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Jia C, Li C, Fu D, Chu M, Zan L, Wang H, Liang C, Yan P. Identification of genetic loci associated with growth traits at weaning in yak through a genome-wide association study. Anim Genet 2019; 51:300-305. [PMID: 31877578 DOI: 10.1111/age.12897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
A multilocus GWAS was performed to explore the genetic architecture of four growth traits in yak. In total, 354 female yaks for which measurements of body weight (BW), withers height (WH), body length (BL) and chest girth (CG) at weaning were available underwent genotyping with the Illumina BovineHD BeadChip (770K). After quality control, we retained 98 688 SNPs and 354 animals for GWAS analysis. We identified seven, 18, seven and nine SNPs (corresponding to seven, 17, seven and eight candidate genes) associated with BW, WH, BL and CG at weaning respectively. Interestingly, most of these candidate genes were reported to be involved in growth-related processes such as muscle formation, lipid deposition, feed efficiency, carcass composition and development of the central and peripheral nervous system. Our results offer novel insight into the molecular architecture underpinning yak growth traits. Further functional analyses are thus warranted to explore the molecular mechanisms whereby these genes affect these traits of interest.
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Affiliation(s)
- C Jia
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - C Li
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - D Fu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - M Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - L Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - H Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - C Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - P Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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Taye M, Kim J, Yoon SH, Lee W, Hanotte O, Dessie T, Kemp S, Mwai OA, Caetano-Anolles K, Cho S, Oh SJ, Lee HK, Kim H. Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef. BMC Genet 2017; 18:11. [PMID: 28183280 PMCID: PMC5301378 DOI: 10.1186/s12863-016-0467-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/20/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. RESULTS We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. CONCLUSION Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.
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Affiliation(s)
- Mengistie Taye
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Bahir Dar University, College of Agriculture and Environmental Sciences, PO Box 79, Bahir Dar, Ethiopia
| | - Jaemin Kim
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Wonseok Lee
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Olivier Hanotte
- The University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK
- International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia
| | - Stephen Kemp
- International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya
- The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya
| | | | - Seoae Cho
- C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea
| | - Sung Jong Oh
- National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Hak-Kyo Lee
- The Animal Molecular Genetics & Breeding Center, Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.
- C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea.
- Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.
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