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Identification of genetic variants the CCKAR gene and based on body measurement and carcass quality characteristics in Qinchuan beef cattle (Bos taurus). ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Yang X, Ning Y, Mei C, Zhang W, Sun J, Wang S, Zan L. The role of BAMBI in regulating adipogenesis and myogenesis and the association between its polymorphisms and growth traits in cattle. Mol Biol Rep 2020; 47:5963-5974. [PMID: 32740798 DOI: 10.1007/s11033-020-05670-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022]
Abstract
Bone morphogenic protein and activin membrane-bound inhibitor (BAMBI) is a transmembrane protein that affects the growth, development and muscle regeneration of the body by regulating the TGF-β, BMP and Wnt signaling pathways. Studies have found that BAMBI has important regulatory functions in skeletal muscle and preadipocytes in vivo and in vitro. However, research on this protein in cattle is lacking. In this study, to determine the role of BAMBI in the growth and development of cattle, we first found that the expression of BAMBI in adipose tissue and longissimus muscle of newborn and adult Qinchuan beef cattle was significantly different. Then we showed that BAMBI knockdown promoted the differentiation of bovine preadipocytes and suppressed myoblast myogenesis, as indicated by the increased lipid droplets and the decreased myotubes, as well as the corresponding significant changes in the expression of PPARγ, C/EBPα, C/EBPβ, FABP4, MyoD, MyoG and Myf6. Finally, to further verify the effect of BAMBI on the growth performance of cattle, we identified seven novel SNPs in the BAMBI genomic region, which were significantly correlated with one or more growth traits (p < 0.05). Furthermore, individuals with haplotype H1H4 (TC-GA-CT-CA-AT-AT-AG) had a higher body and carcass quality than those with other haplotypes (p < 0.05). In brief, BAMBI may be a functional gene for the differentiation of bovine preadipocytes and myoblasts, and variations in the BAMBI genomic region, especially the combined haplotype H1H4, may benefit marker-assisted selection in cattle.
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Affiliation(s)
- Xinran Yang
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yue Ning
- College of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, 712000, Shaanxi, China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling, 712100, Shaanxi, China
| | - Weiyi Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Jingchun Sun
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Sihu Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, Shaanxi, China. .,National Beef Cattle Improvement Center, Yangling, 712100, Shaanxi, China.
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Genetic variants in MYF5 affected growth traits and beef quality traits in Chinese Qinchuan cattle. Genomics 2020; 112:2804-2812. [PMID: 32220486 DOI: 10.1016/j.ygeno.2020.03.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/07/2020] [Accepted: 03/22/2020] [Indexed: 12/14/2022]
Abstract
Myogenic factor 5 plays actively roles in the regulation of myogenesis. The aims of this study are to identify the evolution information of MYF5 protein among 10 domestic and mammalian animals, to uncover the expression patterns of MYF5 gene in calves and adults of Qinchuan cattle, and to expose the genetic variants of the MYF5 gene and explore its effect on cattle growth traits and beef quality traits in Qinchuan cattle. The bioinformatics results showed that the MYF5 proteins highly conserved in different mammalian or domestic animals apart from chicken. The expression level of MYF5 gene in the heart, muscle, lung, large intestine and liver was greater than that of other tissues. PCR amplicons sequencing identified four novel SNPs at g.5738A>G, g.5785C>T and g.5816A>G in the 3rd exon region and g.6535A>G in the 3' UTR. Genotypic frequencies of g.5785C>T was harshly deviated from the HWE (P < .05). Genetic diversity was low or intermediate for the four SNPs and those SNPs were in the weak linkage disequilibrium. Association analysis results indicated g.5785C>T, g.5816A>G and g.6535A>G significant effect on growth performance and beef quality traits of Qinchuan cattle. H1H3 diplotype had greater body size and better beef quality. All the results implicate that the MYF5 gene might be applied as a promising candidate gene in Qinchuan cattle breeding.
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Khan R, Raza SHA, Guo H, Xiaoyu W, Sen W, Suhail SM, Rahman A, Ullah I, Abd El-Aziz AH, Manzari Z, Alshawi A, Zan L. Genetic variants in the TORC2 gene promoter and their association with body measurement and carcass quality traits in Qinchuan cattle. PLoS One 2020; 15:e0227254. [PMID: 32059009 PMCID: PMC7021310 DOI: 10.1371/journal.pone.0227254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 11/27/2019] [Indexed: 11/19/2022] Open
Abstract
The TORC2 gene is responsible for nutrient metabolism, gluconeogenesis, myogenesis and adipogenesis through the PI3K-Akt, AMPK, glucagon and insulin resistance signaling pathways. Sequencing of PCR amplicons explored three novel SNPs at loci g.16534694G>A, g.16535011C>T, and g.16535044A>T in the promoter region of the TORC2 gene in the Qinchuan breed of cattle. Allelic and genotypic frequencies of these SNPs deviated from Hardy-Weinberg equilibrium (HWE) (P < 0.05). SNP1 genotype GG, SNP2 genotype CT and SNP3 genotype AT showed significantly (P <0.05) larger body measurement and improved carcass quality traits. Haplotype H1 (GCA) showed significantly (p<0.01) higher transcriptional activity (51.44%) followed by H4 (ATT) (34.13%) in bovine preadipocytes. The diplotypes HI-H3 (GG-CC-AT), H1-H2 (GG-CT-AT) and H3-H4 (GA-CT-TT) showed significant (P<0.01) associations with body measurement and improved carcass quality traits. Analysis of the relative mRNA expression level of the TORC2 gene in different tissues within two different age groups revealed a significant increase (P<0.01) in liver, small intestine, muscle and fat tissues with growth from calf stage to adult stage. We can conclude that variants mapped within TORC2 can be used in marker-assisted selection for carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.
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Affiliation(s)
- Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Wang Xiaoyu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Wu Sen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Syed Muhammad Suhail
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Abdur Rahman
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Irfan Ullah
- College of Bio-medical Engineering, Chongqing University, Chongqing, China
| | - Ayman Hassan Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Zeinab Manzari
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Akil Alshawi
- School of Life Science University of Nottingham, Nottingham, United Kingdom
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
- National Beef Cattle Improvement Research Center, Yangling, China
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Expression of the bovine KLF6 gene polymorphisms and their association with carcass and body measures in Qinchuan cattle (Bos Taurus). Genomics 2020; 112:423-431. [DOI: 10.1016/j.ygeno.2019.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 02/02/2023]
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Shishay G, Liu G, Jiang X, Yu Y, Teketay W, Du D, Jing H, Liu C. Variation in the Promoter Region of the MC4R Gene Elucidates the Association of Body Measurement Traits in Hu Sheep. Int J Mol Sci 2019; 20:E240. [PMID: 30634446 PMCID: PMC6358852 DOI: 10.3390/ijms20020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 12/30/2018] [Indexed: 12/15/2022] Open
Abstract
The melanocortin 4 receptor (MC4R) gene is expressed in the appetite-regulating areas of the brain and is engaged in the leptin signaling pathway. Although previous studies have identified variants in the coding region of the sheep MC4R gene showing significant associations with birth weight, weaning weight, and backfat thickness, no such associations have been reported for the promoter region. Besides, the essential promoter region of the sheep MC4R has not been delineated. In this study, to better understand the transcriptional regulation of MC4R and to elucidate the association between regulatory variants and haplotypes with body measurement traits in sheep, we cloned and characterized the MC4R promoter. We found that the minimal promoter of the gene is located within the region -1207/-880 bp upstream of the first exon. Real-time quantitative PCR (RT-qPCR) data revealed the mRNA expression of the MC4R gene had a significant difference between sex and age. In the association analysis, eight single nucleotide polymorphisms (SNPs) had a significant association with one or more traits (p < 0.05); of these, two SNPs were novel. Notably, individuals with haplotype H1H2 (CT-GA-GT-GA-GT-GA-GA-CG) were heavier in body weight than other haplotypes. Altogether, variations in the MC4R gene promoter, most notably haplotype H1H2, may greatly benefit marker-assisted selection in sheep.
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Affiliation(s)
- Girmay Shishay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Yu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wassie Teketay
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dandan Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huang Jing
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenghui Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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Wu S, Wang Y, Ning Y, Guo H, Wang X, Zhang L, Khan R, Cheng G, Wang H, Zan L. Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle. Int J Mol Sci 2018; 19:ijms19041035. [PMID: 29596388 PMCID: PMC5979584 DOI: 10.3390/ijms19041035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy-Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle.
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Affiliation(s)
- Sen Wu
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yaning Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yue Ning
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Le Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
- National Beef Cattle Improvement Center of Northwest A & F University, Yangling 712100, China.
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Shen C, Li X, Zhang R, Lin Z. Genome-wide recombination rate variation in a recombination map of cotton. PLoS One 2017; 12:e0188682. [PMID: 29176878 PMCID: PMC5703465 DOI: 10.1371/journal.pone.0188682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/10/2017] [Indexed: 01/03/2023] Open
Abstract
Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species’ genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.
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Affiliation(s)
- Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Agronomy and Plant Protection, Qingdao Agricultural University/Shandong Key Laboratory of Dryland Farming Technology, Qingdao, Shandong, China
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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Zhang H, Li X, Zhou L, Zhang K, Zhang Q, Li J, Wang N, Jin M, Wu N, Cong M, Qiu C. A novel haplotype of low-frequency variants in the aldosterone synthase gene among northern Han Chinese with essential hypertension. Medicine (Baltimore) 2017; 96:e8150. [PMID: 28953657 PMCID: PMC5626300 DOI: 10.1097/md.0000000000008150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Low-frequency variants showed that there is more power to detect risk variants than to detect protective variants in complex diseases. Aldosterone plays an important role in the renin-angiotensin-aldosterone system, and aldosterone synthase catalyzes the speed-controlled steps of aldosterone biosynthesis. Polymorphisms of the aldosterone synthase gene (CYP11B2) have been reported to be associated with essential hypertension (EH). CYP11B2 polymorphisms such as -344T/C, have been extensively reported, but others are less well known. This study aimed to assess the association between human CYP11B2 and EH using a haplotype-based case-control study. A total of 1024 EH patients and 956 normotensive controls, which consist of north Han population peasants, were enrolled. Seven single nucleotide polymorphisms (SNPs) (rs28659182, rs10087214, rs73715282, rs542092383, rs4543, rs28491316, and rs7463212) covering the entire human CYP11B2 gene were genotyped as markers using the MassARRAY system. The major allele G frequency of rs542092383 was found to be risk against hypertension [odds ratio (OR) 3.478, 95% confidence interval (95% CI) 1.407-8.597, P = .004]. The AG genotype frequency of SNP rs542092383 was significantly associated with an increased risk of hypertension (OR 4.513, 95% CI 1.426-14.287, P = .010). In the haplotype-based case-control analysis, the frequency of the T-G-T haplotype was higher for EH patients than for controls (OR 5.729, 95% CI 1.889-17.371, P = .000495). All |D'| values of the seven SNPs were >0.9, and r values for rs28659182- rs10087214-rs28491316-rs7463212 SNPs were >0.8 and showed strong linkage intensity. Haplotype T-G-T may therefore be a useful genetic marker for EH.
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Affiliation(s)
- Hao Zhang
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Xueyan Li
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Li Zhou
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Keyong Zhang
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Qi Zhang
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Jingping Li
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Ningning Wang
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Ming Jin
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Nan Wu
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Mingyu Cong
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
| | - Changchun Qiu
- Institute of Polygenic Disease, Qiqihar Medical University, Qiqihar, Heilongjiang Province
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (Peking Union) Medical College (CAMS/PUMC), Beijing, P. R. China
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Gion JM, Hudson CJ, Lesur I, Vaillancourt RE, Potts BM, Freeman JS. Genome-wide variation in recombination rate in Eucalyptus. BMC Genomics 2016; 17:590. [PMID: 27507140 PMCID: PMC4979139 DOI: 10.1186/s12864-016-2884-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 07/06/2016] [Indexed: 11/25/2022] Open
Abstract
Background Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Results Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = −0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = −0.75). Conclusions The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.
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Affiliation(s)
| | - Corey J Hudson
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.,Present address: Tasmanian Alkaloids, P.O. Box 130, Westbury, TAS, 7303, Australia
| | | | - René E Vaillancourt
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Brad M Potts
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Jules S Freeman
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
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An X, Song Y, Bu S, Ma H, Gao K, Hou J, Wang S, Lei Z, Cao B. Association of polymorphisms at the microRNA binding site of the caprine KITLG 3'-UTR with litter size. Sci Rep 2016; 6:25691. [PMID: 27168023 PMCID: PMC4863368 DOI: 10.1038/srep25691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/21/2016] [Indexed: 01/23/2023] Open
Abstract
This study identified three novel single nucleotide polymorphisms (SNPs) (c.1389C > T, c.1457A > C and c.1520G > A) in the caprine KITLG 3'-UTR through DNA sequencing. The three SNP loci were closely linked in Guanzhong dairy (GD) goats. Two alleles of the c.1457A > C SNP introduced two miRNA sites (chi-miR-204-5p and chi-miR-211). Individuals with combined genotype TT-CC-AA had a higher litter size compared with those with combined genotypes CC-AA-GG, TC-CC-GA and CC-AC-GG (P < 0.05). Luciferase assays showed that chi-miR-204-5p and chi-miR-211 suppressed luciferase expression in the presence of allele 1457A compared with negative control (NC) and allele 1457C (P < 0.05). Western blot revealed that KITLG significantly decreased in the granulosa cells (GCs) of genotype AA compared with that in the GCs of genotype CC and NC (P < 0.05). The KITLG mRNA levels of the CC-AA-GG carriers significantly decreased compared with those of the TT-CC-AA, TC-CC-GA and CC-AC-GG carriers. In addition, cell proliferation was reduced in haplotype C-A-G GCs compared with that in haplotype T-C-A GCs. These results suggest that SNPs c.1389C > T, c.1457A > C and c.1520G > A account for differences in the litter size of GD goats because chi-miR-204-5p and chi-miR-211 could change the expression levels of the KITLG gene and reduce GC proliferation.
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Affiliation(s)
- Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shuhai Bu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Haidong Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Kexin Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jinxing Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhang Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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An X, Hou J, Gao T, Lei Y, Li G, Song Y, Wang J, Cao B. Single-nucleotide polymorphisms g.151435C>T and g.173057T>C in PRLR gene regulated by bta-miR-302a are associated with litter size in goats. Theriogenology 2015; 83:1477-1483.e1. [DOI: 10.1016/j.theriogenology.2015.01.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 01/19/2015] [Accepted: 01/24/2015] [Indexed: 01/22/2023]
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Gibson J, Tapper W, Ennis S, Collins A. Exome-based linkage disequilibrium maps of individual genes: functional clustering and relationship to disease. Hum Genet 2012; 132:233-43. [PMID: 23124193 DOI: 10.1007/s00439-012-1243-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/20/2012] [Indexed: 11/26/2022]
Abstract
Exome sequencing identifies thousands of DNA variants and a proportion of these are involved in disease. Genotypes derived from exome sequences provide particularly high-resolution coverage enabling study of the linkage disequilibrium structure of individual genes. The extent and strength of linkage disequilibrium reflects the combined influences of mutation, recombination, selection and population history. By constructing linkage disequilibrium maps of individual genes, we show that genes containing OMIM-listed disease variants are significantly under-represented amongst genes with complete or very strong linkage disequilibrium (P = 0.0004). In contrast, genes with disease variants are significantly over-represented amongst genes with levels of linkage disequilibrium close to the average for genes not known to contain disease variants (P = 0.0038). Functional clustering reveals, amongst genes with particularly strong linkage disequilibrium, significant enrichment of essential biological functions (e.g. phosphorylation, cell division, cellular transport and metabolic processes). Strong linkage disequilibrium, corresponding to reduced haplotype diversity, may reflect selection in utero against deleterious mutations which have profound impact on the function of essential genes. Genes with very weak linkage disequilibrium show enrichment of functions requiring greater allelic diversity (e.g. sensory perception and immune response). This category is not enriched for genes containing disease variation. In contrast, there is significant enrichment of genes containing disease variants amongst genes with more average levels of linkage disequilibrium. Mutations in these genes may less likely lead to in utero lethality and be subject to less intense selection.
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Affiliation(s)
- Jane Gibson
- Genetic Epidemiology and Genomic informatics Group, Human Genetics, University of Southampton, Southampton General Hospital, Southampton, UK
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