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Cai W, Xu Y, Bai Z, Lin G, Wang L, Dou X, Han D, Wang Z, Wang J, Zhang X, Zhang Y, Qin Y, Gu M, Sun Y, Wu Y, Chen R, Wang Z. Association analysis for SNPs of BAAT and COL1A1 genes with cashmere production performance and other production traits in Liaoning cashmere goats. Anim Biotechnol 2023; 34:2324-2335. [PMID: 35749728 DOI: 10.1080/10495398.2022.2088550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study aimed to investigate the relationship between the polymorphism of bile acid-CoA: amino acid N-acyltransferase (BAAT) and collagen type I alpha 1 chain (COL1A1) genes and the production performance of Liaoning Cashmere goat (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence comparison of BAAT and COL1A1 genes and PCR-Seq polymorphism, and the effect of SNPs on production performance was analyzed by SPSS software. The results showed that three SNPs loci were detected in BAAT gene: G7900A, T7967C, C7998T, and one SNP locus T6716C was detected in COL1AL gene. At G7900A locus, the dominant genotype for cashmere performance was GG, and the dominant genotype for body measurement traits and milk production traits was AG. At T7967C locus, the dominant genotype for cashmere performance was TT, and the dominant genotype for body measurement traits and milk production traits was CC. At C7998T locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. At the T6716C locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. H1H1: AACC is the dominant haplotype combination. Therefore, this study will provide a reliable reference for future research on cashmere production performance, body measurement traits, and milk production traits of LCG.
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Affiliation(s)
- Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - 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
| | - 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
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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2
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Tarasova EI, Frolov AN, Lebedev SV, Romanov MN. Landmark native breed of the Orenburg goats: progress in its breeding and genetics and future prospects. Anim Biotechnol 2023; 34:5139-5154. [PMID: 36495096 DOI: 10.1080/10495398.2022.2154221] [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: 12/14/2022]
Abstract
This paper reviews information about a unique and iconic breed of the Orenburg Oblast, the homeland and the only place where the best herds of Orenburg down-hair goats in Russia are concentrated. Three types of these small ruminant animals are widespread on the territory of the region: Orenburg purebred gray goats, Orenburg purebred white goats, as well as crossbred white goats of F1 White Don × White Orenburg. Currently, at the farms of the Orenburg region, animals are selected according to their phenotype, with selected traits being color, weight and length of down hair. In recent years, the Orenburg goat breed has become an object of genetic research using various marker systems including immunogenetic, microsatellite, mtDNA and SNP markers. Overall, these studies evidence about the uniqueness of the allele pool in the landmark native breed of the Orenburg goats, which is a complex dynamic genetic system, prioritizing its further in-depth genome research and breeding applications.
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Affiliation(s)
- Ekaterina I Tarasova
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Alexey N Frolov
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Svyatoslav V Lebedev
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
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3
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Alsarai TM. Effect of the prolactin gene polymorphism on quantity and quality of milk in Iraqi goats. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Domestic goats in Iraq are one of the oldest domesticated animals in Mesopotamia. Their adaptation characterizes them to harsh environmental conditions such as heat in the summer and cold in the winter. Still, they suffer from neglect and the lack of genetic research that would improve the production of this animal, which is considered a multi-production (milk production, meat production, hair production). And because the prolactin gene is crucial, the current study focused on how the prolactin gene (PRL) affects milk yield and its composition. We obtained three genotypes of the prolactin gene exon 5: AA, AB, and BB. The hybrid genotype AB had the highest daily milk yield in domestic goats, although the recessive type BB had a more significant fat percentage. The genetic approach is advised if breeding aims to enhance milk output daily. So select hybrid genotype AB to exon 5 for the (PRL) gene.
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Keywords: Domestic Iraqi goats; prolactin gene; milk production
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Affiliation(s)
- Tamarah M. Alsarai
- Department of Animal Production, College of Agriculture Engineering Science, University of Baghdad, Baghdad, Iraq
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4
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Abioja M, Logunleko M, Majekodunmi B, Adekunle E, Shittu O, Odeyemi A, Nwosu E, Oke O, Iyasere O, Abiona J, Williams T, James I, Smith O, Daramola J. Roles of Candidate Genes in the Adaptation of Goats to Heat Stress: A Review. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Wu Y, Zhang Y, Qin Y, Cai W, Zhang X, Xu Y, Dou X, Wang Z, Han D, Wang J, Lin G, Wang L, Hao J, Fu S, Chen R, Sun Y, Bai Z, Gu M, Wang Z. Association analysis of single-nucleotide polymorphism in prolactin and its receptor with productive and body conformation traits in Liaoning cashmere goats. Arch Anim Breed 2022; 65:145-155. [PMID: 35505666 PMCID: PMC9051658 DOI: 10.5194/aab-65-145-2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The results of this study showed that the single-nucleotide polymorphism (SNP) sites of the PRL and PRLR genes have
a certain association with the milk production performance, body size and
cashmere performance of Liaoning cashmere goats (LCGs). Through our designed
experiment, the potential SNPs of LCG were
detected by sequence alignment, and two SNPs were found on two genes. The CC
genotype of the PRL gene is the dominant genotype among the three genotypes.
The GG genotype of the PRLR gene is the dominant genotype among the two
genotypes. At the same time, the two genotypes also have good performance in
cashmere production and body size. Through the screening of haplotype
combination, the milk fat rate > 7.6 %, the milk protein
rate > 5.6 %, the milk somatic cell number < 1500 × 103 mL-1, the cashmere fineness < 15.75 µm, the
chest girth > 105 cm, the chest depth > 33 cm, and the waist
height > 67.5 cm are considered as screening indexes for
comprehensive production performance of Liaoning cashmere goats. It is
concluded that the GCGC type is the dominant haplotype combination.
According to our research data, we found that the biological indicators of
Liaoning cashmere goat milk are higher than the national standards, so we
think it is very significant to study the milk production performance of our
experiment. Further research can be done on goat milk production and body
conformation traits around PRL gene and PRLR gene.
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Affiliation(s)
- Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xinjiang Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction
Engineering Center, Liaoyang 110000, China
| | - Jianjun Hao
- Administration Bureau of Zhungeer Banner, Ordos City, Inner Mongolia
010399, China
| | - Shuqing Fu
- Lantian Sub-district Office, Zhungeer Banner, Ordos City, Inner Mongolia
010399, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural
University, Shenyang 110866, China
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6
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Mao C, Akhatayeva Z, Cheng H, Zhang G, Jiang F, Meng X, Yao Y, Elnour IE, Lan X, Song E. A novel 23 bp indel mutation in PRL gene is associated with growth traits in Luxi Blackhead sheep. Anim Biotechnol 2020; 32:740-747. [PMID: 32293991 DOI: 10.1080/10495398.2020.1753757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Prolactin is a highly versatile pituitary hormone with multiple biological functions. PRL expression is regulated by POU1F1 and the prophet of POU1F1 (PROP1). The aim of this study was to investigate the indel variations in ovine PRL and the directly related (PROP1 and POU1F1) genes, and their associations with growth traits in Luxi Blackhead (LXBH) sheep. A monomorphism in PROP1 and POU1F1 genes, and one novel 23-bp insertion mutation in the PRL gene, were identified in LXBH sheep. The 23 bp insertion mutation within PRL gene was significantly associated with several body measurements (e.g., body weight, body height) in sheep of different ages (p < 0.05). Ram lambs (p = 0.036) of genotype insertion/insertion (II) had significantly higher body weights. Weaners (p = 0.018) of genotypes insertion/insertion (II) and insertion/deletion (ID) also had significantly higher body weights compared with male sheep of deletion/deletion (DD) genotype. Moreover, among ewe lambs, individuals of genotype insertion/insertion (II) had a higher paunch girth compared to those with other genotypes (p = 0.044). These findings indicate that a 23 bp indel variant of the ovine PRL gene is correlated with body measurements in LXBH sheep. The findings have potential utility for sheep breeding programs based on marker-assisted selection.
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Affiliation(s)
- Cui Mao
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 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, Shandong, 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, Shandong, 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, Shandong, 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, Shandong, 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, Shandong, China
| | - Ibrahim Elsaeid Elnour
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College 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, Shandong, China.,College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
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7
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Abdel-Aziem SH, Mahrous KF, Abd El-Hafez MAM, Abdel Mordy M. Genetic variability of myostatin and prolactin genes in popular goat breeds in Egypt. J Genet Eng Biotechnol 2017; 16:89-97. [PMID: 30647710 PMCID: PMC6296629 DOI: 10.1016/j.jgeb.2017.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 09/25/2017] [Accepted: 10/05/2017] [Indexed: 11/17/2022]
Abstract
The genetic polymorphisms of two functional genes named: myostatin (MSTN) and prolactin (PRL) were investigated in three goat breeds (Barki, Damascus and Zaraibi) using Sanger nucleotide sequence and restriction fragment length polymorphism (RFLP) methods, in order to differentiate between these breeds. Nucleotide sequencing of 337 bp MSTN gene detected five SNPs in Barki breed, two SNPs in Damascus breed, while the Zaraibi breed did not show any SNPs. Moreover, MSTN-HaeIII/PCR-RFLP gave a single Genotype BB was found in all the studied breeds. Meanwhile, Nucleotide sequencing of 196 bp PRL gene showed two SNPs in Damascus breed, one SNPs in Zaraibi breed, while the Barki breed did not show any SNPs. Moreover, PRL-Eco24I/PCR-RFLP showed three genotypes (AA, AB and BB). The genotype AB showed the maximum frequency in all the studied breeds (0.75, 0.85, and 0.90 for Damascus, Barki and Zaraibi breeds, respectively). Observed heterozygosity (Ho) value was higher than expected heterozygosity (He) value all studied breeds. In addition, the values of both Ho and He were the highest in Zaraibi breed (0.90 and 0.51 respectively). Chi-square (χ2) value revealed a significant variation Hardy-Weinberg equilibrium (P < .05) in the three studied breeds. It is the highest in Zaraibi goats and lowest in Damascus breed. The results demonstrated that the PRL-Eco24I/PCR-RFLP polymorphism may be utilized as effective marker for genetic differentiation between goat breeds, but MSTN-HaeIII/PCR-RFLP revealed no polymorphism or variation, thus it is not recommended in the selection program. Moreover, these results open up interesting prospects for future selection programs, especially marker assisted selection. In addition, the results established that PCR-RFLP method is a suitable tool for calculating genetic variability.
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Affiliation(s)
| | - K F Mahrous
- Department of Cell Biology, National Research Center, Dokki, Giza, Egypt
| | - M A M Abd El-Hafez
- Department of Cell Biology, National Research Center, Dokki, Giza, Egypt
| | - M Abdel Mordy
- Department of Zoology, Faculty of Science, Ain Shams University, Cairo, Egypt
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8
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Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, Li Y, Yuan C, Geng R, Lan X, An X, Tian X, Zhou H, Song J, Jiang Y, Chen Y. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Sci Rep 2016; 6:38932. [PMID: 27941843 PMCID: PMC5150979 DOI: 10.1038/srep38932] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/16/2016] [Indexed: 12/25/2022] Open
Abstract
The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZHp and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.
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Affiliation(s)
- Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, 625000, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Life Science, Yulin University, Yulin, 719000, China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China
| | - Rongqing Geng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Pharmacy, Yancheng Teachers University, Yancheng, 224051, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Huangkai Zhou
- Guangzhou Gene de-novo Biotechnology Co. Ltd. Guangzhou, 510000, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742,USA
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
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9
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Shamsalddini S, Mohammadabadi MR, Esmailizadeh AK. Polymorphism of the prolactin gene and its effect on fiber traits in goat. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Wang L, Zhang Y, Zhao M, Wang R, Su R, Li J. SNP Discovery from Transcriptome of Cashmere Goat Skin. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1235-43. [PMID: 26323515 PMCID: PMC4554862 DOI: 10.5713/ajas.15.0172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/04/2015] [Accepted: 06/13/2015] [Indexed: 11/27/2022]
Abstract
The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.
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11
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Linkage disequilibrium and haplotype distribution of the bovine LHX4 gene in relation to growth. Gene 2014; 538:354-60. [DOI: 10.1016/j.gene.2013.12.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 12/04/2013] [Accepted: 12/12/2013] [Indexed: 11/20/2022]
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12
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GAO YUAN, LIU DONG, MA WEI, LI AIMIN, LAN XIANYONG, ZHANG CHUNLEI, LEI CHUZHAO, CHEN HONG. Two novel SNPs in the coding region of bovine VDR gene and their associations with growth traits. J Genet 2013. [DOI: 10.1007/s12041-013-0244-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Haplotype distribution in the GLI3 gene and their associations with growth traits in cattle. Gene 2013; 513:141-6. [DOI: 10.1016/j.gene.2012.10.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 09/08/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022]
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14
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Chang MT, Cheng YS, Huang MC. Association of prolactin haplotypes with reproductive traits in Tsaiya ducks. Anim Reprod Sci 2012; 135:91-6. [DOI: 10.1016/j.anireprosci.2012.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 07/17/2012] [Accepted: 08/18/2012] [Indexed: 11/30/2022]
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15
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Molecular characterization and haplotype combination of PrRP gene polymorphism and its association with production traits in Chinese native goats. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2012.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Bai WL, Yin RH, Jiang WQ, Luo GB, Yin RL, Li C, Zhao ZH. Molecular Characterization of Prolactin cDNA and Its Expression Pattern in Skin Tissue of Liaoning Cashmere Goat. Biochem Genet 2012; 50:694-701. [DOI: 10.1007/s10528-012-9512-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 01/26/2012] [Indexed: 12/19/2022]
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17
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He XP, Xia JH, Wang CM, Pang HY, Yue GH. Significant associations of polymorphisms in the prolactin gene with growth traits in Asian seabass (Lates calcarifer). Anim Genet 2011; 43:233-6. [DOI: 10.1111/j.1365-2052.2011.02230.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Huang YZ, He H, Sun JJ, Wang J, Li ZJ, Lan XY, Lei CZ, Zhang CL, Zhang EP, Wang JQ, Chen H. Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle. Genome 2011; 54:507-16. [DOI: 10.1139/g11-016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR–RFLP, and forced PCR–RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.
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Affiliation(s)
- Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Jia-Jie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Jing Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Zhuan-Jian Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Chun-Lei Zhang
- Institute of Cellular and Molecular Biology, Xuzhou Normal University, Xuzhou Jiangsu, 221116, China
| | - En-Ping Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Ju-Qiang Wang
- Research Center of Cattle Engineering Technology in Henan, Zhengzhou Henan, 450003, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
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Identification of SNPs within the sheep PROP1 gene and their effects on wool traits. Mol Biol Rep 2010; 38:2723-8. [PMID: 21104025 DOI: 10.1007/s11033-010-0416-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
Regarding mutations of PROP1 (Prophet of POU1F1) gene significantly associating with combined pituitary hormone deficiency (CPHD) in human patients and animals, PROP1 gene is a novel important candidate gene for detecting genetic variation and growth, reproduction, metabolism traits selection and breeding. The aim of this study was to detect PROP1 gene mutation of the exon 1-3 and its association with wool traits in 345 Chinese Merino sheep. In this study, on the basis of PCR-SSCP and DNA sequencing methods, ten novel SNPs within the sheep PROP1 gene, namely, AY533708: g.45A>G resulting in Glu15Glu, g.1198A>G, g.1341G>C resulting in Arg63Ser, g.1389G>A resulting in Ala79Ala, g.1402C>T resulting in Leu84Leu, g.1424A>G resulting in Asn91Ser, g.1522C>T, g.1556A>T, g.1574T>C, g.2430C>G were reported. In addition, association analysis showed that three genotypes of P4 fragment were significantly associated with fiber diameter in the analyzed population (P=0.044). These results strongly suggested that polymorphisms of the PROP1 gene could be a useful molecular marker for sheep breeding and genetics through marker-assisted selection (MAS).
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A large indel mutation of the bovine ADD1/SREBP1c gene and its effects on growth traits in some native cattle breeds from China. Mol Biol Rep 2010; 38:2037-42. [DOI: 10.1007/s11033-010-0327-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
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Huang YZ, Zhang EP, Chen H, Wang J, Li ZJ, Huai YT, Ma L, Lan XY, Ren G, Lei CZ, Fang XT, Wang JQ. Novel 12-bp deletion in the coding region of the bovine NPM1 gene affects growth traits. J Appl Genet 2010; 51:199-202. [PMID: 20453307 DOI: 10.1007/bf03195728] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The nucleophosmin 1 gene (NPM1) encodes a multifunctional nucleolar phosphoprotein that plays a crucial role in the control of various aspects of cell growth and homeostasis. In this study, the coding region of the NPM1 gene was screened in 1035 individuals of 4 Chinese cattle breeds by DNA sequencing and polyacrylamide gel electrophoresis. A novel 12-bp deletion mutation was identified in the coding region of the NPM1 gene. The PCR products of primer NPM1-P2 exhibited 3 genotypes and 2 alleles: 178 bp (denoted as W) and 166 bp (denoted as D). Genotype DD and allele D were predominant in the studied populations. Association analysis with growth traits in the Nanyang breed (N = 265) showed that the animals with genotype DD had significantly greater birth weight, body weight, body length, and heart girth than those with genotype WD (P < 0.01 or P < 0.05) at birth and after 6 months and 12 months, but not at 18 and 24 months of age. Results of this study suggest that the NPM1 gene is a candidate gene for growth traits in cattle.
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Affiliation(s)
- Y-Z Huang
- 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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Lan X, Pan C, Li J, Guo Y, Hu S, Wang J, Liu Y, Hu S, Lei C, Chen H. Twelve novel SNPs of the goat POU1F1 gene and their associations with cashmere traits. Small Rumin Res 2009. [DOI: 10.1016/j.smallrumres.2009.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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