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Lange A, Medugorac I, Ali A, Kessler B, Kurome M, Zakhartchenko V, Hammer SE, Hauser A, Denner J, Dobenecker B, Wess G, Tan PLJ, Garkavenko O, Reichart B, Wolf E, Kemter E. Genetic diversity, growth and heart function of Auckland Island pigs, a potential source for organ xenotransplantation. Xenotransplantation 2024; 31:e12858. [PMID: 38646921 DOI: 10.1111/xen.12858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/28/2024] [Indexed: 04/23/2024]
Abstract
One of the prerequisites for successful organ xenotransplantation is a reasonable size match between the porcine organ and the recipient's organ to be replaced. Therefore, the selection of a suitable genetic background of source pigs is important. In this study, we investigated body and organ growth, cardiac function, and genetic diversity of a colony of Auckland Island pigs established at the Center for Innovative Medical Models (CiMM), LMU Munich. Male and female Auckland Island pig kidney cells (selected to be free of porcine endogenous retrovirus C) were imported from New Zealand, and founder animals were established by somatic cell nuclear transfer (SCNT). Morphologically, Auckland Island pigs have smaller body stature compared to many domestic pig breeds, rendering their organ dimensions well-suited for human transplantation. Furthermore, echocardiography assessments of Auckland Island pig hearts indicated normal structure and functioning across various age groups throughout the study. Single nucleotide polymorphism (SNP) analysis revealed higher runs of homozygosity (ROH) in Auckland Island pigs compared to other domestic pig breeds and demonstrated that the entire locus coding the swine leukocyte antigens (SLAs) was homozygous. Based on these findings, Auckland Island pigs represent a promising genetic background for organ xenotransplantation.
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Affiliation(s)
- Andreas Lange
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Asghar Ali
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Barbara Kessler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Mayuko Kurome
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas Hauser
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Joachim Denner
- Institute of Virology, Free University of Berlin, Berlin, Germany
| | - Britta Dobenecker
- Chair for Animal Nutrition, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Gerhard Wess
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | | | | | - Bruno Reichart
- Walter-Brendel-Center for Experimental Medicine, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
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Hervás-Rivero C, Srihi H, López-Carbonell D, Casellas J, Ibáñez-Escriche N, Negro S, Varona L. Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs. Genes (Basel) 2023; 14:1941. [PMID: 37895290 PMCID: PMC10606707 DOI: 10.3390/genes14101941] [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: 09/25/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.
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Affiliation(s)
- Carlos Hervás-Rivero
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - Houssemeddine Srihi
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - David López-Carbonell
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - Joaquim Casellas
- Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Noelia Ibáñez-Escriche
- Instituto Universitario de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sara Negro
- Programa de Mejora Genética “Castua”, INGA FOOD S. A. (Nutreco), 06200 Almendralejo, Spain
| | - Luis Varona
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
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Du T, Li P, Niu Q, Pu G, Wang B, Liu G, Li P, Niu P, Zhang Z, Wu C, Hou L, Hedemann MS, Zhao Q, Huang R. Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs. Microorganisms 2023; 11:2474. [PMID: 37894132 PMCID: PMC10609096 DOI: 10.3390/microorganisms11102474] [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: 08/22/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.
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Affiliation(s)
- Taoran Du
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Pinghua Li
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Qing Niu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guang Pu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Binbin Wang
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Gensheng Liu
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Pinghui Li
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Chengwu Wu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Liming Hou
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | | | - Qingbo Zhao
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
| | - Ruihua Huang
- Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pig) of Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China; (T.D.); (P.L.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
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Lan Q, Deng Q, Qi S, Zhang Y, Li Z, Yin S, Li Y, Tan H, Wu M, Yin Y, He J, Liu M. Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs. Genes (Basel) 2023; 14:522. [PMID: 36833449 PMCID: PMC9957351 DOI: 10.3390/genes14020522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.
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Affiliation(s)
- Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qiuchun Deng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shijin Qi
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulian Li
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Hong Tan
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Maisheng Wu
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
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Vaishnav S, Chauhan A, Ajay A, Saini BL, Kumar S, Kumar A, Bhushan B, Gaur GK. Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits. Mol Biol Rep 2023; 50:3705-3721. [PMID: 36642776 DOI: 10.1007/s11033-022-08168-5] [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: 08/03/2022] [Accepted: 12/01/2022] [Indexed: 01/17/2023]
Abstract
Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.
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Affiliation(s)
| | - Anuj Chauhan
- Indian Veterinary Research Institute, Bareilly, India.
| | - Argana Ajay
- Indian Veterinary Research Institute, Bareilly, India
| | | | - Subodh Kumar
- Indian Veterinary Research Institute, Bareilly, India
| | - Amit Kumar
- Indian Veterinary Research Institute, Bareilly, India
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Chi C, He J, Du Z, Zheng Y, D’Alessandro E, Chen C, Moawad AS, Asare E, Song C, Wang X. Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation. Life (Basel) 2022; 12:life12101650. [PMID: 36295085 PMCID: PMC9604734 DOI: 10.3390/life12101650] [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: 08/31/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
It has been established that through binding to bone morphogenetic proteins (BMPs), bone morphogenetic protein receptor I B (BMPR1B) can mediate transforming growth factor β (TGF-β) signal transduction, and is involved in the regulation of several biological processes, such as bone and muscle formation and homeostasis, as well as folliculogenesis. Also known as FecB, BMPR1B has been reported as the major gene for sheep prolificacy. A number of previous studies have analyzed the relationship between single nucleotide polymorphisms (SNPs) in this gene and its related performance. In recent years, with the illustration of the effect of retrotransposon insertion on the expression of the proximal genes or phenotypic variation, retrotransposon insertion polymorphisms (RIPs) have been used as a novel type of molecular marker in the evaluation of evolution, population structure and breeding of plant and domestic animals. In this study, the RIPs in porcine BMPR1B gene were excavated, and thereafter verified using a comparative genome and polymerase chain reaction (PCR). The potential effects of phenotype, gene expression and functions related to RIPs were also explored. The results showed that 13 distinct RIPs were identified in introns of porcine BMPR1B. Among these, only BMPR1B-SINE-RIP9 and BMPR1B-LINE-RIP13 displayed a close relationship with the growth traits of Large White pigs. Moreover, the total number of BMPR1B-SINE+/+-RIP9 individuals born was found to be significantly higher than that of SINE−/− (p < 0.05). These two RIPs showed an obvious distribution pattern among Chinese indigenous breeds and Western commercial breeds. The expression of BMPR1B in ovaries of adult BMPR1B-SINE+/+-RIP9 Sushan pigs was found to be significantly higher in comparison to those of BMPR1B-SINE−/−-RIP9 (p < 0.05). SINE insertion of BMPR1B-SINE-RIP9 and LINE insertion of BMPR1B-LINE-RIP13 were observed to significantly increase the activity of Octamer binding transcription factor 4 (OCT4) minipromoter in CHO and C2C12 cells (p < 0.01). Therefore, these two RIPs could serve as useful molecular markers for modulating the growth or reproductive traits in assisted selection of pig breeding, while the mechanisms of the insertion function should be studied further.
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Affiliation(s)
- Chenglin Chi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Jia He
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhanyu Du
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Yao Zheng
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Enrico D’Alessandro
- Department of Veterinary Science, Division of Animal Production, University of Messina, 98168 Messina, Italy
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel./Fax: +86-013511768881
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Mary N, Iannuccelli N, Petit G, Bonnet N, Pinton A, Barasc H, Amélie F, Calgaro A, Grosbois V, Servin B, Ducos A, Riquet J. Genome‐wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig. Evol Appl 2022; 15:1115-1128. [PMID: 35899256 PMCID: PMC9309462 DOI: 10.1111/eva.13432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/19/2022] [Accepted: 05/31/2022] [Indexed: 11/15/2022] Open
Abstract
The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub‐species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the “hybrid” status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 “outliers” (3.6%), for which the proportion of the genome of “domestic” origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of “wild” origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.
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Affiliation(s)
- Nicolas Mary
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | | | | | - Nathalie Bonnet
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Alain Pinton
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Harmonie Barasc
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Faure Amélie
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Anne Calgaro
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | | | - Bertrand Servin
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Alain Ducos
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
| | - Juliette Riquet
- GenPhySE Université de Toulouse INRAE, ENVT Castanet Tolosan France
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Chen J, Wu Z, Chen R, Huang Z, Han X, Qiao R, Wang K, Yang F, Li XJ, Li XL. Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies. Animals (Basel) 2022; 12:ani12121584. [PMID: 35739920 PMCID: PMC9219640 DOI: 10.3390/ani12121584] [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: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
The reproductive traits of sows are one of the important economic traits in pig production, and their performance directly affects the economic benefits of the entire pig industry. In this study, a total of 895 French Large White pigs were genotyped by GeneSeek Porcine 50K SNP Beadchip and four phenotypic traits of 1407 pigs were recorded, including total number born (TNB), number born alive (NBA), number healthy piglets (NHP) and litter weight born alive (LWB). To identify genomic regions and genes for these traits, we used two approaches: a single-locus genome-wide association study (GWAS) and a single-step GWAS (ssGWAS). Overall, a total of five SNPs and 36 genomic regions were identified by single-locus GWAS and ssGWAS, respectively. Notably, fourof all five significant SNPs were located in 10.72–11.06 Mb on chromosome 7, were also identified by ssGWAS. These regions explained the highest or second highest genetic variance in the TNB, NBA and NHP traits and harbor the protein coding gene ENSSSCG00000042180. In addition, several candidate genes associated with litter traits were identified, including JARID2, PDIA6, FLRT2 and DICER1. Overall, these novel results reflect the polygenic genetic architecture of the litter traits and provide a theoretical reference for the following implementation of molecular breeding.
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Gong Y, Zhang HY, Yuan Y, He Y, Zhang W, Han Y, Na R, Zeng Y, Luo J, Yang H, Huang Y, Zhao Y, Zhao Z, E GX. Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa. Animals (Basel) 2022; 12:ani12081037. [PMID: 35454283 PMCID: PMC9030587 DOI: 10.3390/ani12081037] [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: 01/18/2022] [Revised: 02/23/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.
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10
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Xu G, Hu Y, Yu D, Chen X, Li X, Duan S, Zhang N, Xu G, Hu J, Yang G, Sun S, Liu Y. Discovery of Differentially Expressed MicroRNAs in Porcine Ovaries With Smaller and Larger Litter Size. Front Genet 2022; 13:762124. [PMID: 35222529 PMCID: PMC8864311 DOI: 10.3389/fgene.2022.762124] [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: 08/21/2021] [Accepted: 01/03/2022] [Indexed: 12/14/2022] Open
Abstract
The number of live births in a litter is an important reproductive trait, and is one of the main indicators which reflect the production level and economic benefit of a pig farm. The ovary is an important reproductive organ of the sow, and it undergoes a series of biological processes during each estrous cycle. A complex transcriptional network containing coding and non-coding RNAs in the ovary closely regulates the reproductive capability of sows. However, the molecular regulation mechanisms affecting sow litter size are still unclear. We investigated the expression profiles of microRNAs (miRNAs) in porcine ovaries from sows with smaller than average litter sizes (SLS) and those with larger litter sizes (LLS). In total, 411 miRNAs were identified, and of these 17 were significantly down-regulated and 16 miRNAs were up-regulated when comparing sows with LLS and SLS, respectively. We further characterized the role of miR-183 which was one of the most up-regulated miRNAs. CCK-8, EdU incorporation and western blotting assays demonstrated that miR-183 promoted the proliferation of granulosa cells (GCs) in pig ovaries. Moreover, miR-183 inhibited the synthesis of estradiol in GCs and promoted the synthesis of progesterone. These results will help in gaining understanding of the role of miRNAs in regulating porcine litter size.
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Affiliation(s)
- Gaoxiao Xu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Yamei Hu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Dongling Yu
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Xingfa Chen
- Nanning Dabeinong Feed Technology Co., Ltd., Nanning, China
| | - Xiao Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Saixing Duan
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Ning Zhang
- Nanning Dabeinong Feed Technology Co., Ltd., Nanning, China
| | - Gaoyu Xu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Jianhong Hu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Gongshe Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Shiduo Sun
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yong Liu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
- *Correspondence: Yong Liu,
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11
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Ran X, Hu F, Mao N, Ruan Y, Yi F, Niu X, Huang S, Li S, You L, Zhang F, Tang L, Wang J, Liu J. Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs. Porcine Health Manag 2021; 7:52. [PMID: 34470660 PMCID: PMC8411529 DOI: 10.1186/s40813-021-00226-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although lots of quantitative trait loci (QTLs) and genes present roles in litter size of some breeds, the information might not make it clear for the huge diversity of reproductive capability in pig breeds. To elucidate the inherent mechanisms of heterogeneity of reproductive capability in litter size of Xiang pig, we performed transcriptome analysis for the expression profile in ovaries using RNA-seq method. RESULTS We identified 1,419 up-regulated and 1,376 down-regulated genes in Xiang pigs with large litter size. Among them, 1,010 differentially expressed genes (DEGs) were differently spliced between two groups with large or small litter sizes. Based on GO and KEGG analysis, numerous members of genes were gathered in ovarian steroidogenesis, steroid biosynthesis, oocyte maturation and reproduction processes. CONCLUSIONS Combined with gene biological function, twelve genes were found out that might be related with the reproductive capability of Xiang pig, of which, eleven genes were recognized as hub genes. These genes may play a role in promoting litter size by elevating steroid and peptide hormones supply through the ovary and facilitating the processes of ovulation and in vivo fertilization.
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Affiliation(s)
- Xueqin Ran
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fengbin Hu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Ning Mao
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Yiqi Ruan
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fanli Yi
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Xi Niu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Shihui Huang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Sheng Li
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Longjiang You
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fuping Zhang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Liangting Tang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Jiafu Wang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China.
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
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12
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Yuan X, Zhou X, Qiao X, Wu Q, Yao Z, Jiang Y, Zhang H, Zhang Z, Wang X, Li J. FoxA2 and p53 regulate the transcription of HSD17B1 in ovarian granulosa cells of pigs. Reprod Domest Anim 2020; 56:74-82. [PMID: 33111336 DOI: 10.1111/rda.13850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/10/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
The oestrogens have been highly implicated in the fertility of female animals. It is widely known that the oestrogens are primarily synthetized by the ovarian granulosa cells (GCs), and the final and essential step of this process is to catalyse the oestrone to the more active oestradiol by the protein coded by hydroxysteroid 17-beta dehydrogenase 1 (HSD17B1) gene. However, the molecular mechanism regarding the transcription of HSD17B1 remains to be fully elucidated in ovarian GCs. In this study, the 5'-deletion, luciferase assay and chromatin immunoprecipitation (ChIP) were utilized to explore the molecular regulation of transcription of HSD17B1 with the porcine ovarian GCs as the cellular model. After the deletions with -2105 to -1754 bp, -1753 to -1429 bp, -1430 to -1081 bp and -1082 to -730 bp, the relative luciferase activity of HSD17B1 promoter did not change significantly, but the deletion of -731 to -332 bp significantly increased the relative luciferase activity of HSD17B1 promoter, and an insertion (GTTT) that might raise the transcription of HSD17B1 was identified at -401 bp of HSD17B1. These findings suggested the region from -731 to +38 bp was the core promoter of HSD17B1, and the region between -731 to -332 bp might be a silence element for HSD17B1. Furthermore, the forkhead box A2 (FoxA2) directly bound at -412 to -401 bp to negatively but p53 bound at -383 to -374 bp to positively regulate the transcription and translation of HSD17B1 in ovarian GCs. These findings will improve our understanding on HSD17B1-mediated oestrogens and provide useful information for further investigations into fertility of females.
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Affiliation(s)
- Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Xiaofeng Zhou
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiwu Qiao
- Guangzhou Customs Technology Center, Guangzhou, Guangdong, China
| | - Qi Wu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhixiang Yao
- Guangdong Dexing Food Co., Ltd, Guangzhou, China
| | - Yao Jiang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hao Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xilong Wang
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
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13
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Bakoev S, Getmantseva L, Bakoev F, Kolosova M, Gabova V, Kolosov A, Kostyunina O. Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig. Genes (Basel) 2020; 11:E491. [PMID: 32365801 PMCID: PMC7291110 DOI: 10.3390/genes11050491] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/26/2022] Open
Abstract
Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as "Genome map association". Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.
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Affiliation(s)
- Siroj Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
| | - Lyubov Getmantseva
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
| | - Faridun Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344006, Russia;
| | - Maria Kolosova
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biotechnology, Don State Agrarian University, Persianovski 346493, Russia
| | - Valeria Gabova
- Department of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344006, Russia;
| | - Anatoly Kolosov
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biotechnology, Don State Agrarian University, Persianovski 346493, Russia
| | - Olga Kostyunina
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
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14
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Ding Y, Ding C, Wu X, Wu C, Qian L, Li D, Zhang W, Wang Y, Yang M, Wang L, Ding J, Zhang X, Gao Y, Yin Z. Porcine LIF gene polymorphisms and their association with litter size traits in four pig breeds. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2018-0228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Leukemia inhibitory factor (LIF) is an important productivity-related gene in pigs. We found two polymorphisms — g.6646C>T and g.6988C>T — in exon 3 of LIF in pigs by using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism. Three genotypes were obtained and associated with litter size traits in Anqing Six-end-white (AQ), Wei (W), Wannan Black (WNB), and Large White (LW) pigs. At locus g.6646C>T, the g.6646C allele frequency variation was 0.6869 (AQ), 0.7473 (W), 1 (WNB), and 0.6852 (LW). In AQ pigs, sows with the TT genotype had higher total number of piglets born (TNB) and number of piglets born alive (NBA) in the first parity and multiparities (P < 0.01). In W and LW pigs, sows with the CC genotype had higher TNB and NBA in multiparities (P < 0.01). At locus g.6988C>T, the g.6988C allele frequency variation was 1 (AQ), 0.6154 (W), 1 (WNB), and 0.6667 (LW). The CC genotype significantly differed from CT or TT genotypes (P < 0.01) for TNB and NBA in W and LW pigs. Thus, LIF was shown to have a significant influence on litter size. Therefore, g.6646C>T and g.6988C>T loci of LIF could be potential marker-assisted selection tools for improving litter size in pig production.
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Affiliation(s)
- Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Chong Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Chaodong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Li Qian
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Dengtao Li
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Wei Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Yuanlang Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Min Yang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Li Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Jian Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
| | - Yafei Gao
- Anhui Haoxiang Agriculture and Animal Husbandry Co., Ltd., Bozhou, Anhui 236700, People’s Republic of China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, People’s Republic of China
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15
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Zhang Q, Huang R, Ma X, Jiang N, Zhou W, Gao C, Zhao M, Niu P, Zhang Z, Li Q, Zhou J, Li P. Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs. Animals (Basel) 2019; 10:ani10010011. [PMID: 31861561 PMCID: PMC7023200 DOI: 10.3390/ani10010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.
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Affiliation(s)
- Qian Zhang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Xiang Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Nengjing Jiang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Wuduo Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Chen Gao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Moran Zhao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Qiang Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Juan Zhou
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
- Correspondence:
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16
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Du X, Guo J, Cao QY, Yao W, Li QF. A haplotype variant of Hu sheep follicle-stimulating hormone receptor promoter region decreases transcriptional activity. Anim Genet 2019; 50:407-411. [PMID: 31094009 DOI: 10.1111/age.12794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
Abstract
In sheep, increased expression of the follicle-stimulating hormone receptor (FSHR) in the ovary is a common feature of ewes that carry the prolific allele. In this study, we demonstrated that polymorphisms in the core promoter of the FSHR gene are associated with the reproductive performance of Hu sheep and are involved in the transcriptional activity of FSHR. An approximately 1.5-kb region of the 5' flanking sequence of the Hu sheep FSHR gene was isolated and characterized, and its core promoter was located in the 5' regulatory region, from nucleotides -580 to -342. Four variants (c.-518T>C, c.-466C>T, c.-414A>G and c.-365C>T) were detected in this region, and six genotypes and three haplotypes were found in the Hu sheep population (n = 245). An association analysis revealed that these polymorphisms are associated with the litter size of Hu ewes. Furthermore, a luciferase assay showed that the T-C-A-C- and C-T-G-T-type core promoters have higher transcriptional activity than does the T-C-G-C type. Notably, the putative binding site for the transcription factor Yin Yang 1 (YY1) was present at the A allele of nucleotide -414, but YY1 can significantly increase the transcriptional activity of the FSHR core promoter, which contains three different haplotypes. Taken together, our results establish that these variants might be involved in regulating the transcriptional activity of FSHR and litter size in Hu ewes and may provide a novel candidate marker for marker-assisted selection in sheep breeding.
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Affiliation(s)
- X Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - J Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Q Y Cao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - W Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Q F Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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Ma X, Li P, Zhang Q, He L, Su G, Huang Y, Lu Z, Hu W, Ding H, Huang R. Transcriptome analysis of the endometrium from Chinese Erhualian sows that differ in calcium ion concentration and litter size. Anim Genet 2019; 50:326-333. [PMID: 31058330 DOI: 10.1111/age.12788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2019] [Indexed: 12/31/2022]
Abstract
Embryonic survival rate, an important factor in the fecundity of sows, is affected by endometrium-secreting histotroph. A higher concentration of calcium ion has been observed in the uterus of highly prolific Erhualian sows (EH) compared with those of less prolific (EL) sows. This suggests that EH sows have better establishment and maintenance of pregnancies, thus increasing embryonic survival rate during the peri-implantation period. To understand the mechanisms of how the endometrium-secreting histotroph affects embryonic survival rate during the Erhualian peri-implantation period, the expression patterns of endometrial mRNA in the EH and EL sows on day 12 of gestation were analyzed using RNA sequencing technology. A total of 164 differentially expressed genes (DEGs) were identified (Padj < 0.05, |log2 (FC)| ≥ 1), including 46 upregulated and 118 downregulated genes in EH compared to EL. Gene Ontology enrichment indicated that a subset of DEGs was involved in calcium ion binding and cell adhesion. Solute carrier family 8 member A3 and solute carrier family 24 member 4, identified as upregulated genes (Padj < 0.05) in EH, were considered key candidate genes expressed in the endometrium affecting embryonic survival rate during the peri-implantation period. The results improve understanding of the genetic mechanism underlying the variation in litter size of Erhualian pigs during the peri-implantation period.
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Affiliation(s)
- X Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - P Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Q Zhang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - L He
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - G Su
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - Y Huang
- Changzhou Jiaoxi Cooperatives of Erhualian Pigs, Changzhou, 213116, China
| | - Z Lu
- Changshu Animal Husbandry and Veterinary Station, Suzhou, 215500, China
| | - W Hu
- Changshu Animal Husbandry and Veterinary Station, Suzhou, 215500, China
| | - H Ding
- Changshu Agriculture Committee, Suzhou, 215500, China
| | - R Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
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