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Liu C, Hou L, Zhao Q, Zhou W, Liu K, Liu Q, Zhou T, Xu B, Li P, Huang R. The selected genes NR6A1, RSAD2-CMPK2, and COL3A1 contribute to body size variation in Meishan pigs through different patterns. J Anim Sci 2023; 101:skad304. [PMID: 37703114 PMCID: PMC10548407 DOI: 10.1093/jas/skad304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023] Open
Abstract
The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.
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Affiliation(s)
- Chenxi Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Liming Hou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Qingbo Zhao
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Wuduo Zhou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiyue Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Tengbin Zhou
- Kunshan Animal Disease Prevention and Control Center, Suzhou 215000, China
| | - Binbin Xu
- Kunshan Meishan Pig Breeding Co., Ltd., Suzhou 215000, China
| | - Pinghua Li
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223001, China
| | - Ruihua Huang
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
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Kondo T, Inoue I, Umeyama K, Watanabe M, Matsunari H, Uchikura A, Nakano K, Tsukita K, Imamura K, Nagashima H, Inoue H. A Transgenic Pig Model With Human Mutant SOD1 Exhibits the Early Pathology of Amyotrophic Lateral Sclerosis. J Transl Med 2023; 103:100013. [PMID: 37039150 DOI: 10.1016/j.labinv.2022.100013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 01/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) causes progressive degeneration of the motor neurons. In this study, we delivered the genetic construct including the whole locus of human mutant superoxide dismutase 1 (SOD1) with the promoter region of human SOD1 into porcine zygotes using intracytoplasmic sperm injection-mediated gene transfer, and we thereby generated a pig model of human mutant SOD1-mediated familial ALS. The established ALS pig model exhibited an initial abnormality of motor neurons with accumulated misfolded SOD1. The ALS pig model, with a body size similar to that of human beings, will provide opportunities for cell and gene therapy platforms in preclinical translational research.
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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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Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis. Animals (Basel) 2022; 12:ani12141839. [PMID: 35883386 PMCID: PMC9312078 DOI: 10.3390/ani12141839] [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: 06/16/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023] Open
Abstract
This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.
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Jiayuan M, Yujie L, Kuirong C, Siran Z, Wenjing Q, Lingli F, Xiaoxiao L, Liang L, Ganqiu L, Jing L. Identifying selection signatures and runs of homozygosity for spine curvature in Chinese indigenous pigs. Anim Genet 2022; 53:513-517. [PMID: 35634679 DOI: 10.1111/age.13224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/03/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
Abstract
In China there are approximately 100 pig breeds, which show great diversity in their appearance. However, information on genome selection signatures, such as spine curvature, is scarce. Therefore, we used the fixation index (FST ) and cross-population extended haplotype homozygosity (XPEHH) methods to explore the genome selection signatures of spine curvature in six breeds of Chinese indigenous pig. We identified 396 and 389 single nucleotide polymorphisms using the FST and XPEHH methods, respectively. We detected 19 selection signatures and 28 genes located in the selected regions. Five candidate genes (MAP3K7, CUX1, GRIN2B, ALPL and MACF1) were identified in the selection signatures. Additionally, 719 high-frequency runs of homozygosity regions, 17 unique runs of homozygosity regions, 78 genes and 27 pathways were identified in the runs of homozygosity analysis. The TGF-beta signaling pathway and eight genes related to the spine formation, spine defects and intervertebral disk degeneration were identified, comprising ACVR1, FMOD, ITGA4, MAPK8, PDGF, RPL3, SULF1 and UBE2D1. In summary, we identified 13 candidate genes related to spine curvature in Chinese indigenous pigs.
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Affiliation(s)
- Mo Jiayuan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lu Yujie
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chen Kuirong
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhu Siran
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qi Wenjing
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Feng Lingli
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liu Xiaoxiao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liang Liang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lan Ganqiu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liang Jing
- College of Animal Science and Technology, Guangxi University, Nanning, China
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Li J, Peng S, Zhong L, Zhou L, Yan G, Xiao S, Ma J, Huang L. Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs. Genet Sel Evol 2021; 53:94. [PMID: 34906088 PMCID: PMC8670072 DOI: 10.1186/s12711-021-00689-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Carcass length is very important for body size and meat production for swine, thus understanding the genetic mechanisms that underly this trait is of great significance in genetic improvement programs for pigs. Although many quantitative trait loci (QTL) have been detected in pigs, very few have been fine-mapped to the level of the causal mutations. The aim of this study was to identify potential causal single nucleotide polymorphisms (SNPs) for carcass length by integrating a genome-wide association study (GWAS) and functional assays. Results Here, we present a GWAS in a commercial Duroc × (Landrace × Yorkshire) (DLY) population that reveals a prominent association signal (P = 4.49E−07) on pig chromosome 17 for carcass length, which was further validated in two other DLY populations. Within the detected 1 Mb region, the BMP2 gene stood out as the most likely causal candidate because of its functions in bone growth and development. Whole-genome gene expression studies showed that the BMP2 gene was differentially expressed in the cartilage tissues of pigs with extreme carcass length. Then, we genotyped an additional 267 SNPs in 500 selected DLY pigs, followed by further whole-genome SNP imputation, combined with deep genome resequencing data on multiple pig breeds. Reassociation analyses using genotyped and imputed SNP data revealed that the rs320706814 SNP, located approximately 123 kb upstream of the BMP2 gene, was the strongest candidate causal mutation, with a large association with carcass length, with a ~ 4.2 cm difference in length across all three DLY populations (N = 1501; P = 3.66E−29). This SNP segregated in all parental lines of the DLY (Duroc, Large White and Landrace) and was also associated with a significant effect on body length in 299 pure Yorkshire pigs (P = 9.2E−4), which indicates that it has a major value for commercial breeding. Functional assays showed that this SNP is likely located within an enhancer and may affect the binding affinity of transcription factors, thereby regulating BMP2 gene expression. Conclusions Taken together, these results suggest that the rs320706814 SNP on pig chromosome 17 is a putative causal mutation for carcass length in the widely used DLY pigs and has great value in breeding for body size in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00689-0.
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Affiliation(s)
- Jing Li
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Song Peng
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liepeng Zhong
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lisheng Zhou
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guorong Yan
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junwu Ma
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Fang J, Zhang D, Cao JW, Zhang L, Liu CX, Xing YP, Wang F, Xu HY, Wang SC, Ling Y, Wang W, Zhang YR, Zhou HM. Pathways involved in pony body size development. BMC Genomics 2021; 22:58. [PMID: 33461495 PMCID: PMC7814589 DOI: 10.1186/s12864-020-07323-1] [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: 03/02/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The mechanism of body growth in mammals is poorly understood. Here, we investigated the regulatory networks involved in body growth through transcriptomic analysis of pituitary and epiphyseal tissues of smaller sized Debao ponies and Mongolian horses at the juvenile and adult stages. RESULTS We found that growth hormone receptor (GHR) was expressed at low levels in long bones, although growth hormone (GH) was highly expressed in Debao ponies compared with Mongolian horses. Moreover, significant downregulated of the GHR pathway components m-RAS and ATF3 was found in juvenile ponies, which slowed the proliferation of bone osteocytes. However, WNT2 and PLCβ2 were obviously upregulated in juvenile Debao ponies, which led to premature mineralization of the bone extracellular matrix. Furthermore, we found that the WNT/Ca2+ pathway may be responsible for regulating body growth. GHR was demonstrated by q-PCR and Western blot analyses to be expressed at low levels in long bones of Debao ponies. Treatment with WNT antagonistI decreased the expression of WNT pathway components (P < 0.05) in vitro. Transduction of ATDC5 cells with a GHR-RNAi lentiviral vector decreased the expression of the GHR pathway components (P < 0.05). Additionally, the expression of the IGF-1 gene in the liver was lower in Debao ponies than in Mongolian horses at the juvenile and adult stages. Detection of plasma hormone concentrations showed that Debao ponies expressed higher levels of IGF-1 as juveniles and higher levels of GH as adults than Mongolian horses, indicating that the hormone regulation in Debao ponies differs from that in Mongolian horses. CONCLUSION Our work provides insights into the genetic regulation of short stature growth in mammals and can provide useful information for the development of therapeutic strategies for small size.
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Affiliation(s)
- Jun Fang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Dong Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Jun Wei Cao
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Li Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Chun Xia Liu
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Yan Ping Xing
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Feng Wang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Hong Yang Xu
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Shi Chao Wang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Yu Ling
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Wei Wang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China
| | - Yan Ru Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China.
| | - Huan Min Zhou
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018, China.
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Oyelami FO, Zhao Q, Xu Z, Zhang Z, Sun H, Zhang Z, Ma P, Wang Q, Pan Y. Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed. Front Genet 2020; 11:752. [PMID: 33101353 PMCID: PMC7498712 DOI: 10.3389/fgene.2020.00752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/23/2020] [Indexed: 11/19/2022] Open
Abstract
The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r2 > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched (p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms (p-value < 0.01), and 2 KEGG pathways (p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyang Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qishan Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
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Reimer C, Ha NT, Sharifi AR, Geibel J, Mikkelsen LF, Schlather M, Weigend S, Simianer H. Assessing breed integrity of Göttingen Minipigs. BMC Genomics 2020; 21:308. [PMID: 32299342 PMCID: PMC7161115 DOI: 10.1186/s12864-020-6590-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Göttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of stratification which might compromise the identity of the breed and its usability as an animal model for biomedical and human disease. We conducted whole genome re-sequencing of two DNA-pools per colony to assess genomic differentiation within and between colonies. We added publicly available samples from 13 various pig breeds and discovered overall about 32 M loci, ~ 16 M. thereof variable in GMPs. Individual samples were virtually pooled breed-wise. FST between virtual and DNA pools, a phylogenetic tree, principal component analysis (PCA) and evaluation of functional SNP classes were conducted. An F-test was performed to reveal significantly differentiated allele frequencies between colonies. Variation within a colony was quantified as expected heterozygosity. RESULTS Phylogeny and PCA showed that the GMP is easily discriminable from all other breads, but that there is also differentiation between the GMP colonies. Dependent on the contrast between GMP colonies, 4 to 8% of all loci had significantly different allele frequencies. Functional annotation revealed that functionally non-neutral loci are less prone to differentiation. Annotation of highly differentiated loci revealed a couple of deleterious mutations in genes with putative effects in the GMPs . CONCLUSION Differentiation and annotation results suggest that the underlying mechanisms are rather drift events than directed selection and limited to neutral genome regions. Animal exchange seems not yet necessary. The Relliehausen colony appears to be the genetically most unique GMP sub-population and could be a valuable resource if animal exchange is required to maintain uniformity of the GMP.
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Affiliation(s)
- Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Ngoc-Thuy Ha
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Ahmad Reza Sharifi
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | | | - Martin Schlather
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Institute of Mathematics, University of Mannheim, B6 26, 68131 Mannheim, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Institute of Farm Animal Genetics of the Friedrich-Loeffler-Institut, Höltystraße 10, 31535 Neustadt, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
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Li X, Ye J, Han X, Qiao R, Li X, Lv G, Wang K. Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs. Genomics 2019; 112:199-206. [PMID: 30707936 DOI: 10.1016/j.ygeno.2019.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/05/2019] [Accepted: 01/22/2019] [Indexed: 11/24/2022]
Abstract
Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5, BMP6, BMP7, ACVR1, INHBA, ZFYVE9, TGFBR2, DCN, ID4, BAMBI, and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9, SLC39A11, SNCA, and UNC5D are candidate genes for reproduction traits.
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Affiliation(s)
- Xinjian Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Jianwei Ye
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xuelei Han
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Ruimin Qiao
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xiuling Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Gang Lv
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China.
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