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Li Y, Shi R, Yuan R, Jiang Y. Comprehensive transcriptional analysis of pig facial skin development. PeerJ 2023; 11:e15955. [PMID: 37663277 PMCID: PMC10470455 DOI: 10.7717/peerj.15955] [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: 05/16/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Background Skin development is a complex process that is influenced by many factors. Pig skin is used as an ideal material for xenografts because it is more anatomically and physiologically similar to human skin. It has been shown that the skin development of different pig breeds is different, and some Chinese pig breeds have the characteristics of skin thickness and facial skin folds, but the specific regulatory mechanism of this skin development is not yet clear. Methods In this study, the facial skin of Chenghua sows in the four developmental stages of postnatal Day 3 (D3) , Day 90 (D90) , Day 180 (D180), and Year 3 (Y3) were used as experimental materials, and RNA sequencing (RNA-seq) analysis was used to explore the changes in RNA expression in skin development at the four developmental stages, determine the differentially expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), and perform functional analysis of related genes by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results A pairwise comparison of the four developmental stages identified several differentially expressed genes (DEGs) and found that the number of differentially expressed RNAs (DE RNAs) increased with increasing developmental time intervals. Elastin (ELN) is an important component of the skin. Its content affects the relaxation of the epidermis and dermal connection, and its expression is continuously downregulated during the four developmental stages. The functions of DEGs at different developmental stages were examined by performing GO and KEGG analyses, and the GO terms and enrichment pathways of mRNAs, lncRNAs, miRNAs, and circRNAs highly overlapped, among which the PPAR signaling pathway, a classical pathway for skin development, was enriched by DEGs of D3 vs. D180, D90 vs. D180 and D180 vs. Y3. In addition, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA interaction networks and found genes that may be associated with skin development, but their interactions need further study. Conclusions We identified a number of genes associated with skin development, performed functional analyses on some important DEGs and constructed interaction networks that facilitate further studies of skin development.
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Affiliation(s)
- Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
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2
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Zhou C, Cheng X, Meng F, Wang Y, Luo W, Zheng E, Cai G, Wu Z, Li Z, Hong L. Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs. BMC Genomics 2023; 24:412. [PMID: 37488487 PMCID: PMC10364396 DOI: 10.1186/s12864-023-09414-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/29/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND One of the most critical periods for the loss of pig embryos is the 12th day of gestation when implantation begins. Recent studies have shown that non-coding RNAs (ncRNAs) play important regulatory roles during pregnancy. Circular RNAs (circRNAs) are a kind of ubiquitously expressed ncRNAs that can directly regulate the binding proteins or regulate the expression of target genes by adsorbing micro RNAs (miRNA). RESULTS We used the Illumina Novaseq6,000 technology to analyze the circRNA expression profile in the endometrium of three Erhualian (EH12) and three Yorkshire (YK12) pigs on day 12 of gestation. Overall, a total of 22,108 circRNAs were identified. Of these, 4051 circRNAs were specific to EH12 and 5889 circRNAs were specific to YK12, indicating a high level of breed specificity. Further analysis showed that there were 641 significant differentially expressed circRNAs (SDEcircRNAs) in EH12 compared with YK12 (FDR < 0.05). Functional enrichment of differential circRNA host genes revealed many pathways and genes associated with reproduction and regulation of embryo development. Network analysis of circRNA-miRNA interactions further supported the idea that circRNAs act as sponges for miRNAs to regulate gene expression. The prediction of differential circRNA binding proteins further explored the potential regulatory pathways of circRNAs. Analysis of SDEcircRNAs suggested a possible reason for the difference in embryo survival between the two breeds at the peri-implantation stage. CONCLUSIONS Together, these data suggest that circRNAs are abundantly expressed in the endometrium during the peri-implantation period in pigs and are important regulators of related genes. The results of this study will help to further understand the differences in molecular pathways between the two breeds during the critical implantation period of pregnancy, and will help to provide insight into the molecular mechanisms that contribute to the establishment of pregnancy and embryo loss in pigs.
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Affiliation(s)
- Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Xinyan Cheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China
| | - Yongzhong Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Wanyun Luo
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China
- Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China
- Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China
- Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China.
- Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China.
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China.
- Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China.
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Yin S, Song G, Gao N, Gao H, Zeng Q, Lu P, Zhang Q, Xu K, He J. Identifying Genetic Architecture of Carcass and Meat Quality Traits in a Ningxiang Indigenous Pig Population. Genes (Basel) 2023; 14:1308. [PMID: 37510213 PMCID: PMC10378861 DOI: 10.3390/genes14071308] [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: 05/11/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Ningxiang pig is a breed renowned for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 min and 24 h) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30~0.80) for carcass traits and from low to high (0.11~0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the GRM4 gene emerged as a pleiotropic gene that correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold the potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Gang Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Hu Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Peng Lu
- Center of Ningxiang Animal Husbandry and Fishery Affairs, Ningxiang 410625, China
| | - Qin Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- College of Animal Science and Technology, China Agricultural University, Beijing 100091, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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Fu M, Zhou X, Liu Z, Wang T, Liu B. Genome-wide association study reveals a genomic region on SSC7 simultaneously associated with backfat thickness, skin thickness and carcass length in a Large White × Tongcheng advanced generation intercross resource population. Anim Genet 2023; 54:216-219. [PMID: 36511585 DOI: 10.1111/age.13285] [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: 01/19/2022] [Revised: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
In order to identify important genetic markers associated with backfat thickness, skin thickness and carcass length, we first constructed Large White × Tongcheng (Chinese local breed), an advanced generation intercross population, then performed a genome-wide association study (GWAS) to reveal the key genomic region associated with these traits through whole genome sequencing. The GWAS results of backfat thickness, skin thickness and carcass length showed that all the most significant SNPs associated with these three traits were located on SSC7, and that 14.9, 27.0 and 21.1% of phenotypic variances were explained by these three SNPs, respectively. Through linkage disequilibrium analysis, we found that a 66.9 kb (30.23-30.31 Mb) genetic region was overlapped among these three traits, and that NUDT3 and HMGA1 were identified as major candidate genes for backfat thickness and carcass length, and GRM4 as a potential candidate gene for skin thickness. In addition, 13 highly linked SNPs significantly associated with the three traits were also identified in overlapped region, and three completely linked SNPs formed two haplotypes Q and q. The backfat thickness of individuals with the qq genotype was significantly lower than that of individuals with the QQ genotype, but their carcass length and skin thickness were significantly higher than those with the QQ genotype. Our detected candidate genes and SNPs will provide the foundation for genetic improvement of these three traits.
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Affiliation(s)
- Ming Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement, Wuhan, China
| | - Zuhong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Tengfei Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement, Wuhan, China
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Tan X, Liu L, Liu X, Cui H, Liu R, Zhao G, Wen J. Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens. Genes (Basel) 2021; 13:genes13010003. [PMID: 35052342 PMCID: PMC8774586 DOI: 10.3390/genes13010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.
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Affiliation(s)
- Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
| | - Lu Liu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311302, China;
| | - Xiaojing Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.T.); (X.L.); (H.C.); (R.L.); (G.Z.)
- Correspondence:
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Liu H, Wang L, Guo Z, Xu Q, Fan W, Xu Y, Hu J, Zhang Y, Tang J, Xie M, Zhou Z, Hou S. Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks. Genet Sel Evol 2021; 53:98. [PMID: 34930109 PMCID: PMC8690979 DOI: 10.1186/s12711-021-00684-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 12/30/2022] Open
Abstract
Background As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks. Results Feed conversation ratio (FCR) was positively correlated with feed intake but negatively correlated with egg-related traits, including egg weight and egg production, both phenotypically and genetically. Estimates of pedigree-based heritability were higher than 0.2 for all traits investigated, except hip-width. Based on whole-genome sequencing data, we conducted genome-wide association studies to identify genomic regions associated with these traits. In total, 11 genomic regions were associated with FCR. No genomic regions were identified as significantly associated with hip-width, total feed intake, average daily feed intake, and total egg production. Analysis of selective sweeps between mallard and Pekin ducks confirmed three of these genomic regions on chromosomes 13, 3 and 6. Within these three regions, variants in candidate genes that were in linkage disequilibrium with the GWAS leader single nucleotide polymorphisms (SNPs) (Chr13:2,196,728, P = 7.05 × 10–14; Chr3:76,991,524, P = 1.06 × 10–12; Chr6:20,356,803, P = 1.14 × 10–10) were detected. Thus, we identified 31 potential candidate genes associated with FCR, among which the strongest candidates are those that are highly expressed in tissues involved in reproduction and nervous system functions of ducks: CNTN4, CRBR, GPR63, KLHL32, FHL5, TRNT1, MANEA, NDUFAF4, and SCD. Conclusions For the first time, we report the identification of genomic regions that are associated with FCR in ducks and our results illustrate the genomic changes that occurred during their domestication and are involved in egg production efficiency. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00684-5.
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Affiliation(s)
- Hehe Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Zhanbao Guo
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Wenlei Fan
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yaxi Xu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Hu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunsheng Zhang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ming Xie
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhengkui Zhou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Xiaoli L, Fengbin H, Shihui H, Xi N, Sheng L, Zhou W, Xueqin R, Jiafu W. Detection of genomic structure variants associated with wrinkled skin in Xiang pig by next generation sequencing. Aging (Albany NY) 2021; 13:24710-24739. [PMID: 34837693 PMCID: PMC8660620 DOI: 10.18632/aging.203711] [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: 12/30/2020] [Accepted: 08/02/2021] [Indexed: 11/25/2022]
Abstract
Wrinkling is prominent manifestation of aging skin. A mutant phenotype characterized by systemic wrinkles and thickened skin was discovered in Xiang pig populations with incidence about 1-3%. The feature in histological structure was epidermal hyperplasia and thickening, collagen fibers disorder. To uncover genetic mechanisms for the mutant phenotype of Xiang pigs with systemic wrinkle (WXP), a genome-wide of structural variations (SVs) in WXP was described by next generation resequencing, taking Xiang pigs (XP) and European pigs (EUP) as compares. Total of 32,308 SVs were detected from three pig groups and 965 SVs were identified specifically from WXP, involving 481 protein-coding genes. These genes were mainly enriched in nuclear structure, ECM components and immunomodulatory pathways. According to gene function and enrichment analysis, we found that 65 candidate SVs in 59 protein genes were probably related with the systemic wrinkle of WXP. Of these, several genes are reported to be associate with aging, such as EIF4G2, NOLC1, XYLT1, FUT8, MDM2 and so on. The insertion/deletion and duplication variations of SVs in these genes resulted in the loss of stop-codon or frameshift mutation, and aberrant alternative splicing of transcripts. These genes are involved in cell lamin filament, intermediate filament cytoskeleton, supramolecular complex, cell differentiation and regulation of macromolecule metabolic process etc. Our study suggested that the loss of function or aberrant expression of these genes lead to structural disorder of nuclear and the extracellular matrix (ECM) in skin cells, which probably was the genetic mechanisms for the mutant phenotype of systemic skin wrinkle of Xiang pig.
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Affiliation(s)
- Liu Xiaoli
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Hu Fengbin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Huang Shihui
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Niu Xi
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Li Sheng
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Zhou
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Ran Xueqin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Jiafu
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
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8
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Guo L, Sun H, Zhao Q, Xu Z, Zhang Z, Liu D, Qadri QR, Ma P, Wang Q, Pan Y. Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data. Anim Genet 2021; 52:143-154. [PMID: 33458851 DOI: 10.1111/age.13034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.
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Affiliation(s)
- L Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - D Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q R Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
| | - Y Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
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Huang Y, Zhou L, Zhang J, Liu X, Zhang Y, Cai L, Zhang W, Cui L, Yang J, Ji J, Xiao S, Ai H, Chen C, Ma J, Yang B, Huang L. A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds. Meat Sci 2020; 168:108182. [DOI: 10.1016/j.meatsci.2020.108182] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 01/26/2023]
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