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Bayraktar M. Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data. Anim Biotechnol 2024; 35:2329106. [PMID: 38497403 DOI: 10.1080/10495398.2024.2329106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.
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Affiliation(s)
- Mervan Bayraktar
- Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
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Colombi D, Perini F, Bettini S, Mastrangelo S, Abeni F, Conte G, Marletta D, Cassandro M, Bernabucci U, Ciampolini R, Lasagna E. Genomic responses to climatic challenges in beef cattle: A review. Anim Genet 2024. [PMID: 39219301 DOI: 10.1111/age.13474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Climate change is a major concern for the near future and for livestock breeding. Cattle breeding, due to its greenhouse gas emissions, is one of the most implicated industries. Consequently, the main future goals are to breed animals resilient to climate change, with the aim of lowering the livestock impact on the environment and selecting animals that will be able to resist different, unsuitable, and changing climates. The aim of this literature review is to compare the most recent studies on the response and adaptation of beef cattle breeds to extreme environments, in terms of genes and pathways involved. Beef breeding is just starting to implement genomics in its selection plans, and shedding light on the genomic responses to extreme climates could speed up and simplify the adaptation of these breeds to climate change. This review discusses the genes involved in climatic stress responses, including those related to extremely cold climates, in beef and dual-purpose cattle breeds. Genes were associated with productive traits, coat and skin structure and development, thermotolerance, cellular physiology and DNA repair mechanisms, immune system, and fertility traits. The knowledge of genes and pathways involved in climate resilience should be taken into consideration for further selection in beef cattle breeding and could promote the valorization of local breeds adapted to extreme environmental conditions. The use of local or resilient breeds could enhance the environmental and social sustainability, animal welfare, and production, compared with the introduction of cosmopolitan breeds with uncertain adaptation in uncontrolled environmental areas.
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Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Stefano Bettini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Fabio Abeni
- Centro di Ricerca Zootecnia e Acquacoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Lodi, Italy
| | - Giuseppe Conte
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Donata Marletta
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Umberto Bernabucci
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture and Forest Sciences, Università Della Tuscia, Viterbo, Italy
| | - Roberta Ciampolini
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
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Becker GM, Thorne JW, Burke JM, Lewis RM, Notter DR, Morgan JLM, Schauer CS, Stewart WC, Redden RR, Murdoch BM. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genet Sel Evol 2024; 56:56. [PMID: 39080565 PMCID: PMC11290166 DOI: 10.1186/s12711-024-00905-7] [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: 07/19/2023] [Accepted: 04/23/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
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Affiliation(s)
- Gabrielle M Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
| | - Jacob W Thorne
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David R Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Christopher S Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, USA
| | - Whit C Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - R R Redden
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA.
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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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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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Yi W, Hu M, Shi L, Li T, Bai C, Sun F, Ma H, Zhao Z, Yan S. Whole genome sequencing identified genomic diversity and candidated genes associated with economic traits in Northeasern Merino in China. Front Genet 2024; 15:1302222. [PMID: 38333624 PMCID: PMC10851152 DOI: 10.3389/fgene.2024.1302222] [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: 09/26/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction: Northeast Merino (NMS) is a breed developed in Northeast China during the 1960s for wool and meat production. It exhibits excellent traits such as high wool yield, superior meat quality, rapid growth rate, robust disease resistance, and adaptability to cold climates. However, no studies have used whole-genome sequencing data to investigate the superior traits of NMS. Methods: In this study, we investigated the population structure, genetic diversity, and selection signals of NMS using whole-genome sequencing data from 20 individuals. Two methods (integrated haplotype score and composite likelihood ratio) were used for selection signal analysis, and the Fixation Index was used to explore the selection signals of NMS and the other two breeds, Mongolian sheep and South African meat Merino. Results: The results showed that NMS had low inbreeding levels, high genomic diversity, and a pedigree of both Merino breeds and Chinese local breeds. A total length of 14.09 Mb genomic region containing 287 genes was detected using the two methods. Further exploration of the functions of these genes revealed that they are mainly concentrated in wool production performance (IRF2BP2, MAP3K7, and WNT3), meat production performance (NDUFA9, SETBP1, ZBTB38, and FTO), cold resistance (DNAJC13, LPGAT1, and PRDM16), and immune response (PRDM2, GALNT8, and HCAR2). The selection signals of NMS and the other two breeds annotated 87 and 23 genes, respectively. These genes were also mainly focused on wool and meat production performance. Conclusion: These results provide a basis for further breeding improvement, comprehensive use of this breed, and a reference for research on other breeds.
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Affiliation(s)
- Wenfeng Yi
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Ting Li
- College of Animal Science, Jilin University, Changchun, China
| | - Chunyan Bai
- College of Animal Science, Jilin University, Changchun, China
| | - Fuliang Sun
- College of Agriculture, Yanbian University, Yanji, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
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Vahedi SM, Salek Ardestani S, Banabazi MH, Clark KF. Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison). Sci Rep 2024; 14:1035. [PMID: 38200094 PMCID: PMC10781757 DOI: 10.1038/s41598-023-51039-7] [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: 07/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case-control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770-98,281 kb and chr1:114,133-120,473) and one on chromosome 6 (chr6:37,953-44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Bible Hill, NS, B2N5E3, Canada
| | | | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden.
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI),, Agricultural Research, Education & Extension Organization (AREEO), Karaj, 3146618361, Iran.
| | - K Fraser Clark
- Department of Animal Science and Aquaculture, Dalhousie University, Bible Hill, NS, B2N5E3, Canada.
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [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: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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10
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Whole-body adipose tissue multi-omic analyses in sheep reveal molecular mechanisms underlying local adaptation to extreme environments. Commun Biol 2023; 6:159. [PMID: 36755107 PMCID: PMC9908986 DOI: 10.1038/s42003-023-04523-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
The fat tail of sheep is an important organ that has evolved to adapt to extreme environments. However, the genetic mechanisms underlying the fat tail phenotype remain poorly understood. Here, we characterize transcriptome and lipidome profiles and morphological changes in 250 adipose tissues from two thin-tailed and three fat-tailed sheep populations in summer and winter. We implement whole-genome selective sweep tests to identify genetic variants related to fat-tails. We identify a set of functional genes that show differential expression in the tail fat of fat-tailed and thin-tailed sheep in summer and winter. These genes are significantly enriched in pathways, such as lipid metabolism, extracellular matrix (ECM) remodeling, molecular transport, and inflammatory response. In contrast to thin-tailed sheep, tail fat from fat-tailed sheep show slighter changes in adipocyte size, ECM remodeling, and lipid metabolism, and had less inflammation in response to seasonal changes, indicating improved homeostasis. Whole-genome selective sweep tests identify genes involved in preadipocyte commitment (e.g., BMP2, PDGFD) and terminal adipogenic differentiation (e.g., VEGFA), which could contribute to enhanced adipocyte hyperplasia. Altogether, we establish a model of regulatory networks regulating adipose homeostasis in sheep tails. These findings improve our understanding of how adipose homeostasis is maintained, in response to extreme environments in animals.
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11
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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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12
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong 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
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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13
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How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds. Animals (Basel) 2022; 12:ani12172198. [PMID: 36077919 PMCID: PMC9454691 DOI: 10.3390/ani12172198] [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: 06/30/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary In this paper, we study the inter-relationships among geography, climate, and genetics in Italian local cattle and sheep breeds. In terms of genetic diversity, geography (latitude and longitude) appears to play a larger role in sheep (26.4%) than that in cattle (13.8%). Once geography is accounted for, 10.1% of cattle genomic diversity and 13.3% of that of sheep are attributable to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher predomestication genetic variability together with biological and productive specializations. The climate alone seems to have had less impact on the current genetic diversity in both species even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions. Abstract Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribed to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher pre-domestication genetic variability together with biological and productive specificities. Climate alone seems to have had less impact on current genetic diversity in both species, even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions.
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Zhao Y, Zhang D, Zhang X, Li F, Xu D, Zhao L, Li X, Zhang Y, Wang J, Yang X, Wang W. Expression features of the ovine FTO gene and association between FTO polymorphism and tail fat deposition related-traits in Hu sheep. Gene X 2022; 826:146451. [PMID: 35358654 DOI: 10.1016/j.gene.2022.146451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/24/2022] [Accepted: 03/18/2022] [Indexed: 11/25/2022] Open
Abstract
Fat mass and obesity associated (FTO) gene is a famous dominant predictor of obesity, and plays pivotal roles in the regulating fatty acid transport and fat metabolism. In the current study, the quantitative real-time PCR (qRT-PCR), DNA-pooled sequencing and KAspar assay were performed to detect the expression features of FTO and the polymorphisms of FTO associated with the tail fat weight related-traits of Hu sheep. The results indicated that the expression of FTO gene is widely expressed in the tissues tested, and the expression level of FTO in tail fat tissue was evidently higher compared with that in the other tissues. In addition, FTO showed the highest expression level in tail fat tissue at three months. The expression of FTO mRNA was lower in the large-tail fat group compared with that in the small-tail fat group in 6 months old. Subsequently, the polymorphism loci g. 23704451C > A detected in the FTO gene was confirmed to be significantly related to the tail length and the weight of tail fat. These results suggested that the polymorphism might be regarded as novel molecular marker for the breeding of small tail sheep.
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Affiliation(s)
- Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobing Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weiming Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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15
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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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16
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Jin M, Fei X, Li T, Lu Z, Chu M, Di R, He X, Wang X, Wang Y, Yuan Z, Quan K, Wang H, Wei C. Oar-miR-432 Regulates Fat Differentiation and Promotes the Expression of BMP2 in Ovine Preadipocytes. Front Genet 2022; 13:844747. [PMID: 35559046 PMCID: PMC9087340 DOI: 10.3389/fgene.2022.844747] [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: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The fat tail is a unique characteristic of sheep that represents energy reserves and is a complex adaptative mechanism of fat-tailed sheep to environmental stress. MicroRNA plays a significant role as regulators at the posttranscriptional level, but no studies have explained the molecular mechanisms of miRNA which regulate fat deposition in sheep tails. In this study, mRNA and miRNA analysis examined tail fat tissue from three Hu fat-tailed and three Tibetan thin-tailed sheep. After aligning to the reference sequences, 2,108 differentially expressed genes and 105 differential expression miRNAs were identified, including 1,247 up- and 861 downregulated genes and 43 up- and 62 downregulated miRNAs. Among these differentially expressed miRNAs, oar-miR-432 was one of the most downregulated miRNAs between Hu sheep and Tibetan sheep, and 712 genes were predicted to be targeted by oar-miR-432, 80 of which overlapped with DEGs. The Gene Ontology analysis on these genes showed that BMP2, LEP, GRK5, BMP7, and RORC were enriched in fat cell differentiation terms. The genes for BMP2 targeted by oar-miR-432 were examined using dual-luciferase assay. The oar-miR-432 mimic transfected into preadipocytes resulted in increased expression of BMP2. The marker gene PPAR-γ of fat differentiation had a lower expression than the negative control on days 0, 2, and 4 after induced differentiation. The decrease in the number of lipids in the oar-miR-432 mimic group detected by oil red O stain was also less than that in the negative control. This is the first study to reveal the fat mechanisms by which oar-miR-432 inhibits fat differentiation and promotes the expression of BMP2 in sheep tails.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaojuan Fei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Yuan Z, Ge L, Sun J, Zhang W, Wang S, Cao X, Sun W. Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PeerJ 2021; 9:e12454. [PMID: 34760406 PMCID: PMC8571958 DOI: 10.7717/peerj.12454] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023] Open
Abstract
Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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18
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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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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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20
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Kalds P, Luo Q, Sun K, Zhou S, Chen Y, Wang X. Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways. Anim Genet 2021; 52:799-812. [PMID: 34472112 DOI: 10.1111/age.13133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Abstract
Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation(s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.
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Affiliation(s)
- P Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Q Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - K Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - S Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - X Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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21
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Baazaoui I, Bedhiaf-Romdhani S, Mastrangelo S, Ciani E. Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area. Animal 2021; 15:100193. [PMID: 33715983 DOI: 10.1016/j.animal.2021.100193] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/21/2022] Open
Abstract
Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58-49.61 Mbp). These results were confirmed using FST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.
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Affiliation(s)
- I Baazaoui
- Faculty of Sciences of Bizerte, University of Carthage, 7021 Zarzouna, Bizerte, Tunisia
| | - S Bedhiaf-Romdhani
- Institut National de la Recherche Agronomique de Tunisie, Laboratoire des Productions Animales et Fourragères, Université de Carthage, 2049 Ariana, Tunisie..
| | - S Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - E Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70121 Bari, Italy
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22
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Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics 2021; 113:1407-1415. [PMID: 33705888 DOI: 10.1016/j.ygeno.2021.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Arash Javanmard
- Departement of Animal Sceince, Faculty of Agriculture, University of Tabriz, PB 5166616471,Tabriz, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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23
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Han J, Guo T, Yue Y, Lu Z, Liu J, Yuan C, Niu C, Yang M, Yang B. Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs. PLoS One 2021; 16:e0246279. [PMID: 33529214 PMCID: PMC7853479 DOI: 10.1371/journal.pone.0246279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.
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Affiliation(s)
- Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
- * E-mail: (MY); (BY)
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
- * E-mail: (MY); (BY)
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24
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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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25
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Ciani E, Mastrangelo S, Da Silva A, Marroni F, Ferenčaković M, Ajmone-Marsan P, Baird H, Barbato M, Colli L, Delvento C, Dovenski T, Gorjanc G, Hall SJG, Hoda A, Li MH, Marković B, McEwan J, Moradi MH, Ruiz-Larrañaga O, Ružić-Muslić D, Šalamon D, Simčič M, Stepanek O, Curik I, Cubric-Curik V, Lenstra JA. On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools. Genet Sel Evol 2020; 52:25. [PMID: 32408891 PMCID: PMC7227234 DOI: 10.1186/s12711-020-00545-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/30/2020] [Indexed: 11/26/2022] Open
Abstract
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed \documentclass[12pt]{minimal}
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\begin{document}$$f_{4}$$\end{document}f4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds. Conclusions Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.
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Affiliation(s)
- Elena Ciani
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, Universita. degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Universita Studi di Palermo, Palermo, Italy
| | - Anne Da Silva
- Université de Limoges, INRAE, Pereine EA7500, USC1061 Gamaa, 87000, Limoges, France
| | - Fabio Marroni
- Dipartamento Scienze Agroalimentari, Ambientali e Animali, Universita Udine, Udine, Italy
| | | | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Mario Barbato
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Chiara Delvento
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, Universita. degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Toni Dovenski
- Department of Reproduction and Biomedicine, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Gregor Gorjanc
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, Scotland, UK
| | | | - Anila Hoda
- Department of Animal Production, Faculty of Agriculture and Environment, Agricultural University ofTirana, Tirana, Albania
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | | | - John McEwan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Mohammad H Moradi
- Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Otsanda Ruiz-Larrañaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of Basque Country, Leioa, Spain
| | | | - Dragica Šalamon
- Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Ino Curik
- Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | | | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Lu Z, Liu J, Han J, Yang B. Association Between BMP2 Functional Polymorphisms and Sheep Tail Type. Animals (Basel) 2020; 10:ani10040739. [PMID: 32340359 PMCID: PMC7223367 DOI: 10.3390/ani10040739] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Bone morphogenetic protein 2 (BMP2) is strongly selected in both fat-tailed and thin-tailed sheep and may be a candidate gene for sheep tail type selection. However, the mechanism of action of BMP2 in sheep tail fat deposition remains unclear. This study investigated genetic variation and haplotype combinations of the BMP2 gene in sheep with different tail types, aiming to reveal the molecular mechanism of BMP2 in sheep tail fat deposition. We detected a total of three single nucleotide polymorphisms (SNPs) (g.48401619 T > A, g.48401272 C > A, and g.48401136 C > T) among 533 sheep. The alleles and genotype frequencies of these SNPs were in Hardy-Weinberg equilibrium and showed significant correlations with tail length. Linkage disequilibrium existed between the g.48401272 C > A and g.48401136 C > T sites, where CACT was the predominant genotype. At the cellular level, the expression levels of peroxisome proliferator-activated receptor gamma (PPARγ) and lipoprotein lipase (LPL) were upregulated after BMP2 overexpression; there were significantly higher levels of PPARγ than controls at 0 d and 1 d, and of LPL than controls at 1 d and 7 d. These results indicate that the BMP2 gene may participate in sheep tail fat deposition and could be used for molecular-marker-assisted selection of sheep tail type.
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Affiliation(s)
- Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (J.L.); (J.H.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (J.L.); (J.H.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (J.L.); (J.H.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (J.L.); (J.H.)
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Correspondence: ; Tel.: +86-931-211-5272
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27
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Li Q, Lu Z, Jin M, Fei X, Quan K, Liu Y, Ma L, Chu M, Wang H, Wei C. Verification and Analysis of Sheep Tail Type-Associated PDGF-D Gene Polymorphisms. Animals (Basel) 2020; 10:ani10010089. [PMID: 31935823 PMCID: PMC7022463 DOI: 10.3390/ani10010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/25/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary PDGF-D can be considered a candidate gene for selection for sheep tail type. This study investigated genetic variation of the PDGF-D gene in sheep with different tail types verified at a cellular level and revealed the molecular mechanism of PDGF-D in sheep tail fat deposition. We detected a total of two SNPs among 533 sheep. g.4122606 C > G site was significantly correlated with tail length, and g.3852134 C > T site was significantly correlated with tail width. In addition, overexpression of PDGF-D in sheep preadipocytes can promote adipogenic differentiation. The PDGF-D gene may participate in sheep tail fat deposition and could be used for molecular marker-assisted selection of sheep tail type. Abstract The aim of this study was to examine the correlation between the platelet-derived growth factor-D (PDGF-D) gene and sheep tail type character and explore the potential underlying mechanism. A total of 533 sheep were included in this study. Polymorphic sites were examined by Pool-seq, and individual genotype identification and correlation analysis between tail type data were conducted using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) method. JASPART website was used to predict transcription factor binding sites in the promoter region with and without PDGF-D gene mutation. The effect of PDGF-D on adipogenic differentiation of sheep preadipocytes was investigated. Two single nucleotide polymorphism sites were identified: g.4122606 C > G site was significantly correlated with tail length, and g.3852134 C > T site was significantly correlated with tail width. g.3852134 C > T was located in the promoter region. Six transcription factor binding sites were eliminated after promoter mutation, and three new transcription factor binding sites appeared. Expression levels of peroxisome proliferator-activated receptor gamma (PPARγ) and lipoproteinlipase (LPL) were significantly up-regulated upon PDGF-D overexpression. Oil red O staining showed increased small and large oil drops in the PDGF-D overexpression group. Together these results indicate the PDGF-D gene is an important gene controlling sheep tail shape and regulating sheep tail fat deposition to a certain degree.
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Affiliation(s)
- Qing Li
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Meilin Jin
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
| | - Xiaojuan Fei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yongbin Liu
- Inner Mongolia Academy of Animal Husbandry Science, Hohhot 010031, China
| | - Lin Ma
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
| | - Huihua Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
- Correspondence: (H.W.); (C.W.)
| | - Caihong Wei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.L.); (M.J.); (X.F.); (L.M.); (M.C.)
- Correspondence: (H.W.); (C.W.)
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
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