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Kwon SG, Bae GH, Hong JH, Choi JW, Choi JH, Lim NS, Jeon C, Mali NM, Jun MS, Shin J, Kim J, Cho ES, Han MH, Oh JW. Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 2024; 35:645-656. [PMID: 39177814 DOI: 10.1007/s00335-024-10058-z] [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] [Received: 06/14/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
Abstract
Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research.
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Affiliation(s)
- Seong Gyu Kwon
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Geon Hue Bae
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joo Hee Hong
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Woo Choi
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - June Hyug Choi
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nam Seop Lim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - CheolMin Jeon
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nanda Maya Mali
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mee Sook Jun
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - JaeEun Shin
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - JinSoo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun-Seok Cho
- Department of Livestock Resource Development, National Institute of Animal Science, Jeonbuk, Republic of Korea
| | - Man-Hoon Han
- Department of Pathology, Kyungpook National University Hospital, Daegu, Republic of Korea.
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Absolute DNA, Inc., Daegu, Republic of Korea.
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Jiang J, Xu L, Zhuang Y, Wei X, Zhang Z, Zhao W, Wang Q, Ye X, Gu J, Cao C, Sun J, He K, Zhang Z, Wang Q, Pan Y, Wang Z. MeHA: A Computational Framework in Revealing the Genetic Basis of Animal Mental Health Traits Under an Intensive Farming System-A Case Study in Pigs. BIOLOGY 2024; 13:843. [PMID: 39452151 PMCID: PMC11504952 DOI: 10.3390/biology13100843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 09/29/2024] [Accepted: 10/14/2024] [Indexed: 10/26/2024]
Abstract
Intensively farmed animals such as pigs inevitably experience a certain degree of psychological stress, which leads to a reduction in production performance. Mental health traits are currently difficult to measure, resulting in a gap in understanding their genetic basis. To address this challenge, we propose a computational framework called mental health of animals (MeHA), capable of revealing genes related to animal mental health traits. Using MeHA, we identified 109 candidate genes associated with pig mental health and discovered their intricate connections with critical functions, such as memory, cognition, and neural development, which are essential components of mental health and cognitive performance. Importantly, our findings provide evidence of the potential impact of these genes on economically important traits, including meat quality and piglet survival. This research underscores the importance of genetic studies in enhancing our understanding of animal behavior and cognition, as well as promoting agricultural practices. By applying our approach to study the genetic basis of mental health in pigs as a case, we confirmed that our framework is an effective way to reveal genetic factors affecting animal mental health traits, which contributes to animal welfare and has potential implications for understanding human mental disorders.
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Affiliation(s)
- Jinyun Jiang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Lingyao Xu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Yizheng Zhuang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Wei Zhao
- SciGene Biotechnology Co., Ltd., Hefei 230031, China;
| | - Qingyu Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Xiaowei Ye
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Jiamin Gu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Kan He
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, China;
- Traditional Chinese Medicine Research Centre, School of Life Sciences, Anhui University, Hefei 230601, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.J.); (L.X.); (Y.Z.); (X.W.); (Z.Z.); (Q.W.); (X.Y.); (J.G.); (C.C.); (J.S.); (Z.Z.); (Q.W.); (Y.P.)
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Bolner M, Bovo S, Ballan M, Schiavo G, Taurisano V, Ribani A, Bertolini F, Fontanesi L. A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome. Genet Sel Evol 2024; 56:64. [PMID: 39285356 PMCID: PMC11403998 DOI: 10.1186/s12711-024-00930-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/26/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. RESULTS We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5-10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. CONCLUSIONS This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species.
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Affiliation(s)
- Matteo Bolner
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Samuele Bovo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Mohamad Ballan
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Valeria Taurisano
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Francesca Bertolini
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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Kwon D, Ahn J, Kim H, Kim H, Kim J, Wy S, Ko Y, Kim J. Convergent dwarfism consequences of minipigs under independent artificial selections. BMC Genomics 2024; 25:761. [PMID: 39107730 PMCID: PMC11301983 DOI: 10.1186/s12864-024-10677-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Currently, diverse minipigs have acquired a common dwarfism phenotype through independent artificial selections. Characterizing the population and genetic diversity in minipigs is important to unveil genetic mechanisms regulating their body sizes and effects of independent artificial selections on those genetic mechanisms. However, full understanding for the genetic mechanisms and phenotypic consequences in minipigs still lag behind. RESULTS Here, using whole genome sequencing data of 41 pig breeds, including eight minipigs, we identified a large genomic diversity in a minipig population compared to other pig populations in terms of population structure, demographic signatures, and selective signatures. Selective signatures reveal diverse biological mechanisms related to body size in minipigs. We also found evidence for neural development mechanism as a minipig-specific body size regulator. Interestingly, selection signatures within those mechanisms containing neural development are also highly different among minipig breeds. Despite those large genetic variances, PLAG1, CHM, and ESR1 are candidate key genes regulating body size which experience different differentiation directions in different pig populations. CONCLUSIONS These findings present large variances of genetic structures, demographic signatures, and selective signatures in the minipig population. They also highlight how different artificial selections with large genomic diversity have shaped the convergent dwarfism.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jiyeong Ahn
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Gyeonggi-Do, 17035, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Florio M, Cimini C, Bennato F, Ianni A, Grotta L, Martino G. Evaluation of Chemical and Nutritional Characteristics of Ricotta Cheese from Two Different Breeds: The Endangered Italian Teramana Goat and the Cosmopolitan Saneen Goat. Foods 2024; 13:1239. [PMID: 38672910 PMCID: PMC11048775 DOI: 10.3390/foods13081239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The present study aimed to compare the qualitative features of ricotta cheese produced by Teramana goats and Saanen goats raised in similar breeding systems and environmental conditions. The analyses were performed on ricotta after 0 (T0) and 5 (T5) days of storage at 4 °C. Ricotta cheese samples were subjected to chemical and physical analyses. The Teramana goat ricotta cheese was found to have a high-fat content characterized by a marked percentage of conjugates of linoleic acid (CLA). The reduction inketones and carboxylic acid revealed that Teramana goat ricotta cheese had greater oxidative stability during storage. According to the physical analyses, there are no differences between the two breeds in terms of color characteristics. Our findings underscore the importance of advocating for indigenous breeds, as evidenced by the compelling results observed in the production of ricotta cheese from Teramana goats.
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Affiliation(s)
| | | | | | | | | | - Giuseppe Martino
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy; (M.F.); (C.C.); (F.B.); (A.I.); (L.G.)
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6
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Fabbri MC, Lozada-Soto E, Tiezzi F, Čandek-Potokar M, Bovo S, Schiavo G, Fontanesi L, Muñoz M, Ovilo C, Bozzi R. Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study. Animal 2024; 18:101070. [PMID: 38401921 DOI: 10.1016/j.animal.2023.101070] [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] [Received: 09/15/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/26/2024] Open
Abstract
Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbreeding is implemented when leveraging autochthonous and cosmopolitan breeds to obtain most of the hybrid vigor.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, United States
| | - Francesco Tiezzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| | | | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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7
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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [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] [Received: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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8
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Bolner M, Bertolini F, Bovo S, Schiavo G, Fontanesi L. Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets. Animals (Basel) 2023; 14:5. [PMID: 38200737 PMCID: PMC10778222 DOI: 10.3390/ani14010005] [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: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions.
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Affiliation(s)
| | | | | | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (M.B.); (S.B.); (G.S.)
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Poklukar K, Mestre C, Škrlep M, Čandek-Potokar M, Ovilo C, Fontanesi L, Riquet J, Bovo S, Schiavo G, Ribani A, Muñoz M, Gallo M, Bozzi R, Charneca R, Quintanilla R, Kušec G, Mercat MJ, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Servin B. A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits. Genet Sel Evol 2023; 55:88. [PMID: 38062367 PMCID: PMC10704730 DOI: 10.1186/s12711-023-00858-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. RESULTS Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. CONCLUSIONS In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | - Camille Mestre
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | | | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - Ricardo Bozzi
- DAGRI-Animal Science Section, Università Di Firenze, Via Delle Cascine 5, 50144, Florence, Italy
| | - Rui Charneca
- MED- Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
| | - Goran Kušec
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - Marie-José Mercat
- IFIP Institut du Porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Christoph Zimmer
- Bauerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, 74549, Wolpertshausen, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, 82317, Baisogala, Lithuania
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, 11080, Belgrade-Zemun, Serbia
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France.
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Feng X, Diao S, Liu Y, Xu Z, Li G, Ma Y, Su Z, Liu X, Li J, Zhang Z. Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools. BMC Genomics 2023; 24:743. [PMID: 38053015 PMCID: PMC10699062 DOI: 10.1186/s12864-023-09848-7] [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] [Received: 02/23/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation. To uncover population genetic diversity, migration events, and artificial selection signatures in Chinese domestic pigs, we sampled 111 Yunnan pigs from four breeds in Yunnan which is considered to be one of the centres of livestock domestication in China, and genotyped them using Illumina Porcine SNP60K BeadChip. We then leveraged multiple bioinformatics database tools to further investigate the signatures and associated complex traits. RESULTS Population structure and migration analyses showed that Diannanxiaoer pigs had different genetic backgrounds from other Yunnan pigs, and Gaoligongshan may undergone the migration events from Baoshan and Saba pigs. Intriguingly, we identified a possible common target of sharing artificial selection on a 265.09 kb region on chromosome 5 in Yunnan indigenous pigs, and the genes on this region were associated with cardiovascular and immune systems. We also detected several candidate genes correlated with dietary adaptation, body size (e.g., PASCIN1, GRM4, ITPR2), and reproductive performance. In addition, the breed-sharing gene MMP16 was identified to be a human-mediated gene. Multiple lines of evidence at the mammalian genome, transcriptome, and phenome levels further supported the evidence for the causality between MMP16 variants and the metabolic diseases, brain development, and cartilage tissues in Chinese pigs. Our results suggested that the suppression of MMP16 would directly lead to inactivity and insensitivity of neuronal activity and skeletal development in Chinese indigenous pigs. CONCLUSION In this study, the population genetic analyses and identification of artificial selection signatures of Yunnan indigenous pigs help to build an understanding of the effect of human-mediated selection mechanisms on phenotypic traits in Chinese indigenous pigs. Further studies are needed to fully characterize the process of human-mediated genes and biological mechanisms.
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Affiliation(s)
- Xueyan Feng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuqi Diao
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yuqiang Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiting Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Guangzhen Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ye Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhanqin Su
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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11
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Hayah I, Talbi C, Chafai N, Houaga I, Botti S, Badaoui B. Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs. Front Genet 2023; 14:1229741. [PMID: 38034497 PMCID: PMC10687199 DOI: 10.3389/fgene.2023.1229741] [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: 05/26/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Background: The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication of meat and dairy products, and the preservation and improvement of pig breeds. By identifying breed informative markers, we aimed to gain insights into the genetic mechanisms that influence production traits, enabling informed decisions in animal management and promoting sustainable pig production to meet the growing demand for animal products. Methods: Our dataset consists of 300 coding SNPs genotyped from three Italian commercial pig populations: Landrace, Yorkshire, and Duroc. Firstly, we analyzed the genetic diversity among the populations. Then, we applied a discriminant analysis of principal components to identify the most informative SNPs for discriminating between these populations. Lastly, we conducted a functional enrichment analysis to identify the most enriched pathways related to the genetic variation observed in the pig populations. Results: The alpha diversity indexes revealed a high genetic diversity within the three breeds. The higher proportion of observed heterozygosity than expected revealed an excess of heterozygotes in the populations that was supported by negative values of the fixation index (FIS) and deviations from the Hardy-Weinberg equilibrium. The Euclidean distance, the pairwise FST, and the pairwise Nei's GST genetic distances revealed that Yorkshire and Landrace breeds are genetically the closest, with distance values of 2.242, 0.029, and 0.033, respectively. Conversely, Landrace and Duroc breeds showed the highest genetic divergence, with distance values of 2.815, 0.048, and 0.052, respectively. We identified 28 significant SNPs that are related to phenotypic traits and these SNPs were able to differentiate between the pig breeds with high accuracy. The Functional Enrichment Analysis of the informative SNPs highlighted biological functions related to DNA packaging, chromatin integrity, and the preparation of DNA into higher-order structures. Conclusion: Our study sheds light on the genetic underpinnings of phenotypic variation among three Italian pig breeds, offering potential insights into the mechanisms driving breed differentiation. By prioritizing breed-specific coding SNPs, our approach enables a more focused analysis of specific genomic regions relevant to the research question compared to analyzing the entire genome.
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Affiliation(s)
- Ichrak Hayah
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Chouhra Talbi
- Plant and Microbial Biotechnologies, Biodiversity, and Environment (BioBio), Mohammed V University in Rabat, Rabat, Morocco
| | - Narjice Chafai
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Isidore Houaga
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
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Bordonaro S, Chessari G, Mastrangelo S, Senczuk G, Chessa S, Castiglioni B, Tumino S, Marletta D, Criscione A. Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds. Anim Genet 2023; 54:591-605. [PMID: 37381662 DOI: 10.1111/age.13344] [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: 06/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.
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Affiliation(s)
- Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, Torino, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, National Research Council, Lodi, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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Zhao C, Wang D, Teng J, Yang C, Zhang X, Wei X, Zhang Q. Breed identification using breed-informative SNPs and machine learning based on whole genome sequence data and SNP chip data. J Anim Sci Biotechnol 2023; 14:85. [PMID: 37259083 DOI: 10.1186/s40104-023-00880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/05/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Breed identification is useful in a variety of biological contexts. Breed identification usually involves two stages, i.e., detection of breed-informative SNPs and breed assignment. For both stages, there are several methods proposed. However, what is the optimal combination of these methods remain unclear. In this study, using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project, we compared the combinations of three methods (Delta, FST, and In) for breed-informative SNP detection and five machine learning methods (KNN, SVM, RF, NB, and ANN) for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs. In addition, we evaluated the accuracy of breed identification using SNP chip data of different densities. RESULTS We found that all combinations performed quite well with identification accuracies over 95% in all scenarios. However, there was no combination which performed the best and robust across all scenarios. We proposed to integrate the three breed-informative detection methods, named DFI, and integrate the three machine learning methods, KNN, SVM, and RF, named KSR. We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99% in most cases and was very robust in all scenarios. The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases. CONCLUSIONS The current study showed that the combination of DFI and KSR was the optimal strategy. Using sequence data resulted in higher accuracies than using chip data in most cases. However, the differences were generally small. In view of the cost of genotyping, using chip data is also a good option for breed identification.
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Affiliation(s)
- Changheng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Jun Teng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Cheng Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Xinyi Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Xianming Wei
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.
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14
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Ribani A, Taurisano V, Karatosidi D, Schiavo G, Bovo S, Bertolini F, Fontanesi L. Signatures of Admixture and Genetic Uniqueness in the Autochthonous Greek Black Pig Breed Deduced from Gene Polymorphisms Affecting Domestication-Derived Traits. Animals (Basel) 2023; 13:1763. [PMID: 37889646 PMCID: PMC10251807 DOI: 10.3390/ani13111763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 09/29/2023] Open
Abstract
The Greek Black Pig (or Greek Pig) is the only recognized autochthonous pig breed raised in Greece, usually in extensive or semi-extensive production systems. According to its name, the characteristic breed coat color is solid black. In this study, with the aim to start a systematic genetic characterization of the Greek Black Pig breed, we investigated polymorphisms in major genes well known to affect exterior and production traits (MC1R, KIT, NR6A1, VRTN and IGF2) and compared these data with population genetic information available in other Mediterranean and Western Balkan pig breeds and wild boars. None of the investigated gene markers were fixed for one allele, suggesting that, in the past, this breed experienced introgression from wild boars and admixture from cosmopolitan pig breeds, enriching the breed genetic pool that should be further investigated to design appropriate conservation genetic strategies. We identified a new MC1R allele, containing two missense mutations already reported in two other independent alleles, but here present in the same haplotype. This allele might be useful to disclose biological information that can lead to better understanding the cascade transmission of signals to produce melanin pigments. This study demonstrated that autochthonous genetic resources can be an interesting reservoir of unexpected genetic variants.
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Affiliation(s)
- Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
| | - Valeria Taurisano
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
| | - Despoina Karatosidi
- Research Institute of Animal Science, General Directorate of Hellenic Agricultural Organisation “Demeter”, Paralimni Giannitsa, 58100 Pella, Greece;
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (A.R.); (V.T.); (G.S.); (S.B.); (F.B.)
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15
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Florio M, Cimini C, Ianni A, Bennato F, Grotta L, Valbonetti L, Martino G. New Insight into the Quality Traits of Milk and Cheese from Teramana Goats, a Native Italian Breed. Animals (Basel) 2023; 13:ani13081344. [PMID: 37106907 PMCID: PMC10135095 DOI: 10.3390/ani13081344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The preservation and enhancement of native breeds is a central issue to initiate new breeding policies, which are sustainable and adapted to climate changes. The aim of this study was the characterisation of the qualitative traits of milk and cheese obtained from Teramana goats compared with Saanen goats reared in the same breeding facilities or environment. The research involved 41 Teramana goats and 40 Saanen goats. The milk of each group was collected and used to produce cheese, which was analysed fresh and after 30 and 60 days of ripening. Cheese samples were subjected to evaluations of the physical parameters, including colour and the TPA test, in addition to chemical evaluations that were focused on the determination of total lipids, fatty acids composition, volatile profile and proteolysis. The results showed the Teramana goat to be rich in fat, characterised by a significant increase in conjugates of linoleic acid (CLA), which are attributed to important health benefits. The analysis of volatile compounds showed more oxidative stability of Teramana goats' cheeses during the ripening. The results from sensory analyses indicated an improved hardness and yellowness, which could be accompanied by an improvement in customer acceptance. In conclusion, our study shows interesting results regarding the milk and cheese from the Teramana goat, as well as a positive evaluation by consumers, findings that encourage the importance of promoting native breeds.
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Affiliation(s)
- Marco Florio
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Costanza Cimini
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Andrea Ianni
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Francesca Bennato
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Lisa Grotta
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Luca Valbonetti
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
- Institute of Biochemistry and Cell Biology (CNRIBBC/EMMA/Infrafrontier/IMPC), National Research Council, 00015 Rome, Italy
| | - Giuseppe Martino
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
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Suárez-Mesa R, Ros-Freixedes R, Laghouaouta H, Pena RN, Hernández-Ortiz B, Rondón-Barragán I, Estany J. Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing. Trop Anim Health Prod 2023; 55:154. [PMID: 37041265 PMCID: PMC10089996 DOI: 10.1007/s11250-023-03557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
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Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Houda Laghouaouta
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Byron Hernández-Ortiz
- Research and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
| | - Joan Estany
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
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Boitard S, Liaubet L, Paris C, Fève K, Dehais P, Bouquet A, Riquet J, Mercat MJ. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines. Genet Sel Evol 2023; 55:13. [PMID: 36864379 PMCID: PMC9979506 DOI: 10.1186/s12711-023-00789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes. METHODS We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence. RESULTS French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others). CONCLUSIONS These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.
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Affiliation(s)
- Simon Boitard
- CBGP, CIRAD, INRAE, Institut Agro, IRD, Université de Montpellier, Montferrier-sur-Lez, France. .,GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France.
| | - Laurence Liaubet
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Cyriel Paris
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Katia Fève
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Patrice Dehais
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Alban Bouquet
- IFIP Institut du porc/Alliance R & D, Le Rheu, France
| | - Juliette Riquet
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
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18
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Fontanesi L. Genetics and genomics of pigmentation variability in pigs: A review. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Sá P, Santos D, Chiaia H, Leitão A, Cordeiro JM, Gama LT, Amaral AJ. Lost pigs of Angola: Whole genome sequencing reveals unique regions of selection with emphasis on metabolism and feed efficiency. Front Genet 2022; 13:1003069. [PMID: 36353101 PMCID: PMC9639768 DOI: 10.3389/fgene.2022.1003069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Angola, in the western coast of Africa, has been through dramatic social events that have led to the near-disappearance of native swine populations, and the recent introduction of European exotic breeds has also contributed to the erosion of this native swine repertoire. In an effort to investigate the genetic basis of native pigs in Angola (ANG) we have generated whole genomes from animals of a remote local pig population in Huambo province, which we have compared with 78 genomes of European and Asian pig breeds as well as European and Asian wild boars that are currently in public domain. Analyses of population structure showed that ANG pigs grouped within the European cluster and were clearly separated from Asian pig breeds. Pairwise FST ranged from 0.14 to 0.26, ANG pigs display lower levels of genetic differentiation towards European breeds. Finally, we have identified candidate regions for selection using a complementary approach based on various methods. All results suggest that selection towards feed efficiency and metabolism has occurred. Moreover, all analysis identified CDKAL1 gene, which is related with insulin and cholesterol metabolism, as a candidate gene overlapping signatures of selection unique to ANG pigs. This study presents the first assessment of the genetic relationship between ANG pigs and other world breeds and uncovers selection signatures that may indicate adaptation features unique to this important genetic resource.
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Affiliation(s)
- Pedro Sá
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Dulce Santos
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Hermenegildo Chiaia
- Faculdade de Medicina Veterinária, Universidade José Eduardo dos Santos, Huambo, Angola
| | - Alexandre Leitão
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - José Moras Cordeiro
- Faculdade de Medicina Veterinária, Universidade José Eduardo dos Santos, Huambo, Angola
| | - Luís T. Gama
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Andreia J. Amaral
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
- *Correspondence: Andreia J. Amaral,
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20
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Mo J, Lu Y, GangYan, Wang Y, Zhang K, Zhang S, Wang M, Chen X, Lan G, Liang J. Identifying selection signatures for litter size in Guangxi Bama Xiang pigs. Reprod Domest Anim 2022; 57:1536-1543. [PMID: 35989556 DOI: 10.1111/rda.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yujie Lu
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - GangYan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yubing Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Kun Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Shuai Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Mengying Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Xingfa Chen
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning, China
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21
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Banos G, Talenti A, Chatziplis D, Sánchez-Molano E. Genomic analysis of the rare British Lop pig and identification of distinctive genomic markers. PLoS One 2022; 17:e0271053. [PMID: 35960784 PMCID: PMC9374264 DOI: 10.1371/journal.pone.0271053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Concentration of production on a few commercial pig breeds has led to the marginalization of many native, numerically small breeds, increasing their risk of endangerment. In the UK, one such rare breed is the British Lop, a lop-eared breed, of similar origin to the Welsh breed. The objective of the present study was to address the genomic status of the British Lop and its relationship with other breeds and identify a small set of genomic markers that uniquely characterize and distinguish British Lop animals. Results have shown that the British Lop is a relatively distinct population with reduced genomic diversity and effective size consistent with its status as a rare breed. Furthermore, we demonstrated the genetic closeness of the British Lop to phenotypically similar breeds such as Landrace and Welsh as well Large White, Middle White and Pietrain. Finally, a set of 75 Single Nucleotide Polymorphisms distributed across multiple chromosomes were identified and validated as markers that can consistently distinguish British Lops from other closely related breeds. Results may inform breeding and management strategies aiming to enhance diversity as well as the development of a breed purity test.
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Affiliation(s)
- Georgios Banos
- Scotland’s Rural College (SRUC), Department of Animal and Veterinary Sciences, The Roslin Institute Building, Edinburgh, United Kingdom
| | - Andrea Talenti
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Dimitrios Chatziplis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Sindos, Greece
| | - Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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22
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Berghöfer J, Khaveh N, Mundlos S, Metzger J. Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs. BMC Genomics 2022; 23:564. [PMID: 35933356 PMCID: PMC9357325 DOI: 10.1186/s12864-022-08801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes. RESULTS Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation. CONCLUSIONS The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.
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Affiliation(s)
- Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Stefan Mundlos
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Charité-Universitätsmedizin Berlin, BCRT, Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
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23
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Ianni A, Bennato F, Martino C, Di Luca A, Martino G. Qualitative attributes of meat from Teramana goat kids, an Italian native breed of the Abruzzo region. Anim Biosci 2022; 35:1091-1099. [PMID: 34991229 PMCID: PMC9271378 DOI: 10.5713/ab.21.0352] [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: 08/08/2021] [Accepted: 10/14/2021] [Indexed: 11/27/2022] Open
Abstract
Objective: The aim of this work was the characterization of the qualitative aspects of meat obtained from Teramana goats, an Italian indigenous breed of the Abruzzo region. Specifically, the study included a comparison with meat samples deriving from Saanen goat kids reared in the same environment and applying the same feeding protocol.Methods: Upon reaching about 7 months of age the animals were slaughtered and samples of muscle tissue were collected to be analyzed. Specifically, meat samples were subjected to evaluations of the physical parameters, including color and the meat ability to retain water, in addition to chemical evaluations that were focused to the determination of the total lipids amount, fatty acids composition, lipid oxidation, and volatile profile.Results: The meat samples obtained from the indigenous breed showed a less intense reddish color and no significant variations for the muscle tissue tendency to retain water, both regarding fresh and cooked meat. Several differences were instead observed in the fatty acid profile. The Teramana samples were richer in saturated fatty acids (p<0.01) and interestingly showed higher concentrations of rumenic acid (p<0.05), a conjugate of linoleic acid that has been associated with important health benefits for the consumers. Another important finding for these meat samples was the marked resistance to oxidative events, as evidenced by the thiobarbituric acid reactive substances-test (p<0.05) and by the characterization of the volatile profile that highlighted a strong reduction in the relative percentage of hexanal (p<0.05), commonly associated to lipid oxidation and the development of unpleasant aromatic notes.Conclusion: The collected data, therefore appeared useful for the valorization of the food product derived from the Teramana goat, although no sensory information has been collected to define the degree of acceptability by the consumers.
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Chakraborty D, Sharma N, Kour S, Sodhi SS, Gupta MK, Lee SJ, Son YO. Applications of Omics Technology for Livestock Selection and Improvement. Front Genet 2022; 13:774113. [PMID: 35719396 PMCID: PMC9204716 DOI: 10.3389/fgene.2022.774113] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 05/16/2022] [Indexed: 12/16/2022] Open
Abstract
Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals’ actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.
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Affiliation(s)
- Dibyendu Chakraborty
- Division of Animal Genetics and Breeding, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
| | - Neelesh Sharma
- Division of Veterinary Medicine, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
- *Correspondence: Neelesh Sharma, ; Young Ok Son,
| | - Savleen Kour
- Division of Veterinary Medicine, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Ranbir Singh Pura, India
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Mukesh Kumar Gupta
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, India
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Life Sciences, Kangwon National University, Chuncheon-si, South Korea
| | - Young Ok Son
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, South Korea
- *Correspondence: Neelesh Sharma, ; Young Ok Son,
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Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages. Animals (Basel) 2022; 12:ani12111356. [PMID: 35681821 PMCID: PMC9204547 DOI: 10.3390/ani12111356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/07/2022] [Accepted: 05/23/2022] [Indexed: 12/16/2022] Open
Abstract
Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.
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Jiang Y, Li X, Liu J, Zhang W, Zhou M, Wang J, Liu L, Su S, Zhao F, Chen H, Wang C. Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data. BMC Genomics 2022; 23:373. [PMID: 35581549 PMCID: PMC9115978 DOI: 10.1186/s12864-022-08583-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (FROH) and homozygosity (FHOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. FROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, FROH and FHOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08583-9.
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Affiliation(s)
- Yao Jiang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaojin Li
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jiali Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jieru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongquan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data. Sci Rep 2022; 12:7346. [PMID: 35513520 PMCID: PMC9072372 DOI: 10.1038/s41598-022-10698-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.
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Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. Genet Sel Evol 2022; 54:30. [PMID: 35484510 PMCID: PMC9052598 DOI: 10.1186/s12711-022-00718-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). RESULTS The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. CONCLUSIONS Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.
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Hall SJG. Genetic Differentiation among Livestock Breeds-Values for F st. Animals (Basel) 2022; 12:1115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Affiliation(s)
- Stephen J G Hall
- Department of Environmental Protection and Landscape, Estonian University of Life Sciences, Kreutzwaldi 5, 51014 Tartu, Estonia
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30
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Kim YM, Seong HS, Kim YS, Hong JK, Sa SJ, Lee J, Lee JH, Cho KH, Chung WH, Choi JW, Cho ES. Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon. Front Genet 2022; 13:779152. [PMID: 35186025 PMCID: PMC8847790 DOI: 10.3389/fgene.2022.779152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/07/2022] [Indexed: 02/03/2023] Open
Abstract
A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.
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Affiliation(s)
- Yong-Min Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ha-Seung Seong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Young-Sin Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Joon-Ki Hong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Soo-Jin Sa
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Jun-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Kyu-Ho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, South Korea
| | - Jung-Woo Choi
- Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
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31
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Ballan M, Bovo S, Schiavo G, Schiavitto M, Negrini R, Fontanesi L. Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data. Genet Sel Evol 2022; 54:3. [PMID: 35062866 PMCID: PMC8780294 DOI: 10.1186/s12711-022-00696-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00696-9.
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Bertolini F, Moscatelli G, Schiavo G, Bovo S, Ribani A, Ballan M, Bonacini M, Prandi M, Dall'Olio S, Fontanesi L. Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours. J Anim Breed Genet 2021; 139:307-319. [PMID: 34841617 PMCID: PMC9300179 DOI: 10.1111/jbg.12659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/01/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed-specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well-known Protected Designation of Origin Parmigiano-Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome-wide information in comparative FST analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% FST values, a total of 64 markers were detected in the single-marker analysis. The top FST value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window-based analyses, which included 0.5-Mb or 1-Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle.
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Affiliation(s)
- Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giulia Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anisa Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Stefania Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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33
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Knoll A, Nesvadbová M, Urban T. The expression pattern, polymorphisms and association analyses of the porcine NREP gene. J Anim Breed Genet 2021; 139:62-70. [PMID: 34487372 DOI: 10.1111/jbg.12646] [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: 12/15/2020] [Revised: 05/29/2021] [Accepted: 08/20/2021] [Indexed: 11/28/2022]
Abstract
NREP (neuronal regeneration related protein homolog) plays a role in the transformation of neural, muscle, and fibroblast cells and in smooth muscle myogenesis. The NREP gene was selected for detailed study as an expressional and functional candidate gene on the basis of data from the expression microarray, which detected the differences in gene expression between Czech Large White pigs and wild boars in the longissimus lumborum et thoracis and biceps femoris muscle tissues. Quantitative real-time PCR results confirmed that porcine NREP was expressed in both skeletal muscles and significantly overexpressed in Czech Large White pigs compared with wild boars (14.5- and 11.6-fold; p < .05). We identified 9 polymorphic sites in the genomic DNA of NREP. Six of these polymorphisms were in complete linkage disequilibrium, and therefore, only 4 loci were informative. The associations of the HF571253:g.103G>A, HF571253:g.134G>A, HF571253:g.179T>C and HF571253:g.402_409delT polymorphisms with backfat thickness, lean meat content and average daily gain were assessed in Czech Large White pigs. The GG genotypes HF571253:g.103G>A and HF571253:g.134G>A, the TT genotypes HF571253:g.179T>C and 67 HF571253:g.402_409delT genotypes had favourable effects on the studied traits. Our results indicate the possibility of utilizing the variability of the NREP gene in marker-assisted selection in order to improve meat production in pigs.
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Affiliation(s)
- Aleš Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic.,CEITEC MENDELU, Mendel University in Brno, Brno, Czech Republic
| | - Michaela Nesvadbová
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Tomáš Urban
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic.,CEITEC MENDELU, Mendel University in Brno, Brno, Czech Republic
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Bakoev S, Getmantseva L, Kostyunina O, Bakoev N, Prytkov Y, Usatov A, Tatarinova TV. Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia. PeerJ 2021; 9:e11595. [PMID: 34249494 PMCID: PMC8256806 DOI: 10.7717/peerj.11595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
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Affiliation(s)
- Siroj Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia
| | - Lyubov Getmantseva
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Olga Kostyunina
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Nekruz Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Yuri Prytkov
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, United States of America.,Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia.,Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute for General Genetics, Moscow, Russia
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35
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Bovo S, Ballan M, Schiavo G, Ribani A, Tinarelli S, Utzeri VJ, Dall'Olio S, Gallo M, Fontanesi L. Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds. Anim Genet 2021; 52:440-450. [PMID: 34096632 PMCID: PMC8362157 DOI: 10.1111/age.13095] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
The number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.
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Affiliation(s)
- S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Ballan
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - S Tinarelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy.,Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, Roma, 00198, Italy
| | - V J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - S Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, Roma, 00198, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
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Nosková A, Bhati M, Kadri NK, Crysnanto D, Neuenschwander S, Hofer A, Pausch H. Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs. BMC Genomics 2021; 22:290. [PMID: 33882824 PMCID: PMC8061004 DOI: 10.1186/s12864-021-07610-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. RESULTS Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. CONCLUSIONS We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland.
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
| | | | - Danang Crysnanto
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
| | | | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
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Pork Quality of Two Lithuanian Breeds: Effects of Breed, Gender and Feeding Regimen. Animals (Basel) 2021; 11:ani11041103. [PMID: 33921472 PMCID: PMC8069488 DOI: 10.3390/ani11041103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary A few highly selected commercial pig breeds have been developed and many different local breeds have been replaced by these modern breeds. With the aim to preserve rare local breeds, the necessity has arisen to find and create the conditions under which local breeds could be more widely used. Therefore, the performance and production qualities of local breeds should be evaluated and highlighted. As the quality of pig production is associated with breeds and effects of other different conditions, the objective of this experiment was to investigate the effects of breed, gender, and feeding level in the finishing phase on the carcass and meat quality of Lithuanian White and Lithuanian Indigenous Wattle pigs reared indoors. Feed restriction during the finishing phase and gender both affected the growth and fatness of pigs. The breed and gender appeared to have an effect on the parameters of meat quality including fatty acid composition. The breed and gender effects on fatty acid composition showed more favorable lipid indices in relation to healthy nutrition in the ham muscles of Lithuanian White pigs compared with Lithuanian Indigenous Wattle pigs and also in the ham muscle and backfat of females compared with castrated males. Abstract The diversity of breeds is an important factor influencing carcass and meat quality traits that are also associated with other different effects. The objective of this study was to investigate the effects of breed, gender, and feeding level in the finishing phase on the carcass and meat quality of Lithuanian White and Lithuanian Indigenous Wattle pigs reared indoors. After 60 kg weight, half of the animals from both breeds were fed a restricted diet of approximately 82% of average ad libitum feeding intake, and the other half of pigs were further fed ad libitum to the end of the experiment. Feed restriction during the finishing phase decreased daily gain and weight of pigs at slaughter, and backfat thickness at the tenth rib (p ˂ 0.001, p ˂ 0.01, and p ˂ 0.05, respectively). Lithuanian White pigs demonstrated higher (p ˂ 0.001) growth rate, live body weight at slaughter and carcass weight, and had a higher (p ˂ 0.01) length of carcass and loin area and lower (p ˂ 0.05) backfat thickness at the last rib and at two points at the lumbar area compared with Lithuanian Indigenous Wattle pigs. The semimembranosus muscle of Lithuanian White pigs had relatively (8.1%) lower (p ˂ 0.001) proportions of saturated and 41.2% higher (p ˂ 0.001) proportions of polyunsaturated fatty acids compared with the pigs of the Lithuanian Indigenous Wattle breed, whereas in the longissimus muscle and subcutaneous tissue, the breed only affected the n-6/n-3 ratio (p ˂ 0.01 and p ˂ 0.001, respectively). Gender showed an effect on saturated fatty acids in all the studied tissues, however, the effects on polyunsaturated fatty acids were found in the semimembranosus muscle and subcutaneous tissue (p ˂ 0.05 and p ˂ 0.001) and the effects on monounsaturated fatty acids was found only in the semimembranosus muscle (p ˂ 0.01). These differences in the fatty acid composition of the semimembranosus muscle and subcutaneous tissue of females exhibited more favorable lipid quality indices compared with castrated males (p ˂ 0.001). The semimembranosus muscle of Lithuanian White pigs also showed more favorable lipid quality indices in relation to healthy nutrition compared with Lithuanian Indigenous Wattle pigs (p ˂ 0.001). This study is one of the steps toward the development and utilization of endangered breeds. The obtained information can be used to increase choice in pork production and consumption, and provides new insights for research into the conservation of local breeds.
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Tinarelli S, Ribani A, Utzeri VJ, Taurisano V, Bovo C, Dall’Olio S, Nen F, Bovo S, Schiavo G, Gallo M, Fontanesi L. Redefinition of the Mora Romagnola Pig Breed Herd Book Standard Based on DNA Markers Useful to Authenticate Its "Mono-Breed" Products: An Example of Sustainable Conservation of a Livestock Genetic Resource. Animals (Basel) 2021; 11:ani11020526. [PMID: 33670521 PMCID: PMC7923016 DOI: 10.3390/ani11020526] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Autochthonous breeds are, in general, well adapted to their production systems in which they have been constituted but they are usually less efficient than commercial breeds. Therefore, conservation strategies of livestock genetic resources should be designed to assure profitability to the farmers. The development of “mono-breed” brand products is one of the most effective actions towards this aim. These products are usually sold at a higher price compared to undifferentiated ones, as the consumers consider positively the link between these breeds and the perceived quality of their products. The premium price, however, also attracts fraudsters that unscrupulously see an economic advantage by selling mis-labelled products to obtain an unjustified additional economic gain. These frauds undermine the whole strategy designed to support a sustainable conservation of autochthonous genetic resources. Mora Romagnola is a local pig breed raised in the north of Italy. Mono-breed pork products derived from this breed are part of an important niche value chain that is intrinsically linked to the conservation of this local genetic resource. In this study we present how the Mora Romagnola Herd Book standard integrated information of DNA markers of two genes (MC1R and NR6A1), affecting morphological traits, to allow the authentication of mono-breed products of this breed. This is one of the first examples of sustainable conservation of a pig genetic resource designed starting from the genotype of the animals registered to the breed herd book, with the specific purpose to combat frauds. Abstract Mora Romagnola is an autochthonous pig breed, raised in the north of Italy. Mono-breed pork products of this breed are part of important niche value chain that is intrinsically linked to the conservation of this local genetic resources that can only survive due to the premium price that these products can obtain on the market. However, the added value attracts fraudsters that unscrupulously sell mis-labelled Mora Romagnola products, causing consumer distrust that, in turn, undermines the conservation strategy of this breed. To monitor and better characterise this local breed, we phenotyped 826 Mora Romagnola pigs for three breed-specific traits. Then, we genotyped almost all living sows and boars registered to the Herd Book (n. = 357 animals) for polymorphisms in the MC1R and NR6A1 genes (affecting coat colour and vertebral number, respectively). The results were used to re-define the breed descriptors of the Mora Romagnala breed that included information on the allowed genotypes at these two genes. A few pigs that did not carry the allowed genotypes were excluded from its Herd Book. Finally, we evaluated the usefulness of these DNA markers to authenticate Mora Romagnola meat against meat derived from other 11 pig breeds and wild boars. To our knowledge, the Mora Romagnola Herd Book is one of the first examples that established a direct link between a genetic standard of a breed with the possibility to authenticate mono-breed products using DNA markers with the specific purpose to combat frauds and, indirectly, support the conservation of a livestock genetic resource.
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Affiliation(s)
- Silvia Tinarelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
- Associazione Nazionale Allevatori Suini, Via Nizza 53, 00198 Roma, Italy; (F.N.); (M.G.)
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Valeria Taurisano
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Claudio Bovo
- Associazione Regionale Allevatori dell’Emilia-Romagna, Viale Della Mercanzia 240-242-244, 40050 Funo di Argelato (BO), Italy;
| | - Stefania Dall’Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Francesco Nen
- Associazione Nazionale Allevatori Suini, Via Nizza 53, 00198 Roma, Italy; (F.N.); (M.G.)
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, 00198 Roma, Italy; (F.N.); (M.G.)
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy; (S.T.); (A.R.); (V.J.U.); (V.T.); (S.D.); (S.B.); (G.S.)
- Correspondence: ; Tel.: +39-051-2096535
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Bovo S, Schiavo G, Ribani A, Utzeri VJ, Taurisano V, Ballan M, Muñoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Djurkin Kušec I, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Škrlep M, Usai G, Zimmer C, Ovilo C, Fontanesi L. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources. Sci Rep 2021; 11:3359. [PMID: 33564056 PMCID: PMC7873263 DOI: 10.1038/s41598-021-82956-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Valerio J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Valeria Taurisano
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Mohamad Ballan
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Estefania Alves
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Riccardo Bozzi
- DAGRI - Animal Science Section, University of Florence, Via delle Cascine 5, 50144, Florence, Italy
| | - Rui Charneca
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Federica Di Palma
- Biodiversity School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47UH, UK
| | - Ivona Djurkin Kušec
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - Graham Etherington
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR47UZ, UK
| | - Ana I Fernandez
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Fabián García
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Juan García-Casco
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - José Manuel Martins
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Marie-José Mercat
- IFIP Institut du porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, 11080, Belgrade-Zemun, Serbia
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Juliette Riquet
- Génétique Physiologie et Systèmes d'Elevage (GenPhySE), Université de Toulouse, INRA, Chemin de Borde-Rouge 24, Auzeville Tolosane, 31326, Castanet Tolosan, France
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
| | - Martin Škrlep
- Kmetijski Inštitut Slovenije, Hacquetova 17, 1000, Ljubljana, Slovenia
| | - Graziano Usai
- AGRIS SARDEGNA, Loc. Bonassai, 07100, Sassari, Italy
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria yAlimentaria (INIA), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
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Schiavo G, Bovo S, Muñoz M, Ribani A, Alves E, Araújo JP, Bozzi R, Čandek-Potokar M, Charneca R, Fernandez AI, Gallo M, García F, Karolyi D, Kušec G, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. Anim Genet 2021; 52:155-170. [PMID: 33544919 DOI: 10.1111/age.13045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.
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Affiliation(s)
- G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - A Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - E Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J P Araújo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, Ponte de Lima, 4990-706, Portugal
| | - R Bozzi
- DAGRI - Animal Science Division, Università di Firenze, Via delle Cascine 5, Firenze, 50144, Italy
| | - M Čandek-Potokar
- Kmetijski Inštitut Slovenije, Hacquetova 17, Ljubljana, SI-1000, Slovenia
| | - R Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Polo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - A I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Rome, 00198, Italy
| | - F García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - D Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, Zagreb, 10000, Croatia
| | - G Kušec
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, Osijek, 31000, Croatia
| | - J M Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Polo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - M-J Mercat
- IFIP Institut du porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex, 35651, France
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - R Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona, 08140, Spain
| | - Č Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - V Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania
| | - J Riquet
- GenPhySE, Université de Toulouse, INRA, Chemin de Borde-Rouge 24, Auzeville Tolosane, Castanet Tolosan, 31326, France
| | - R Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - G Usai
- Agris Sardegna, Loc. Bonassai, Sassari, 07100, Italy
| | - V J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - C Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, Wolpertshausen, 74549, Germany
| | - C Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
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Bovo S, Schiavo G, Utzeri VJ, Ribani A, Schiavitto M, Buttazzoni L, Negrini R, Fontanesi L. A genome-wide association study for the number of teats in European rabbits (Oryctolagus cuniculus) identifies several candidate genes affecting this trait. Anim Genet 2021; 52:237-243. [PMID: 33428230 DOI: 10.1111/age.13036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 12/01/2022]
Abstract
In the European rabbit (Oryctolagus cuniculus), a polytocous livestock species, the number of teats indirectly impacts the doe reproduction efficiency and, in turn, the sustainable production of rabbit meat. In this study, we carried out a genome-wide association study (GWAS) for the total number of teats in 247 Italian White does included in the Italian White rabbit breed selection program, by applying a selective genotyping approach. Does had either 8 (n = 121) or 10 teats (n = 126). All rabbits were genotyped with the Affymetrix Axiom OrcunSNP Array. Genomic data from the two extreme groups of rabbits were also analysed with the single-marker fixation index statistic and combined with the GWAS results. The GWAS identified 50 significant SNPs and the fixation index analysis identified a total of 20 SNPs that trespassed the 99.98th percentile threshold, 19 of which confirmed the GWAS results. The most significant SNP (P = 4.31 × 10-11 ) was located on OCU1, close to the NUDT2 gene, a breast carcinoma cells proliferation promoter. Another significant SNP identified as candidate gene NR6A1, which is well known to play an important role in affecting the correlated number of vertebrae in pigs. Other significant markers were close to candidate genes involved in determining body length in mice. Markers associated with increased number of teats could be included in selection programmes to speed up the improvement for this trait in rabbit lines that need to increase maternal performances.
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Affiliation(s)
- S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Contrada Giancola snc, Volturara Appula, Foggia, 71030, Italy
| | - L Buttazzoni
- Research Centre for Animal Production and Aquaculture, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Via Salaria 31, Monterotondo, Rome, 00015, Italy
| | - R Negrini
- Associazione Italiana Allevatori, Via G. Tomassetti 9, Rome, 00161, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
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Schiavo G, Bovo S, Bertolini F, Dall'Olio S, Nanni Costa L, Tinarelli S, Gallo M, Fontanesi L. Runs of homozygosity islands in Italian cosmopolitan and autochthonous pig breeds identify selection signatures in the porcine genome. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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