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Yang C, He J, Mao J, Ren Y, Liu G, Wei C, Zhang G, Tian K, Huang X. Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats. Genes (Basel) 2024; 15:353. [PMID: 38540412 PMCID: PMC10970512 DOI: 10.3390/genes15030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.
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Affiliation(s)
- Cunming Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Junmin He
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Jingyi Mao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Yifan Ren
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Chen Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guoping Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
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Wijayanti D, Zhang S, Bai Y, Pan C, Chen H, Qu L, Guo Z, Lan X. Investigation on mRNA expression and genetic variation within goat SMAD2 gene and its association with litter size. Anim Biotechnol 2023; 34:2111-2119. [PMID: 35584800 DOI: 10.1080/10495398.2022.2077214] [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] [Indexed: 11/01/2022]
Abstract
The SMAD family member 2 (SMAD2), a member of the TGF-beta superfamily, executes a significant part in the oogenesis and ovulation process. A genome-wide selective sweep analysis also found SMAD2 was different in the fertility groups of Laoshan dairy goats; whether this gene was linked to litter size was unknown. Therefore, SMAD2 was chosen to study its effects on Shaanbei white cashmere goat reproduction and mRNA expression profile. Herein, the mRNA expression level of SMAD2 was firstly determined in female goat tissues, revealing significant differences in mRNA levels of different tissues (p < 0.05), including ovary tissue, indicating a potential role for SMAD2 in goat prolificacy. Then, using six pairs of primers, only one indel locus (P3-Del-12-bp) was found to be polymorphic in goat SMAD2 (n = 501). ANOVA also revealed that a P3-Del-12-bp deletion was significantly related to first-born litter size (p = 0.037). The Chi-square (χ2) test revealed that the ID genotype was significantly more prevalent in mothers with multiple lambs (p = 0.01), indicating that heterozygous individuals (ID) are more likely to produce multiple lambs. Our findings suggest that the SMAD2 gene's P3-Del-12-bp deletion could be used to improve goat breeds by assisting with litter size selection.
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Affiliation(s)
- Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, Indonesia
| | - Sihuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Mi F, Wu X, Wang Z, Wang R, Lan X. Relationships between the Mini-InDel Variants within the Goat CFAP43 Gene and Body Traits. Animals (Basel) 2022; 12:ani12243447. [PMID: 36552367 PMCID: PMC9774114 DOI: 10.3390/ani12243447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The cilia- and flagella-associated protein 43 (CFAP43) gene encodes a member of the cilia- and flagellum-associated protein family. Cilia on the cell surface influence intercellular signaling and are involved in biological processes such as osteogenesis and energy metabolism in animals. Previous studies have shown that insertion/deletion (InDel) variants in the CFAP43 gene affect litter size in Shaanbei white cashmere (SBWC) goats, and that litter size and body traits are correlated in this breed. Therefore, we hypothesized that there is a significant relationship between InDel variants within the CFAP43 gene and body traits in SBWC goats. Herein, we first investigated the association between three InDel variant loci (L-13, L-16, and L-19 loci) within CFAP43 and body traits in SBWC goats (n = 1827). Analyses revealed that the L-13, L-16, and L-19 loci were significantly associated with chest depth, four body traits, and three body traits, respectively. The results of this study are in good agreement with those previously reported and could provide useful molecular markers for the selection and breeding of goats for body traits.
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Affiliation(s)
- Fang Mi
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350000, China
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350000, China
- Correspondence: (X.W.); (X.L.)
| | - Zhen Wang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Ruolan Wang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
- Correspondence: (X.W.); (X.L.)
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