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Wu XF, Liu Y, Wang YG, Zhang F, Li WY. A novel 22-bp InDel within FGF7 gene is significantly associated with growth traits in goat. Anim Biotechnol 2024; 35:2262537. [PMID: 37870116 DOI: 10.1080/10495398.2023.2262537] [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: 10/24/2023]
Abstract
Fibroblast growth factor 7 (FGF7) is involved in lipid metabolism, which is considered as a candidate gene with close relation with muscle development by eGWAs and RNA-Seq analyses. To date, limited research has been conducted on the relationship between FGF7 gene and growth traits. The main objective of this work was to further investigate the association between novel InDel within FGF7 gene and growth traits in goat. Herein, FGF7 mRNA expression levels were investigated in various Fuqing goat tissues. We found that FGF7 gene was expressed in six adult goat tissues with the highest mRNA levels in adipose tissue. This result suggested that FGF7 gene might play a critical role in fat deposition. We also detected potential polymorphisms in Fuqing, Nubian and Jianyang Daer breeds. A 22-bp InDel polymorphism in FGF7 gene was detected in 396 goats and the three genotypes were designated as II, ID, and DD. Correlation analysis revealed that InDel polymorphism was significantly associated with growth traits (P < 0.05). Goats with genotypes ID and/or II had superior growth traits compared to those with genotype DD. In summary, our findings suggested that the 22-bp InDel within FGF7 gene could act as a molecular marker to improve the growth traits of goats in breeding programs.
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Affiliation(s)
- Xian-Feng Wu
- Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Yuan Liu
- Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Ying-Gang Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fu Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wen-Yang Li
- Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
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2
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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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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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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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Yang H, Yue B, Yang Y, Tang J, Yang S, Qi A, Qu K, Lan X, Lei C, Wei Z, Huang B, Chen H. Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle. BIOLOGY 2022; 11:biology11020223. [PMID: 35205089 PMCID: PMC8869484 DOI: 10.3390/biology11020223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary It is known that many different breeds of cattle are widely distributed in China. However, due to a lengthy selection of draught direction, there are obvious shortcomings in Chinese cattle, such as less meat production, slow weight gain, poor meat quality, and a lack of specialized beef cattle breeds. Animal breeding heavily benefits from molecular technologies, among which molecular genetic markers were widely used to improve the economic traits of beef cattle. Because the copy number variation (CNV) involves a longer DNA sequence or even the entire functional gene, it may have a greater impact on the phenotype. Recent studies have indicated that CNVs are widespread in the Chinese cattle genome. By investigating the effects of CNVs on gene expression and cattle traits, we aim to find those genomic variations which could significantly affect cattle traits, and which could provide a basis for genetic selection and molecular breeding of local Chinese cattle. Abstract Currently, studies of the SYT11 gene mainly focus on neurological diseases such as schizophrenia and Parkinson’s disease. However, some studies have shown that the C2B domain of SYT11 can interact with RISC components and affect the gene regulation of miRNA, which is important for cell differentiation, proliferation, and apoptosis, and therefore has an impact on muscle growth and development in animals. The whole-genome resequencing data detected a CNV in the SYT11 gene, and this may affect cattle growth traits. In this study, CNV distribution of 672 individuals from four cattle breeds, Yunling, Pinan, Xianan, and Qinchuan, were detected by qPCR. The relationship between CNV, gene expression and growth traits was further investigated. The results showed that the proportion of multiple copy types was the largest in all cattle breeds, but there were some differences among different breeds. The normal type had higher gene expression than the abnormal copy type. The CNVs of the SYT11 gene were significantly correlated with body length, cannon circumference, chest depth, rump length, and forehead size of Yunling cattle, and was significantly correlated with the bodyweight of Xianan cattle, respectively. These data improve our understanding of the effects of CNV on cattle growth traits. Our results suggest that the CNV of SYT11 gene is a protentional molecular marker, which may be used to improve growth traits in Chinese cattle.
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Affiliation(s)
- Haiyan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Binglin Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Yu Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Jia Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Shuling Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Ao Qi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, 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, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Zehui Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
- Correspondence: (Z.W.); (B.H.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China
- Correspondence: (Z.W.); (B.H.); (H.C.)
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
- Correspondence: (Z.W.); (B.H.); (H.C.)
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Yao R, Lu T, Liu J, Li W, Weng X, Yue X, Li F. Variants of ADPGK gene and its effect on the male reproductive organ parameters and sperm count in Hu sheep. Anim Biotechnol 2021:1-8. [PMID: 34730075 DOI: 10.1080/10495398.2021.1995400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ADP-dependent glucokinase (ADPGK) plays an important role instead of hexokinase in regulating energy metabolism via the Embden-Meyerhof-Parnas Pathway. And energy provided via glycolysis promotes testis development and spermatogenesis. In this study, 466 Hu sheep were screened for mutations in the ADPGK gene to examine the association of the ADPGK gene polymorphisms with the testis traits and spermatogenesis. The NC_056060.1: g.31295 C > T SNP was found in the 3'-UTR region, resulting in two genotypes CC and TC type with genotypic frequencies of 0.66 and 0.34, respectively. This mutation was significantly associated with testis weight, testis long circumference, testis short girth, epididymis weight, and sperm concentration (p < 0.05). Moreover, TC genotype individuals had an increased tendency in the expression of the ADPGK gene and had significant reproductive performance advantages compared with CC genotype individuals in the study. And compared with the small testes (<50 g), the ADPGK gene expression of big testes (>160 g) increased significantly. This indicates an association between the ADPGK gene and reproductive organ parameters and sperm count in selected Hu sheep breed, and this SNP may serve as an effective DNA molecular marker for marker-assisted selection in Hu sheep breeding programs.
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Affiliation(s)
- Rongyu Yao
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tingting Lu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiamei Liu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wanhong Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuiu Weng
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiangpeng Yue
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Gansu Runmu Biological Engineering Co., Ltd., Yongchang, China.,Biotechnology Engineering Laboratory of Gansu Meat Sheep Breeding, Minqin, China
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Zhang S, Gao X, Jiang Y, Shen Y, Xie H, Pan P, Huang Y, Wei Y, Jiang Q. Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat. Arch Anim Breed 2021; 64:375-386. [PMID: 34584939 PMCID: PMC8461558 DOI: 10.5194/aab-64-375-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
Litter size is an important component trait of doe
reproduction. By improving it, production efficiency and economic benefits
can be significantly provided. Genetic marker-assisted selection (MAS) based
on proven molecular indicators could enhance the efficacy of goat selection,
as well as litter size trait. Many molecular markers have been identified
that they can be used to improve litter size in different goat breeds.
However, the presence and value of these markers vary among goat breeds. In
the present study, we used the reported loci on other breeds of goat as
candidate loci to detect whether these loci appear in this Nubian goat
population; then we proceed to genotype and detect surrounding loci (50 bp)
by multiplex PCR and sequencing technology. As a result, 69
mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes
in Nubian goat population, 12 loci were significantly associated with
the litter size of first-parity individuals; 5 loci were significantly
associated with the litter size of second-parity individuals; 3 loci
were significantly associated with the litter size of third-parity
individuals. In addition, five loci were significantly associated with the
average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674
C>G in first parity, and GHR: g.32134187G>A in
second parity exceed more than 0.40, and the preponderant alleles are G, C,
A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation
loci shows that 3 haplotype blocks are formed, and the litter size of
combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower
than that of other combinations genotype in first parity (P<0.05). These findings
can provide effective candidate DNA markers for selecting superior
individuals in Nubian goat breeding.
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Affiliation(s)
- Sanbao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Xiaotong Gao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yujian Shen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Hongyue Xie
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Peng Pan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yanna Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yingming Wei
- Institute for New Rural Development, Guangxi University, Nanning 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
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Detection of 15-bp Deletion Mutation within PLAG1 Gene and Its Effects on Growth Traits in Goats. Animals (Basel) 2021; 11:ani11072064. [PMID: 34359192 PMCID: PMC8300177 DOI: 10.3390/ani11072064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Goats have always served as an important domesticated livestock. PLAG1 is a major gene that affects the stature and growth of animals. Body size traits are very important for goats as it directly affects the economic characteristics of meat and cashmere production. This study showed that the 15-base pair (bp) InDel (rs637141549) can significantly affect growth traits such as body weight, height, height at hip cross, chest circumference, hip width and body index of goats through the detection of large samples (n = 1581) in four indigenous breeds. Accordingly, it is suggested that the deletion mutation can be used as a potential molecular marker that significantly affects goat growth traits. Moreover, the 15bp deletion mutation can be used as a potential molecular marker, which significantly affects the growth traits of goats and plays an important role in animal husbandry production. Abstract Stature and weight are important growth and development traits for animals, which also significantly affect the productivity of livestock. Polymorphic adenoma gene 1 (PLAG1) is located in the growth-related quantitative trait nucleotides (QTN), and its variation has been determined to significantly affect the body stature of bovines. This study found that novel 15-bp InDel could significantly influence important growth traits in goats. The frequencies of genotypes of the 15-bp mutation and relationship with core growth traits such as body weight, body height, height at hip cross, chest circumference, hip width and body index were explored in 1581 individuals among 4 Chinese native goat breeds. The most frequent genotypes of Shaanbei white Cashmere goat (SWCG), Inner Mongolia White Cashmere goat (IMCG) and Guanzhong Dairy goat (GZDG) were II genotypes (insertion/insertion), and the frequency of ID genotype (insertion/deletion) was found to be slightly higher than that of II genotype in Hainan Black goat (HNBG), showing that the frequency of the I allele was higher than that of the D allele. In adult goats, there were significant differences between 15-bp variation and body weight, chest circumference and body height traits in SWCG (p < 0.05). Furthermore, the locus was also found to be significantly correlated with the body index of HNBG (p = 0.044) and hip width in GZDG (p = 0.002). In regard to lambs, there were significant differences in height at the hip cross of SWCG (p = 0.036) and hip width in IMWC (p = 0.005). The corresponding results suggest that the 15-bp InDel mutation of PLAG1 is associated with the regulation of important growth characteristics of both adult and lamb of goats, which may serve as efficient molecular markers for goat breeding.
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Ju X, Huang X, Zhang M, Lan X, Wang D, Wei C, Jiang H. Effects of eight InDel variants in FHIT on milk traits in Xinjiang brown cattle. Anim Biotechnol 2020; 32:486-494. [PMID: 32401148 DOI: 10.1080/10495398.2020.1724124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In our previous genome-wide association study (GWAS), we identified the fragile histidine triad diadenosine triphosphatase (FHIT) gene in Xinjiang brown cattle (XJBC) as a candidate gene associated with cattle productive traits, with potential application in mark-assisted selection (MAS) in cattle breeding. FHIT is a prototype of a class of tumor suppressor genes that contain genomic loci mapped to common fragile loci. Here, 388 healthy and unrelated XJBC were selected to identify insertion/deletion (InDel) variants in the bovine FHIT and assess their effects on milk traits. Eight of the thirteen InDel loci were found to be polymorphic in FHIT. The polymorphism information content of the eight loci ranged from 0.061 to 0.375. The correlation analysis showed that all the new InDel variants were significantly related to six different milk traits (p < 0.05). The following variants presented a significant relationship with productive traits: P2-23bp with the 305 milk yield (p = 0.005) in the sixth parity; P3-24bp with the milk fat yield (p = 0.009) in the third parity; P5-21bp with the somatic cell score (p = 0.001) in the first parity and with the milk protein percentage (p = 0.002) in the sixth parity; and P7-26bp with the somatic cell score (p = 0.003) in the sixth parity. These findings will help evaluate InDel genotypes, within and between cattle breeds and identify potential target loci to accelerate progress in MAS in cattle breeding.
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Affiliation(s)
- Xing Ju
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xixia Huang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Menghua Zhang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Dan Wang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Chen Wei
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hui Jiang
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
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10
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He L, Bi Y, Wang R, Pan C, Chen H, Lan X, Qu L. Detection of a 4 bp Mutation in the 3'UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits. Animals (Basel) 2020; 10:ani10040672. [PMID: 32294879 PMCID: PMC7222716 DOI: 10.3390/ani10040672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The sex determining region Y (SRY)-type high mobility group (HMG) box 9 (Sox9) gene is critically important in the formation and development of cartilage and is considered the “main regulator” of chondrogenesis. Additionally, a large number of studies have shown that mutations in a single allele of human Sox9 can lead to campomelic dysplasia syndrome. Therefore, the mutations of Sox9 have been the subject of increasing interest among researchers. However, no studies to date have examined the association between Sox9 gene variants and growth traits in goats. Here, we detected a 4 bp indel in the 3′Untranslated Regions (3′UTR) region of Sox9 in Shaanbei white cashmere (SBWC) goats (n = 1109) and studied the association between this indel and growth traits. The 4 bp indel of Sox9 was significantly associated with body length, heart girth, hip width, and all body measurement indexes (p < 0.05) in SBWC goats. Thus, this deletion could be used as an effective molecular marker for maximizing the growth traits of goats in breeding programs. Abstract The SRY-type HMG box 9 (Sox9) gene plays an important role in chondrocyte development as well as changes in hypertrophic chondrocytes, indicating that Sox9 can regulate growth in animals. However, no studies to date have examined the correlation between variations in Sox9 and growth traits in goats. Here, we found a 4 bp indel in the 3′UTR of Sox9 and verified its association with growth traits in Shaanbei white cashmere goats (n = 1109). The frequencies of two genotypes (ID and II) were 0.397 and 0.603, respectively, and polymorphic information content (PIC) values showed that the indel had a medium PIC (PIC > 0.25). The 4 bp indel was significantly correlated with body length (p = 0.006), heart girth (p = 0.001), and hip width (p = 4.37 × 10 −4). Notably, individuals with the ID genotype had significantly superior phenotypic traits compared with individuals bearing the II genotype. Hence, we speculated that the 4 bp indel is an important mutation affecting growth traits in goat, and may serve as an effective DNA molecular marker for marker-assisted selection in goat breeding programs.
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Affiliation(s)
- Libang He
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
| | - Yi Bi
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
| | - Ruolan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (L.H.)
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China
- Correspondence: (X.L.); (L.Q.); Tel.: +86-137-7207-1502 (X.L.); +86-189-9226-2688 (L.Q.)
| | - Lei Qu
- 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
- Correspondence: (X.L.); (L.Q.); Tel.: +86-137-7207-1502 (X.L.); +86-189-9226-2688 (L.Q.)
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11
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He L, Kang Z, Kang Y, Xiang W, Pan C, Chen H, Zhu H, Qu L, Lan X, Song X. Goat CMTM2: mRNA expression profiles of different alternative spliced variants and associations analyses with growth traits. 3 Biotech 2020; 10:131. [PMID: 32154044 DOI: 10.1007/s13205-020-2125-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
CKLF like MARVEL transmembrane domain containing 2 (CMTM2) plays crucial roles in spermiogenesis, skeletogenous, growth, and development through PI3K/Akt and other pathways. The purpose of this study was to explore the expression profile and variation of different spliced CMTM2 gene in Shaanbei white cashmere goats, as well as to find the relationships between a CMTM2 promoter region 14 bp genetic variant and growth traits in 1366 Shaanbei white cashmere goats. In this study, we identified alternative CMTM2 splicing and detected the effects of the spliced variants on mRNA expression levels in tissues. Meanwhile, an unreported spliced variant of CMTM2 in goat was identified using in CDS cloning and RT-PCR, namely, CMTM2-AS2. Compared with the normal transcript (CMTM2-AS1), the novel variant had the higher expression level in muscle and liver tissues, indicating that it plays an effective role in growth traits. Furthermore, a 14 bp deletion was detected within CMTM2 promoter region, and the different genotypes were significantly associated with growth traits (e.g., body length, circumference of cannon bone) in the large group of 1366 individuals in Shaanbei white cashmere goats. We found that the body length of the individuals with II (n = 571) genotype had better phenotypes than those with DD (n = 118) and ID (n = 650) genotypes. These results have direct guiding significance for goat breeding in the future and provide a new idea for studying the characteristics and functions of CMTM2 gene in goats.
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12
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An 11-bp Indel Polymorphism within the CSN1S1 Gene Is Associated with Milk Performance and Body Measurement Traits in Chinese Goats. Animals (Basel) 2019; 9:ani9121114. [PMID: 31835668 PMCID: PMC6940862 DOI: 10.3390/ani9121114] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/08/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023] Open
Abstract
The casein alpha s1 (CSN1S1) gene encodes α-s1 casein, one of the proteins constituting milk, which affects milk performance, as well as improving the absorption of calcium and bone development in mammals. A previous study found that an 11-bp insertion/deletion (indel) of this gene strongly affected litter size in goats. However, to our knowledge, the relationships between this polymorphism and the milk performance and body measurement traits of goats have not been reported. In this paper, the previously identified indel has been recognized in three Chinese goat breeds, namely the Guanzhong dairy goat (GZDG; n = 235), Shaanbei white cashmere goat (SBWC; n = 1092), and Hainan black goat (HNBG; n = 278), and the following three genotypes have been studied for all of the breeds: insertion/insertion (II), deletion/deletion (DD), and insertion/deletion (ID). The allele frequencies analyzed signified that the frequencies of the "D" allele were higher (47.8%-65.5%), similar to the previous report, which indicates that this polymorphism is genetically stable in different goat breeds. Further analysis showed that this indel was markedly associated with milk fat content, total solids content, solids-not-fat content, freezing point depression, and acidity in GZDG (p < 0.05), and also affected different body measurement traits in all three breeds (p < 0.05). The goats with II genotypes had superior milk performance, compared with the others; however, goats with DD genotypes had better body measurement sizes. Hence, it may be necessary to select goats with an II or DD genotype, based on the desired traits, while breeding. Our study provides information on the potential impact of the 11-bp indel polymorphism of the CSN1S1 gene for improving the milk performance and body measurement traits in goats.
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13
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Tang Q, Zhang X, Wang X, Wang K, Yan H, Zhu H, Lan X, Lei Q, Pan C. Detection of two insertion/deletions (indels) within the ADAMTS9 gene and their associations with growth traits in goat. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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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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15
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Cui W, Liu N, Zhang X, Zhang Y, Qu L, Yan H, Lan X, Dong W, Pan C. A 20-bp insertion/deletion (indel) polymorphism within the CDC25A gene and its associations with growth traits in goat. Arch Anim Breed 2019; 62:353-360. [PMID: 31807646 PMCID: PMC6852853 DOI: 10.5194/aab-62-353-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Cell division cycle 25A (CDC25A), a member of the CDC25 family of phosphatases, is
required for progression from G1 to the S phase of the cell cycle. CDC25A provides an essential function during early embryonic development in mice,
suggesting that it plays an important role in growth and development. In
this study, we used mathematical expectation (ME) methods to identify a
20-bp insertion/deletion (indel) polymorphism of CDC25A gene in Shaanbei White
Cashmere (SBWC) goats. We also investigated the association between this
20-bp indel and growth-related traits in SBWC goats. Association results
showed that the indel was related to growth traits (height at hip cross,
cannon circumference, and cannon circumference index) in SBWC goats. The
height at hip cross of individuals with insertion/insertion (II) genotype
was higher than those with insertion/deletion (ID) genotype (P=0.02); on
the contrary, the cannon circumference and cannon circumference index of
individuals with ID genotype were superior when compared with those with II
genotype (P=0.017 and P=0.009). These findings suggest that the 20-bp
indel in the CDC25A gene significantly affects growth-related traits, and could be
utilized as a candidate marker for marker-assisted selection (MAS) in
the cashmere goat industry.
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Affiliation(s)
- Wenbo Cui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Nuan Liu
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Xuelian Zhang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Yanghai Zhang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Hailong Yan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China.,College of Animals Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
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16
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Zhang S, Cao X, Li Y, Wang K, Yuan M, Lan X. Detection of polled intersex syndrome (PIS) and its effect on phenotypic traits in goats. Anim Biotechnol 2019; 31:561-565. [PMID: 31198087 DOI: 10.1080/10495398.2019.1625782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polled intersex syndrome (PIS), a physiological defect associates polledness and intersexuality, will directly affect the reproduction and other phenotypic traits of goats, thus, it is a hazard to the development of the goat industry. Recent studies have revealed that goat PIS was caused by an 11.7-kb deletion located in chromosome 1q43, but its DNA detection method was little reported. Herein, a total of 503 goats from three goat breeds were used to successfully establish a simple, rapid, accurate and effective method for the detection of goat PIS mutation. Furthermore, based on this assay, the associations between the PIS mutation and growth traits were analyzed in Guanzhong dairy goats. These findings would provide the potential practical application for molecular breeding to accelerate the development of the goat industry.
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Affiliation(s)
- Shaoli Zhang
- Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi, P. R. China.,Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xinyuan Cao
- Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yu Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Ke Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Ming Yuan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
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17
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Wang K, Hui Y, Zhang S, Wang M, Yan H, Zhu H, Qu L, Lan X, Pan C. A deletion mutation within the ATBF1 gene is strongly associated with goat litter size. Anim Biotechnol 2019; 31:174-180. [DOI: 10.1080/10495398.2018.1561459] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ke Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yiqing Hui
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shaoli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hailong Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- Life Science Research Center, Yulin University, Yulin, 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, 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, China
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18
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Wang K, Cui Y, Wang Z, Yan H, Meng Z, Zhu H, Qu L, Lan X, Pan C. One 16 bp insertion/deletion (indel) within the KDM6A gene revealing strong associations with growth traits in goat. Gene 2018; 686:16-20. [PMID: 30408547 DOI: 10.1016/j.gene.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/31/2018] [Accepted: 11/03/2018] [Indexed: 01/02/2023]
Abstract
Lysine demethylase 6A (KDM6A), as a candidate gene associated with skeletal dysplasia and the differentiation of osteogenesis, might affect the growth traits in animals. In the previous study (Cui et al., 2018), one 16 bp intronic insertion/deletion (NW_017189516.1: g.138, 431_138,446delAATGTATAGCTTAAAA) within the KDM6A gene significantly influenced KDM6A gene expression. The objective of this work was to investigate the association between this 16 bp indel and growth-related traits in Shaanbei White Cashmere goat (SWCG). Association analyses showed the 16 bp indel was related to growth traits strongly (body height, chest depth, height across the hip, body length and chest circumference) in SWCG population (n = 1953, P < 0.05). Insertion/insertion (II) genotype individuals (n = 1502) had the best growth traits, by comparison of those of insertion/deletion (ID) (n = 410) and the deletion/deletion (DD) genotypes (n = 41). Particularly, the body weight of II genotype individuals were significantly higher than ID and DD genotypes (P < 0.01). Besides, the remarkable influence of this indel on traits might cause by the change of MEF2 binding site. These findings hinted that the 16 bp deletion mutation in KDM6A gene, which was significantly associated with growth-related traits, could be assigned to an effective molecular marker for growth traits in goat breeding.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Yang Cui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Zhen Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Zhe Meng
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China.
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19
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Yang Q, Zhang S, Li J, Wang X, Peng K, Lan X, Pan C. Development of a touch-down multiplex PCR method for simultaneously rapidly detecting three novel insertion/deletions (indels) within one gene: an example for goat GHR gene. Anim Biotechnol 2018; 30:366-371. [DOI: 10.1080/10495398.2018.1517770] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Qing Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Shaoli Zhang
- Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jie Li
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xinyu Wang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kun Peng
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
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20
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Wei Z, Wang K, Hui Y, Yan H, Zhu H, Qu L, Pan C, Chen H, Lan X. Detection of insertion/deletions (indels) of the <i>ATBF1</i> gene and their effects on growth-related traits in three indigenous goat breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-311-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The AT motif-binding factor (ATBF1), also known as zinc finger homeobox 3
(ZFXH3), is necessary for activating the POU1F1 gene; thus,
the ATBF1 gene greatly affects the grow traits in animals. The
objective of this work was to explore novel indel (insertion/deletion)
variations and their associations with growth traits in three native Chinese
goat breeds. Two indels within the ATBF1 gene were found in the
Shaanbei white cashmere goat (SWCG; n=581), the Guanzhong dairy goat
(GZDG; n=334) and the Hainan black goat (HNBG; n=270) for the first time
using 12 pairs of primers. Association analysis revealed that the P1-12-bp
indel was consistently correlated with the body height of the three breeds,
and individuals with ID (insertion/deletion) and
DD (deletion/deletion) genotypes had a higher body weight than the
II (insertion/insertion) genotype (P=0.036); the P11-6-bp indel
was consistently correlated with chest circumference and hip width of the
three breeds. Moreover, these two loci were associated with other several
growth-related traits in different breeds. Hence, these findings indicated
that the goat ATBF1 gene had marked effects on growth traits and the
growth-trait-related loci, which would contribute to improving the
growth-related traits of local breeds in the goat industry by implementing
marker-assisted selection (MAS).
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21
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Li J, Zhang S, Erdenee S, Sun X, Dang R, Huang Y, Lei C, Chen H, Xu H, Cai Y, Lan X. Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes. Prion 2018; 12:185-196. [PMID: 29695200 DOI: 10.1080/19336896.2018.1467193] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Studies of the ovine prion-related protein (testis-specific) gene (PRNT), including studies of genetic diversity, have highlighted its potential relationship to scrapie infection and economically important ovine traits. PRNT was previously reported to be highly polymorphic in Portuguese sheep. To characterize genetic polymorphisms in this gene in Asian sheep, a direct sequencing method was used to detect polymorphic loci in PRNT in 285 individual sheep from four Chinese and one Mongolian breeds. Seven SNP variants in PRNT were identified, including three novel variants (g.93G>A, g.162G>T, and g.190A>G) and four previously reported variants (g.17 C>T, g.112G>C, g.129C>T, and g.144A>G). In the five breeds that we analyzed, the mutation frequencies of g.190A>G in Lanzhou Fat-tail sheep (LFTS) and g.129C>T in the other four varieties were high (F>0.5). Moreover, thirteen different haplotypes that had a comparable distribution in the tested breeds were also identified; 'C-G-G-C-A-G-A' occurred at the highest frequency in the five sheep breeds. Additionally, we previously explored the significance of relationships between polymorphisms in PRNP or PRND and ovine growth performance. Here, we also performed correlation analysis in all tested loci. These loci polymorphisms were significantly associated with ten different growth traits (P<0.05), except for g.93G>A. Meanwhile, in contrast to a previous study, there was no significant association between the seven SNP loci analyzed and our previously reported sheep PRND or PRNP insertion/deletion mutations. Our findings may provide new insights into polymorphic variation in ovine PRNT, which may contribute to genetic improvements in economic traits that are important for sheep breeding.
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Affiliation(s)
- Jie Li
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China.,b College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an , Shaanxi , China
| | - Shaoli Zhang
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China.,b College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an , Shaanxi , China
| | - Sarantsetseg Erdenee
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Xiuzhu Sun
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Ruihua Dang
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Yongzhen Huang
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Chuzhao Lei
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hong Chen
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hongwei Xu
- c Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Yong Cai
- c Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Xianyong Lan
- a College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
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22
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Wang K, Yan H, Xu H, Yang Q, Zhang S, Pan C, Chen H, Zhu H, Liu J, Qu L, Lan X. A novel indel within goat casein alpha S1 gene is significantly associated with litter size. Gene 2018; 671:161-169. [PMID: 29864495 DOI: 10.1016/j.gene.2018.05.119] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023]
Abstract
The ruminant casein gene family (CSNs, link as CSN1S1-CSN2-CSN1S2-CSN3) is characterized by diverse variations and has been extensively studied for ruminant milk traits, however, studies on insertion/deletion (indel) mutations within this gene family and their effects on prolificacy are extremely limited. This study aimed to detect possible novel indels within CSNs in an indigenous Chinese goat breed-Shaanbei White Cashmere goat (SBWC, n = 3047) and four other Chinese goat breeds (n = 1136) with varied litter size rates (105%-283%) and different estrus types (seasonal vs. perennial), as well as exploring the association between these potential indels and litter size. Only one novel 11-bp indel within the CSN1S1 gene was found. The association analyses uncovered that this novel indel was related to the first-birth litter size of SBWC population (n = 2690) (P < 1.0 E-8). Individuals with the II genotype (n = 676) had the best litter size when compared with those ID genotype (n = 1098) and DD genotype (n = 916) individuals. Animals with the II genotype were found to have higher relative expression level of CSN1S1 gene in the ovary (P < 0.01). Besides, Chi-square tests for different litter size and estrous cycle breeds showed that perennial-estrus breeds and multi-kids breeds had higher "I" allelic frequencies and "II" genotypic frequencies. These findings suggest the 11-bp indel within the CSN1S1 gene is significantly associated with reproduction traits and can be an effective molecular marker for litter size of goat breeding.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Han Xu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China.
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Jinwang Liu
- Station of Veterinary and Animal Husbandry of Tong town of Jiaxian County, Jiaxian, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China.
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23
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Zhao H, Wu M, Wang S, Yu X, Li Z, Dang R, Sun X. Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-71-2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. During the past decades, insertions and deletions (indels) have become
increasingly popular in animal breeding for understanding the relationship
between genotypes and phenotypes. The androgen receptor (AR) plays the
vital role of a bridge on the function of the androgen and has sexual size
dimorphism. For this reason, the objective of this study was to explore the
novel indel variants within the cattle AR gene and to detect their
effects on growth traits in four breeds of Chinese yellow cattle. Herein, we
first confirmed a novel 24 bp indel (AC_000187.1g.4187270-4187293delAATTTATTGGGAGATTATTGAATT) within the intron of
the cattle AR gene. This is consistent with the results predicted
from the NCBI SNP database. The distribution of the indel genotypes of four
Chinese yellow cattle were significantly different from each other
(P < 0.01). After significant correlation analysis, many remarkable
phenotypic differences among the three genotypes were found (P < 0.05).
In conclusion, a novel 24 bp indel within the AR gene
significantly affected growth traits, suggesting that this indel may be a
useful DNA marker for the elimination or selection of excellent individuals for
cattle breeding.
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24
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Li J, Erdenee S, Zhang S, Wei Z, Zhang M, Jin Y, Wu H, Chen H, Sun X, Xu H, Cai Y, Lan X. Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep. Prion 2018; 12:42-53. [PMID: 29394137 DOI: 10.1080/19336896.2017.1405886] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene. In five analyzed breeds, the minor allelic frequencies (MAF) of the above indels were in the range of 0.008 to 0.986 (I1-7bp), 0.113 to 0.336 (I2-15bp), 0.281 to 0.510 (I2-19bp), and 0.040 to 0.238 (3' UTR-7bp). Additionally, there were 15 haplotypes and the haplotype 'II2-15bp-D3'UTR-7bp-DI2-19bp-DI1-7bp' had the highest frequency, which varied from 0.464 to 0.629 in five breeds. Moreover, association analysis revealed that all novel indel polymorphisms were significantly associated with 13 different growth traits (P < 0.05). Particularly, the influences of I2-15bp on chest width (P = 0.001) in Small Tail Han sheep (ewe), 3' UTR-7bp on chest circumference (P = 0.003) in Hu sheep, and I2-19bp on tail length (P = 0.001) in Tong sheep, were highly significant (P < 0.01). These findings may be a further step toward the detection of indel-based typing within and across sheep breeds, and of promising target loci for accelerating the progress of marker-assisted selection in sheep breeding.
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Affiliation(s)
- Jie Li
- a College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an, Shaanxi , China
| | - Sarantsetseg Erdenee
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Shaoli Zhang
- a College of Animal Science and Technology, Innovation Experimental College, Northwest A&F University , Xi'an, Shaanxi , China
| | - Zhenyu Wei
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Meng Zhang
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Yunyun Jin
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hui Wu
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hong Chen
- c Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , China
| | - Xiuzhu Sun
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
| | - Hongwei Xu
- d Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Yong Cai
- d Science Experimental Center, College of Life Science and Engineering, Northwest University for Nationalities , Chengguan District, Lanzhou City in northwest, Lanzhou , Gansu , China
| | - Xianyong Lan
- b College of Animal Science and Technology, Northwest A&F University , Xi'an , Shaanxi , China
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25
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Yan H, Zhang F, Wang K, Liu J, Zhu H, Pan C, Qu L. A novel 12 bp deletion within goat <i>LHX4</i> gene significantly affected litter size. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-1-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract. The LIM homeobox transcription factor 4 (LHX4) gene plays a critical role in regulating the development of the pituitary and the secretion of growth hormone (GH) and prolactin (PRL) associated with reproduction. Thus this gene may affect litter size. Herein, the aim of this study is to detect the novel insertion/deletion (indel) within the LHX4 gene as well as to test its association with litter size in 1149 Shaanbei white cashmere goats. Herein, a novel 12 bp indel (NC_030823.1:g.60001011_60001022delGGGGAGGAGGGG) was firstly found, which was located in the first intron. Meanwhile, three genotypes were detected in Shaanbei white cashmere goats, and the allelic frequencies of I and D were 0.593 and 0.407, respectively. Interestingly, the genotype distributions between mothers of single-lamb (n = 895) and multi-lamb (n = 254) groups within Shaanbei white cashmere goats were significantly different, implying that the 12 bp indel might affect the litter size. Furthermore, the association analysis was carried out to find out that the 12 bp indel was significantly associated with litter size in the analyzed goat population (P < 0.05). The litter sizes of genotype DD and ID individuals were superior to those of genotype II (P < 0.05). These findings suggest that this locus could be considered as a genetic marker for goat breeding, enriching the research category of functional genome of goats.
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26
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Xu H, Zhang S, Zhang X, Dang R, Lei C, Chen H, Lan X. Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-285-2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C>G (SNP1), g.146573T>C (SNP2), g.205468C>T (SNP3), g.205575A>G (SNP4) and g.297690C<T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.
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27
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Li J, Zhu X, Ma L, Xu H, Cao X, Luo R, Chen H, Sun X, Cai Y, Lan X. Detection of a new 20-bp insertion/deletion (indel) within sheep PRND gene using mathematical expectation (ME) method. Prion 2017; 11:143-150. [PMID: 28362554 DOI: 10.1080/19336896.2017.1300740] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Prion-related protein doppel gene (PRND), as an essential member of the mammalian prion gene family, is associated with the scrapie susceptibility as well as phenotype traits, so the genetic variation of the PRND has been highly concerned recently, including the single nucleiotide polymorphism (SNP) and insertion/deletion (indel). Therefore, the objective of present study was to examine the possible indel variants by mathematical expectation (ME) detection method as well as explore its associations with phenotype traits. A novel 20-bp indel was verified in 623 tested individuals representing 4 diversity sheep breeds. The results showed that 3 genotypes were detected and the minor allelic frequency were 0.008 (Lanzhou Fat-Tail sheep, LFTS), 0.084 (Small Tail Han sheep, STHS), 0.021(Tong sheep, TS) and 0.083 (Hu sheep, HS), respectively. Comparing with the traditional method of detecting samples one by one, the reaction times with ME method was decreased by 36.22% (STHS), 37.00% (HS), 68.67% (TS) and 83.33% (LFTS), respectively. Besides, this locus was significantly associated to cannon circumference index (P = 0.012) and trunk index (P = 0.037) in the Hu sheep breed. Notably, it was not concordance with the present result of DNA sequencing (GCTGTCCCTGCAGGGCTTCT) and dbSNPase of NCBI (NC_443194: g.46184887- 46184906delCTGCTGTCCCTGCAGGGCTT). Consequently, it was the first time to detect the new 20-bp indel of sheep PRND gene by ME strategy, which might provide a valuable theoretical basis for marker-assisted selection in sheep genetics and breeding.
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Affiliation(s)
- Jie Li
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China.,b Innovation Experimental College , Northwest A&F University , Yangling , China
| | - Xichun Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Lin Ma
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Hongwei Xu
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xin Cao
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Renyun Luo
- e Ruilin Sci-Tech Cluture and Breeding Limit Company , Yongjing , China
| | - Hong Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Xiuzhu Sun
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yong Cai
- c Science Experimental Center , Northwest University for Nationalities , Lanzhou , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xianyong Lan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
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28
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Zhao H, He S, Zhu Y, Cao X, Luo R, Cai Y, Xu H, Sun X. A novel 29 bp insertion/deletion (indel) variant of the <i>LHX3</i> gene and its influence on growth traits in four sheep breeds of various fecundity. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-79-2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract. Belonging to the same LIM homeobox (LHX) family, LHX3 and LHX4 are key transcription factors in animal growth and reproduction. Insertion/deletion (indel) is a relatively simple and effective DNA marker. Therefore, four sheep breeds of various fecundity were used to explore the novel indel variants within the sheep LHX3 and LHX4 gene, as well as to evaluate their effects on growth traits. Herein, only one novel 29 bp indel (NC_019460.2:g.3107494-3107522delGGCCTGGACTGTGATGGGCACCCTCCGGG) within the sheep LHX3 gene was found, and three genotypes were detected. Interestingly, the increasing trends of II (insertion/insertion) genotype frequency and I allelic frequency were the same as the growth of the fertility character. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (HS, STHS and LFTS) and low-fecundity breed (TS) based on a χ2 test (P < 0.05). Association analyses showed that body length was significantly different in female TS and STHS and that chest width was significantly different for the female TS and male STHS (P < 0.05). These findings suggested that the 29 bp indel could extend the spectrum of genetic variations of the LHX3 gene in sheep and provide a valuable theoretical basis for the marker-assisted selection (MAS) in sheep breeding and genetics.
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29
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Zhang M, Pan C, Lin Q, Hu S, Dang R, Lei C, Chen H, Lan X. Exploration of the exonic variations of the iPSC-related <i>Nanog</i> gene and their effects on phenotypic traits in cattle. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-351-2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract. Nanog is an important pluripotent transcription regulator transforming somatic cells to induced pluripotent stem cells (iPSCs), and its overexpression leads to a high expression of the growth and differentiation factor 3 (GDF3), which affects animal growth traits. Therefore, the aim of this study was to explore the genetic variations within the Nanog gene and their effects on phenotypic traits in cattle. Six novel exonic single nucleotide polymorphisms (SNPs) were found in six cattle breeds. Seven haplotypes were analyzed: TCAACC (0.260), TCAATA (0.039), TCATCC (0.019), TCGACC (0.506), TCGATA (0.137), TCGTCC (0.036), and CTGATA (0.003). There were strong linkage disequilibriums of SNP1 and SNP2 in Jiaxian cattle as well as of SNP5 and SNP6 in both Jiaxian cattle and Nanyang cattle. Moreover, SNP3, SNP4, and SNP5 were associated with phenotypes. The individuals with GG genotype at the SNP3 locus or AA genotype at the SNP4 locus showed better body slanting length and chest circumference or body height and hucklebone width in Nanyang cattle. The superiority of the SNP5-C allele regarding body height and cannon circumference was observed in Jiaxian cattle. The combination of SNP3 and SNP4 (GG–AA) had positive effects on body height, body slanting length, and chest circumference. These findings may indicate that Nanog, as a regulator of bovine growth traits, could be a candidate gene for marker-assisted selection (MAS) in breeding and genetics in cattle.
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