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Zhou Q, Hu H, Yang Y, Kang Y, Lan X, Wu X, Guo Z, Pan C. Insertion/deletion (Indel) variant of the goat RORA gene is associated with growth traits. Anim Biotechnol 2023; 34:2175-2182. [PMID: 35622416 DOI: 10.1080/10495398.2022.2078980] [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
RAR related orphan receptor A (RORA), which encodes the retinoid-acid-related orphan receptor alpha (RORα), is a clock gene found in skeletal muscle. Several studies have shown that RORα plays an important role in bone formation, suggesting that RORA gene may take part in the regulation of growth and development. The purpose of this research is to study the insertion/deletion (indel) variations of the RORA gene and investigate the relationship with the growth traits of Shaanbei white cashmere (SBWC) goats. Herein, the current study identified that the P4-11-bp and P11-28-bp deletion sites are polymorphic among 12 pairs of primers within the RORA gene in the SBWC goats (n = 641). Moreover, the P11-28-bp deletion locus was significantly related to the body height (p = 0.046), height at hip cross (p = 0.012), and body length (p = 0.003). Both of P4-11-bp and P11-28-bp indels showed the moderate genetic diversity (0.25
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Affiliation(s)
- Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huina Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Zhengang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Animal Husbandry and Veterinary Science Institute of Bijie city, Bijie, Guizhou, China
| | - Chuanying Pan
- 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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Gao J, Song X, Wu H, Tang Q, Wei Z, Wang X, Lan X, Zhang B. Detection of rs665862918 (15-bp Indel) of the HIAT1 Gene and its Strong Genetic Effects on Growth Traits in Goats. Animals (Basel) 2020; 10:ani10020358. [PMID: 32102183 PMCID: PMC7070599 DOI: 10.3390/ani10020358] [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: 01/12/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Growth traits are important in goats and can affect their body size and meat production. In this study, the hippocampus abundant transcript 1 (HIAT1) gene, which has been reported as a meat-associated trait in elite goat breeds and a dairy-associated trait in water buffalo, was chosen to detect its correlation with growth traits in goats. The results show that the rs665862918 polymorphism (a 15 bp insertion) in HIAT1 is associated with body length, chest width, chest depth, height at hip cross and heart girth in Shaanbei white cashmere goats (SBWC, n = 1013). Our results reveal that rs665862918 in HIAT1 is relevant to the growth traits of goats and could be used for marker-assisted selection (MAS) as a molecular marker in goat populations. Abstract The hippocampus abundant transcript 1 (HIAT1) gene, which was detected by the genome-wide identification of selective sweeps among elite goat breeds and water buffalo, is proposed to play an important role in meat characteristics. Four indels of the HIAT1 gene selected from the NCBI and Ensembl databases were detected via a pooling and sequencing strategy. A 15 bp insertion (rs665862918) in the first intron of HIAT1 was selected and classified on an electrophoresis platform in the Shaanbei white cashmere goat (SBWC) population. The correlation analysis revealed that rs665862918 is significantly highly associated with chest width (p = 1.57 × 10−5), chest depth (p = 8.85 × 10−5), heart girth (p = 1.05 × 10−7), body length (p = 0.022), and height at hip cross (p = 0.023) in the SBWC population (n = 1013). Further analysis revealed that individuals with a genotype insertion/insertion (II) of the rs665862918 locus exhibited better growth trait performance than individuals with an insertion/deletion (ID) or deletion/deletion (DD). These findings verify that HIAT1 affects the body size of goats and that rs665862918 could be a potential molecular marker for growth traits in goat breeding.
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Affiliation(s)
- Jiayang Gao
- College of Medicine & Forensic, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China;
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, Shaanxi, China;
- Life Science Research Center, Yulin University, Yulin 719000, Shaanxi, China
| | - Hui Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Qi Tang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Zhenyu Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xinyu Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
- Correspondence: (X.L.); (B.Z.)
| | - Bao Zhang
- College of Medicine & Forensic, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China;
- Correspondence: (X.L.); (B.Z.)
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Li WY, Liu Y, Gao CF, Lan XY, Wu XF. A novel duplicated insertion/deletion (InDel) of the CPT1a gene and its effects on growth traits in goat. Anim Biotechnol 2019; 32:343-351. [PMID: 31809636 DOI: 10.1080/10495398.2019.1698433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Carnitine palmitoyltransferase 1a (CPT1a) is a rate-limited enzyme in the mitochondrial fatty acid β-oxidation pathway. It acts as a bridge between PPARα and the fatty acid oxidation pathways and is closely related to ruminant growth and development. In this study, one 12 bp InDel polymorphism of the CPT1a gene was identified in 700 goats, and we designated these three genotypes II, ID, and DD. Association analysis showed that the InDel polymorphism was closely associated with trunk index (p = 0.008) and body length index (p = 0.034) in Hainan black goats, and body length (p = 0.010), chest circumference (p = 0.004), chest depth (p = 0.029), and huckle bone width (p = 0.002) in Nubian goats, as well as the chest circumference (p = 0.016) in the Fuqing goat breed. In both kids and adult goats, qRT-PCR results showed that the CPT1a gene was expressed in all tissues, showing the highest mRNA levels in the liver, lung, spleen, and kidney, followed by the adipose tissue and brain. This indicates an association between the InDel of the CPT1a gene and growth traits in selected goat breeds, which may facilitate marker-assisted selection in goat genetics and breeding.
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Affiliation(s)
- Wen-Yang Li
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Yuan Liu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Chen-Fang Gao
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xian-Feng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
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Jiang E, Kang Z, Wang X, Liu Y, Liu X, Wang Z, Li X, Lan X. Detection of insertions/deletions (InDels) within the goat Runx2 gene and their association with litter size and growth traits. Anim Biotechnol 2019; 32:169-177. [PMID: 31591922 DOI: 10.1080/10495398.2019.1671858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Runt-related transcription factor 2 (Runx2) is characterized by its critical functions in osteoblastic and ovulatory processes. The goal of this study was to explore the insertion/deletion (indel) variants of this gene and to evaluate their association with productive traits. Herein, a 12 bp and 6 bp insertion within the Runx2 gene was uncovered in Shaanbei white cashmere goats (SBWC; n = 1200). Chi-square analysis revealed that the 12 bp insertion was related to litter size (p < 0.01). Further association analysis also found this insertion was significantly associated with litter size (p = 1.1E-5). Interestingly, this insertion was also significantly associated with chest circumference (p = 0.018). Additionally, the 6 bp insertion was associated with body length (p = 0.003), chest width (p = 0.011), and chest circumference (p = 0.005). Furthermore, diplotype associations also uncovered that the combined genotypes of these two indels also significantly affected litter size and growth traits (p < 0.05). These findings suggested that these two insertions within the Runx2 gene were significantly associated with reproduction and growth traits, which would make them beneficial functional DNA markers that can be used in goat breeding.
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Affiliation(s)
- Enhui Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,College of Animal Science and Technology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zihong Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuan Liu
- College of Animal Science and Technology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Xinfeng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangchen Li
- College of Animal Science and Technology, Zhejiang A&F University, Hangzhou, Zhejiang, 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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Zhang S, Zhao H, Lei C, Pan C, Chen H, Lin Q, Lan X. Effects of genetic variations within goat PITX2 gene on growth traits and mRNA expression. Anim Biotechnol 2019; 31:107-114. [PMID: 30652937 DOI: 10.1080/10495398.2018.1551229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Paired-like homeodomain 2 (PITX2), a key gene in hypothalamic-pituitary-adrena axis, influences animal growth and development. The objective of this study was to identify the association of the functional genetic variations within goat PITX2 gene with growth traits and mRNA expression levels. According to the reported single nucleotide polymorphisms (SNPs) information in Guanzhong dairy goat (GZDG), we identified genotypes of the known SNPs in Hainan black goat (HNBG). Association analysis uncovered that the SNPs of AC_000163: g.18117T > C, g.18161C > G and g.18353T > C loci were significantly associated with several growth traits (e.g., body height and body length) in HNBG and GZDG breeds. According to the quantitative real-time PCR assay, β-Actin and ribosomal protein L19 (RPL19) were the most stable expressed housekeeping genes in heart and skeletal muscle, respectively; meanwhile, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the most stable expressed housekeeping gene in the other tissues. Based on the best housekeeping gene of varied tissues, we found the different genotypes of above loci were significantly associated with PITX2 mRNA expression in heart, muscle and small intestine. Briefly, the genetic variants of goat PITX2 associating with mRNA expression affected growth traits significantly, which would benefit for goat breeding in the future.
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Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Haiyu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qing Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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