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Li C, Wang X, Li H, Ahmed Z, Luo Y, Qin M, Yang Q, Long Z, Lei C, Yi K. Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat. Anim Genet 2024; 55:575-587. [PMID: 38806279 DOI: 10.1111/age.13437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.
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Affiliation(s)
- Chuanqing Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianglin Wang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Haobang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Yang Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Mao Qin
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Qiong Yang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Zhangcheng Long
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China
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Zhang Y, Qin Y, Gu M, Xu Y, Dou X, Han D, Lin G, Wang L, Wang Z, Wang J, Sun Y, Wu Y, Chen R, Qiao Y, Zhang Q, Li Q, Wang X, Xu Z, Cong Y, Chen J, Wang Z. Association between the cashmere production performance, milk production performance, and body size traits and polymorphism of COL6A5 and LOC102181374 genes in Liaoning cashmere goats. Anim Biotechnol 2023; 34:4415-4429. [PMID: 36527393 DOI: 10.1080/10495398.2022.2155177] [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: 12/23/2022]
Abstract
The purpose of this study was to analyze the relationship between COL6A5 (collagen type VI alpha 5 chain) and LOC102181374 (alcohol dehydrogenase 1) genes and the production performance of Liaoning cashmere goats by single nucleotide polymorphism (SNP). We have searched for SNP loci of COL6A5 and LOC102181374 genes through sequence alignment and PCR experiments, and have used SPSS and SHEsis software to analyze production data. We obtained five SNP loci in total, including three SNP loci (G50985A, G51140T, G51175A) in COL6A5 gene and two SNP loci (A10067G, T10108C) in LOC102181374 gene. The genotypes G50985A (AG), G51140T (GT), G51175A (AA), A10067G (AA), and T10108C (CC) of these loci have certain advantages in improving the production performance of Liaoning cashmere goats. The haplotype combinations that can improve production performance in COL6A5 gene were H1H5:AGGGAG, H4H4:GGGGAA, and H4H4:GGGGAA. H3H3:GGCC and H2H4:AGTT were the dominant combinations in LOC102181374 gene. At G51175A and A10067G loci, we found that H1H2:AAAG and H1H3:AGAA have dominant effects. These results may provide some support for the molecular breeding of production traits in Liaoning cashmere goats.
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Affiliation(s)
- Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanjun Qiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qiu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qian Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaowei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiguo Xu
- Dalian Modern Agricultural Production Development Service Center, Dalian, China
| | - Yuyan Cong
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jing Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 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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Cai HF, Chen Z, Luo WX. cDNA cloning and analysis of polymorphism of GFI1B gene in GuiZhou white goat. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413110045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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A novel SNP of liver-type fatty acid-binding protein gene in duck and its associations with the intramuscular fat. Mol Biol Rep 2011; 39:1073-7. [PMID: 21573793 DOI: 10.1007/s11033-011-0833-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Liver-type fatty acid-binding protein (L-FABP) is a member of intracellular lipid-binding proteins involved in the transportation of fatty acids. We detected the polymorphisms of duck L-FABP gene and its association with the intramuscular fat (IMF) and other fat-related traits. The complete sequence of duck L-FABP gene (four exons and three introns, 2,542 bp) was obtained in this study. The polymorphism of L-FABP gene was examined with direct DNA sequencing method in 231 individuals from different breeds, and a novel single nucleotide polymorphism in the exon 3 was detected. The polymorphism was shown to be associated with the contents of C16:0, C18:3 and the total IMF in pectoral muscle. The content of C16:0 in genotype CC was significantly higher than CT (P < 0.01) and TT (P < 0.01), and the genotype CT was higher than TT (P < 0.01). The content of C18:3 in genotype TT was significantly higher than CC and CT (P < 0.01), whereas the genotype CC and CT had no significant difference (P > 0.05). The content of IMF in genotype CC was significantly higher than CT (P < 0.01). However, no significant difference was detected between genotype CC and TT or genotype CT and TT (P > 0.05).
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Yue XP, Zhang XM, Wang W, Ma RN, Deng CJ, Lan XY, Chen H, Li F, Xu XR, Ma Y, Lei CZ. The CSN1S1 N and F alleles identified by PCR-SSCP and their associations with milk yield and composition in Chinese dairy goats. Mol Biol Rep 2010; 38:2821-5. [PMID: 21086177 DOI: 10.1007/s11033-010-0428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 11/08/2010] [Indexed: 11/25/2022]
Abstract
A method was depicted to identify null allele CSN1S1 N and low allele CSN1S1 F of the CSN1S1 gene of goat using PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism). First, primer A was designed to amplify the exon 9 of CSN1S1 gene which produced three genotypes AA, AB, and BB. Among these three genotypes, only AA and AB individuals had a cytosine deletion at exon 9 after DNA sequencing, which cannot be used to identify the N and F alleles. Therefore, primer B was used to amplify intron 14 of CSN1S1 of described AA and AB individuals. Genotypes FF, FN and NN were detected within AA individuals and genotypes FO and NO were detected in the above AB individuals. The frequencies of F and N alleles in 708 samples from Xinong Saanen (XS) and Guanzhong (GZ) dairy goat breeds were 0.1139, 0.0927, and 0.2376, 0.1193, respectively. In 268 XS samples, the individuals with NN genotype contained a significant lower protein content than that of other genotypes (P<0.01). Individuals of FF genotype had significant higher milk yield than that of NO genotype in the first milk lactation of 202 XS individuals (P<0.05). Therefore, the variability at CSN1S1 locus contains enough genetic diversity to be potentially useful in improving the quality and production of milk in Chinese dairy goat breeds.
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Affiliation(s)
- X P Yue
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
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Li G, An X, Hou J, Li L, Han D, Yang M, Wang Y, Zhu G, Wang J, Song Y, Cao BY. Study on polymerization effect of polyembryony genes by SSCP marker and family trees in Chinese goats. Mol Biol Rep 2010; 38:739-44. [DOI: 10.1007/s11033-010-0161-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 03/30/2010] [Indexed: 01/12/2023]
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