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Yang R, Zhou D, Tan X, Zhao Z, Lv Y, Tian X, Ren L, Wang Y, Li J, Zhao Y, Zhang J. Genome-Wide Association Study of Body Conformation Traits in Tashi Goats ( Capra hircus). Animals (Basel) 2024; 14:1145. [PMID: 38672293 PMCID: PMC11047570 DOI: 10.3390/ani14081145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was "olfactory transduction", and the most significantly enriched gene ontology (GO) terms were "cellular process", "cellular anatomical entity", and "molecular transducer activity". Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.
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Affiliation(s)
- Rong Yang
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Di Zhou
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Xiaoshan Tan
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Zhonghai Zhao
- Zunyi Animal Husbandry and Fishery Station, Zunyi 563000, China
| | - Yanli Lv
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Xingzhou Tian
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Liqun Ren
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Yan Wang
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Jun Li
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
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Sun H, He Z, Zhao F, Hu J, Wang J, Liu X, Zhao Z, Li M, Luo Y, Li S. Molecular Genetic Characteristics of the Hoxc13 Gene and Association Analysis of Wool Traits. Int J Mol Sci 2024; 25:1594. [PMID: 38338874 PMCID: PMC10855228 DOI: 10.3390/ijms25031594] [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: 12/07/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Homobox C13 (Hoxc13) is an important transcription factor in hair follicle cycle development, and its deletion had been found in a variety of animals leading to abnormal hair growth and disruption of the hair follicle system. In this study, we used immunofluorescence, immunohistochemistry, real-time fluorescence quantitative PCR (RT-qPCR), and Kompetitive Allele-Specific PCR (KASP) genotyping to investigate molecular genetic characteristics of the Hoxc13 gene in Gansu alpine fine-wool sheep. The results revealed that Hoxc13 was significantly expressed during both the anagen and catagen phases (p < 0.05). It was found to be highly expressed predominantly in the dermal papillae and the inner and outer root sheaths, showing a distinct spatiotemporal expression pattern. Two single nucleotide polymorphisms (SNPs) in the exon 1 of Hoxc13, both the individual locus genotypes and the combined haplotypes were found to be correlated with wool length (p < 0.05). It was determined the mutations led to changes in mRNA expression, in which higher expression of this gene was related with longer wool length. In summary, this unique spatiotemporal expression pattern of the Hoxc13 gene may regulate the wool length of Gansu alpine fine-wool sheep, which can be used as a molecular genetic marker for wool traits and thus improve the breed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (Z.H.); (F.Z.); (J.H.); (J.W.); (X.L.); (Z.Z.); (M.L.); (Y.L.)
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Alkhammas AH, Al-Thuwaini TM, Al-Shuhaib MBS, Khazaal NM. Association of Novel C319T Variant of PITX2 Gene 3'UTR Region With Reproductive Performance in Awassi Sheep. Bioinform Biol Insights 2023; 17:11779322231179018. [PMID: 37313032 PMCID: PMC10259137 DOI: 10.1177/11779322231179018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/13/2023] [Indexed: 06/15/2023] Open
Abstract
Several genes influence sheep's reproductive performance, among them the paired-like homeodomain transcription factor 2 (PITX2) gene. Thus, this study aimed to examine whether the variability within the PITX2 gene is associated with the reproductive performance of Awassi ewes. A total of 123 single-progeny ewes and 109 twin ewes were used to extract genomic DNA. An amplicon of 4 sequence fragments from exons 2, 4, 5 (upstream portion), and 5 (downstream portion) of the PITX2 gene was generated by polymerase chain reaction (PCR), 228, 304, 381, and 382 bp, respectively. Three genotypes of 382 bp amplicons were identified: CC, CT, and TT. Sequence analysis revealed a novel mutation in the CT genotype 319C > T. Statistical analysis revealed that single-nucleotide polymorphism (SNP) 319C > T was associated with reproductive performance. Single-nucleotide polymorphism 319C > T-carrying ewes had significantly (P ⩽ .01) lower litter sizes, twinning rates, lambing rates, and more days to lambing than those carrying CT and CC genotypes. Based on a logistic regression analysis, it was confirmed that the 319C > T SNP decreased litter size. Ewes with TT genotype produced fewer lambs than ewes with CT and CC genotypes. According to these results, the variant 319C> T SNP negatively affects the reproductive performance of Awassi sheep. Ewes carrying the 319C > T SNP have a lower litter size and are less prolific than those without the SNP.
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Affiliation(s)
- Ahmed H Alkhammas
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
| | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
| | | | - Neam M Khazaal
- Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
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Guo X, Pei J, Wu X, Bao P, Ding X, Xiong L, Chu M, Lan X, Yan P. Detection of InDel and CNV of SPAG17 gene and their associations with bovine growth traits. Anim Biotechnol 2022; 33:440-447. [PMID: 32820682 DOI: 10.1080/10495398.2020.1803342] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sperm-associated antigen 17 (SPAG17) gene encodes a central pair protein, which is involved in flagellar motility, male fertility and skeletal growth in ruminants. The insertions/deletions (indels) and copy number variations (CNVs) influence phenotypic traits by altering the sequences and copy numbers of functional genes, respectively. This study identified a novel 8-bp indel of SPAG17 gene in 1520 individuals from eight different cattle breeds, as well as a novel CNV region in 355 animals. The correlation analysis of indel showed that the individuals of ID genotype had superior performance traits such as body height (p = 0.038) and body slanting length (p = 0.041) as compared to other genotypes in Xianan cattle. For the CNV, different copy numbers were closely related to the body height in Qinchuan (p = 0.045) and body weight in Xianan (p = 0.036) breeds. Importantly, significant difference was observed between the 8-bp indel and the copy number loss in Xianan breed (p < 0.01). These findings indicated that the variations within the bovine SPAG17 gene can be considered as an effective DNA molecular marker for beef cattle breeding.
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Affiliation(s)
- Xian Guo
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Jie Pei
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xiaoyun Wu
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Pengjia Bao
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xuezhi Ding
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Lin Xiong
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Min Chu
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ping Yan
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
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Shao M, Shi K, Zhao Q, Duan Y, Shen Y, Tian J, He K, Li D, Yu M, Lu Y, Tang Y, Feng C. Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens. Genes (Basel) 2022; 13:genes13050798. [PMID: 35627183 PMCID: PMC9140345 DOI: 10.3390/genes13050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.
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Affiliation(s)
- Minghui Shao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Ying Duan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Jinjie Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kun He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Minli Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China;
| | - Yanfei Tang
- Guangxi Fufeng Agricultural and Animal Husbandry Group Co., Ltd., Nanning 530024, China;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
- Correspondence:
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Bai Y, Yuan R, Luo Y, Kang Z, Zhu H, Qu L, Lan X, Song X. Exploration of Genetic Variants within the Goat A-Kinase Anchoring Protein 12 ( AKAP12) Gene and Their Effects on Growth Traits. Animals (Basel) 2021; 11:ani11072090. [PMID: 34359218 PMCID: PMC8300346 DOI: 10.3390/ani11072090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary AKAP12, the family of A-kinase anchoring proteins (AKAPs), plays an important role in the regulation of growth and development. There have been no corresponding studies of the effect of the AKAP12 gene on growth traits in goats. In our previous study, 7 bp (intron 3) and 13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. This study expected to identify the association between these two genetic variations and growth-related traits in 1405 Shaanbei white cashmere (SBWC) goats. The P1–7 bp indel locus was significantly correlated with height at hip cross (HHC; p < 0.05) and the P2–13 bp indel locus was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). These results prove that the AKAP12 gene plays an important role in the growth and development of goats. Abstract The A-kinase anchoring protein 12 gene (AKAP12) is a scaffold protein, which can target multiple signal transduction effectors, can promote mitosis and cytokinesis and plays an important role in the regulation of growth and development. In our previous study, P1–7 bp (intron 3) and P2–13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. Therefore, this study aimed to identify the association between these two genetic variations and growth-related traits in Shaanbei white cashmere goats (SBWC) (n = 1405). Herein, we identified two non-linkage insertions/deletions (indels). Notably, we found that the P1–7 bp indel mutation was related to the height at hip cross (HHC; p < 0.05) and the P2–13 bp indel was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). Overall, the two indels’ mutations of AKAP12 affected growth traits in goats. Compared to the P1–7 bp indel, the P2–13 bp indel is more suitable for the breeding of goat growth traits.
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Affiliation(s)
- Yangyang Bai
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (Y.B.); (R.Y.); (H.Z.); (L.Q.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (Z.K.)
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Rongrong Yuan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (Y.B.); (R.Y.); (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Yunyun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (Z.K.)
| | - Zihong Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (Z.K.)
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (Y.B.); (R.Y.); (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
- Shaanxi Province “Four Subjects One Union” Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin 719000, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (Y.B.); (R.Y.); (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
- Shaanxi Province “Four Subjects One Union” Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin 719000, 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 712100, China; (Y.L.); (Z.K.)
- Correspondence: (X.L.); (X.S.)
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (Y.B.); (R.Y.); (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
- Shaanxi Province “Four Subjects One Union” Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin 719000, China
- Correspondence: (X.L.); (X.S.)
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Akhatayeva Z, Li H, Mao C, Cheng H, Zhang G, Jiang F, Meng X, Yao Y, Lan X, Song E, Zhang D. Detecting novel Indel variants within the GHR gene and their associations with growth traits in Luxi Blackhead sheep. Anim Biotechnol 2020; 33:214-222. [PMID: 32615865 DOI: 10.1080/10495398.2020.1784184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The growth hormone is important in the regulation of metabolism and energy homeostasis and acts through a growth hormone receptor (GHR). In this work, genetic variations within the ovine GHR gene were identified and tested for associations with body morphometric traits in Chinese Luxi Blackhead (LXBH) sheep. Novel deletion loci in the LXBH GHR gene included P2-del-23 bp and P8-del-23 bp indel variants. The polymorphic information content (PIC) was 0.329 in P2-del-23 bp and 0.257 in P8-del-23 bp. Moreover, both indel polymorphisms were not at Hardy-Weinberg equilibrium (p < 0.05) in the LXBH population. Statistical analyses revealed that the P2-del-23 bp and P8-del-23 bp indels were significantly associated (p < 0.05) with several growth traits in rams and ewes, including body weight, body height, chest depth, chest width, chest circumference, cannon circumference, paunch girth and hip width. Among the tested sheep, the body traits of those with genotype DD were superior to those with II and ID genotypes, suggesting that the 'D' allele was responsible for the positive effects on growth traits. Thus, these results indicate that the P2-del-23 bp and P8-del-23 bp indel sites and the DD genotype can be useful in marker-assisted selection in sheep.
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haixia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Cui Mao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guoping Zhang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fugui Jiang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xianfeng Meng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuni Yao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 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
| | - Enliang Song
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dongfu Zhang
- Shandong Liaocheng Luxi Blackhead Sheep Farm, Liaocheng, Shandong, China
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Cao H, Dong X, Mao H, Xu N, Yin Z. Expression Analysis of the PITX2 Gene and Associations between Its Polymorphisms and Body Size and Carcass Traits in Chickens. Animals (Basel) 2019; 9:ani9121001. [PMID: 31756915 PMCID: PMC6940742 DOI: 10.3390/ani9121001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/16/2019] [Accepted: 11/16/2019] [Indexed: 12/20/2022] Open
Abstract
Simple Summary The Wuliang Mountain Black-bone chicken is a Chinese indigenous breed with good meat quality and strong resistance to disease. Like most of the other Chinese domestic breeds, it has a much slower early growth rate compared with foreign chicken breeds. Therefore, the genetic selection of body size and carcass traits is still the focus of Chinese indigenous chicken breeding. The paired-like homeodomain transcription factor 2 (PITX2) gene, an important transcription factor, plays an important role during the development of the eye, heart, skeletal muscle and other tissues in mammals. In chicken, the PITX2 gene affects the late myogenic differentiation of the limb. The objectives of this study were to detect the expression of the PITX2 gene and analyze the associations between the polymorphisms in the exons of the PITX2 gene and body size as well as carcass traits in chickens. The results could contribute to Chinese chicken breeding based on marker assisted-selection. Abstract PITX2 is expressed in and plays an important role in myocytes of mice, and it has effects on late myogenic differentiation in chickens. However, the expression profile and polymorphisms of PITX2 remain unclear in chickens. Therefore, the aim of the present study was to detect its expression and investigate single nucleotide polymorphisms (SNPs) within its exons and then to evaluate whether these polymorphisms affect body size as well as carcass traits in chickens. The expression analysis showed that the expression level of chicken PITX2 mRNA in the leg muscle and hypophysis was significantly higher (p < 0.01) than those in other tissues. The results of polymorphisms analysis identified two SNPs (i.e., g.9830C > T and g.10073C > T) in exon 1 and 10 SNPs (i.e., g.12713C > T, g.12755C > T, g.12938G > A, g. 3164C > T, g.13019G > A, g.13079G > A, g.13285G > A, g.13335G > A, g.13726A > G and g.13856C > T) in exon 3, including four novel SNPs (i.e., g.9830C > T, g.12713C > T, g.12938G > A and g.13856C > T). In the loci of g.10073C > T and g.12713C > T, chickens with the CT genotype had the highest (p < 0.05 or p < 0.01) breast depth and breast angle, respectively. For the locus of g.13335G > A, chickens with the GG genotype had the highest (p < 0.05 or p < 0.01) breast angle and shank circumference. For the locus of g.13726A > G, chickens with the GG genotype had the highest breast width, fossil keel bone length and shank circumference. The locus of g.12713A > G had significant effects on the PITX2 mRNA expression level in leg muscle. The H1H7 diplotype showed the highest shank circumference, and the H2H8 diplotype showed the highest breast muscle rate. The present research suggested that polymorphisms of the exons of the PITX2 gene were significantly associated with the body size and carcass traits of Wuliang Mountain Black-bone chickens and the PITX2 gene could be a potential candidate gene for molecular marker-aided selection in Wuliang Mountain Black-bone chickens and other chicken breeds.
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