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Yuan Y, Zhang WY, Yang BG, Zhou DK, Xu L, He YM, Zhang HY, Liu CL, Ma YH, Chu MX, Zhang WG, Gao HJ, Jiang L, Zhao FP, Zhang LP, Na RS, Oyungerel B, Han YG, Zeng Y, Wang SZ, Jiang HZ, Zhang HP, Jiang XP, He JN, Liang H, Kaushalendra K, Sun YW, Huang YF, Zhao YJ, Zhao ZQ, E GX, Zhao ZQ, E GX. A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats. Zool Res 2023; 44:303-314. [PMID: 36785897 PMCID: PMC10083219 DOI: 10.24272/j.issn.2095-8137.2022.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The Boer goat is one of the top meat breeds in modern animal husbandry and has attracted widespread attention for its unique growth performance. However, the genetic basis of muscle development in the Boer goat remains obscure. In this study, we identified specific structural variants in the Boer goat based on genome-wide selection signals and analyzed the basis of the molecular heredity of related candidate genes in muscle development. A total of 9 959 autosomal copy number variations (CNVs) were identified through selection signal analysis in 127 goat genomes. Specifically, we confirmed that the highest signal CNV (HSV) was a chromosomal arrangement containing an approximately 1.11 Mb (CHIR17: 60062304-61171840 bp) duplicated fragment inserted in reverse orientation and a 5 362 bp deleted region (CHIR17:60145940-60151302 bp) with overlapping genes (e.g., ARHGAP10, NR3C2, EDNRA, PRMT9, and TMEM184C). The homozygous duplicated HSV genotype (+/+) was found in 96% of Boer goats but was not detected in Eurasian goats and was only detected in 4% of indigenous African goats. The expression network of three candidate genes ( ARHGAP10, NR3C2, and EDNRA) regulating dose transcription was constructed by RNA sequencing. Results indicated that these genes were involved in the proliferation and differentiation of skeletal muscle satellite cells (SMSCs) and their overexpression significantly increased the expression of SAA3. The HSV of the Boer goat contributed to superior skeletal muscle growth via the dose effects of overlapping genes.
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Affiliation(s)
- Ying Yuan
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Wei-Yi Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Dong-Ke Zhou
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Lu Xu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yong-Meng He
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Hao-Yuan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Cheng-Li Liu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ming-Xing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wen-Guang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, China
| | - Hui-Jiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Fu-Ping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lu-Pei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ri-Su Na
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, China
| | - Baatarchogt Oyungerel
- School of Animal Science & Biotechnology, Mongolian University of Life Sciences, Zaisan, Khan-uul, Ulaanbaatar 17024, Mongolia
| | - Yan-Guo Han
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yan Zeng
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Shi-Zhi Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Huai-Zhi Jiang
- Animal Science and Technology College, Jilin Agriculture University, Changchun, Jilin 130118, China
| | - Hong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xun-Ping Jiang
- Key Lab of Agricultural Animal, Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong, Agricultural University, Wuhan, Hubei 430070, China
| | - Jian-Ning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Hao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China
| | | | - Ya-Wang Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Guang-Xin E
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China. E-mail:
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E GX, Zhou DK, Zheng ZQ, Yang BG, Li XL, Li LH, Zhou RY, Nai WH, Jiang XP, Zhang JH, Hong QH, Ma YH, Chu MX, Gao HJ, Zhao YJ, Duan XH, He YM, Na RS, Han YG, Zeng Y, Jiang Y, Huang YF. Identification of a Goat Intersexuality-Associated Novel Variant Through Genome-Wide Resequencing and Hi-C. Front Genet 2021; 11:616743. [PMID: 33633772 PMCID: PMC7901718 DOI: 10.3389/fgene.2020.616743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Polled intersex syndrome (PIS) leads to reproductive disorders in goats and exerts a heavy influence on goat breeding. Since 2001, the core variant of an 11.7 kb deletion at ~129 Mb on chromosome 1 (CHI1) has been widely used as a genetic diagnostic criterion. In 2020, a ~0.48 Mb insertion within the PIS deletion was identified by sequencing in XX intersex goats. However, the suitability of this variation for the diagnosis of intersex goats worldwide and its further molecular genetic mechanism need to be clarified. Results: The whole-genome selective sweep of intersex goats from China was performed with whole-genome next-generation sequencing technology for large sample populations and a case–control study on interbreeds. A series of candidate genes related to the goat intersexuality phenotype were found. We further confirmed that a ~0.48 Mb duplicated fragment (including ERG and KCNJ15) downstream of the ~20 Mb PIS region was reversely inserted into the PIS locus in intersex Chinese goats and was consistent with that in European Saanen and Valais black-necked goats. High-throughput chromosome conformation capture (Hi-C) technology was then used to compare the 3D structures of the PIS variant neighborhood in CHI1 between intersex and non-intersex goats. A newly found structure was validated as an intrachromosomal rearrangement. This inserted duplication changed the original spatial structure of goat CHI1 and caused the appearance of several specific loop structures in the adjacent ~20 kb downstream region of FOXL2. Conclusions: Results suggested that the novel complex PIS variant genome was sufficient as a broad-spectrum clinical diagnostic marker of XX intersexuality in goats from Europe and China. A series of private dense loop structures caused by segment insertion into the PIS deletion might affect the expression of FOXL2 or other neighboring novel candidate genes. However, these structures require further in-depth molecular biological experimental verification. In general, this study provided new insights for future research on the molecular genetic mechanism underlying female-to-male sex reversal in goats.
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Affiliation(s)
- Guang-Xin E
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Dong-Ke Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhu-Qing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bai-Gao Yang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiang-Long Li
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinghuangdao, China
| | - Lan-Hui Li
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China
| | - Rong-Yan Zhou
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China
| | - Wen-Hui Nai
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xun-Ping Jiang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia-Hua Zhang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qiong-Hua Hong
- Department of Herbivore Science, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ming-Xing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hui-Jiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yong-Ju Zhao
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xing-Hai Duan
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Meng He
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ri-Su Na
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan-Guo Han
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Zeng
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong-Fu Huang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
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E GX, Chen LP, Zhou DK, Yang BG, Zhang JH, Zhao YJ, Hong QH, Ma YH, Chu MX, Zhang LP, Basang WD, Zhu YB, Han YG, Na RS, Zeng Y, Zhao ZQ, Huang YF, Han JL. Evolutionary relationship and population structure of domestic Bovidae animals based on MHC-linked and neutral autosomal microsatellite markers. Mol Immunol 2020; 124:83-90. [PMID: 32544655 DOI: 10.1016/j.molimm.2020.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 11/26/2022]
Abstract
Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise FST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean FST was significantly correlated negatively with the number of observed alleles (NA), observed (HO) and expected (HE) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean FST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity.
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Affiliation(s)
- Guang-Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Li-Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Dong-Ke Zhou
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Bai-Gao Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Jia-Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Qiong-Hua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Yue-Hui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ming-Xing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lu-Pei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Bin Zhu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Science (TAAAS)), Lhasa 850002, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Ri-Su Na
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yan Zeng
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Zhong-Quan Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivores, Chongqing Engineering Research Centre for Herbivore Resource Protection and Utilization, Southwest University, Chongqing 400716, China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
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Wang WL, Wu ZH, Sun Q, Wei JF, Chen XF, Zhou DK, Zhou L, Xie HY, Zheng SS. Meta-analysis: the use of carbon dioxide insufflation vs. room air insufflation for gastrointestinal endoscopy. Aliment Pharmacol Ther 2012; 35:1145-54. [PMID: 22452652 DOI: 10.1111/j.1365-2036.2012.05078.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 09/13/2011] [Accepted: 03/07/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Carbon dioxide (CO(2)) insufflation has been proposed as an alternative to air insufflation to distend the lumen in gastrointestinal (GI) endoscopy. AIM To perform a systematic review with meta-analysis of randomised controlled trials (RCTs) in which CO(2) insufflation was compared with room air insufflation in GI endoscopy. METHODS Electronic and manual searches were combined to search RCTs. After methodological quality assessment and data extraction, the efficacy and safety of CO(2) insufflation were systematically assessed. RESULTS Twenty-one RCTs [13 on colonoscopy, four on endoscopic retrograde cholangiopancreatography (ERCP), two on double-balloon enteroscopy (DBE), one on oesophagogastroduodenoscopy, and one on flexible sigmoidoscopy] were identified. For colonoscopy, CO(2) insufflation resulted lower postprocedural pain intensity, and increased the proportion of patient without pain at 1 h (RR: 1.84, 95% CI: 1.37-2.47) and 6 h (RR: 1.28; 95% CI: 1.14-1.44) postprocedure. For ERCP, the pain-releasing effect of CO(2) insufflation was not obvious (SMD: -1.48, 95% CI: -3.56, 0.59). CO(2) insufflation revealed no consistent advantages in the RCTs of DBE, but was shown as safe as air insufflation in oesophagus/stomach endoscopic submucosal dissection in one study. pCO(2) level showed no significant variation during these procedures. CONCLUSIONS Compared with air insufflation, CO(2) insufflation during colonoscopy causes lower postprocedural pain and bowel distension without significant pCO(2) variation. More RCTs are needed to assess its advantages in other GI endoscopic procedures.
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Affiliation(s)
- W L Wang
- Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, China
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