (33.2–35.6 Mb) overlapped with the ECA14 CSS signals and spanned a protocadherin gene cluster. Association tests using higher density SNP genotypes across the ECA14 locus identified a SNP within the PCDHGC5 gene associated with elite racing performance (n = 922). These results indicate that there may be differential selection for racing performance under racing and management conditions that are specific to certain geographic racing regions. In Australia breeders have principally selected horses for favourable genetic variants at loci containing genes that modulate behaviour, locomotion and skeletal muscle physiology that together appear to be contributing to early two-year-old speed.
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