基于转录组测序的大口黑鲈驯食相关SNP开发及其与生长性状的关联分析
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摘要
大口黑鲈为肉食性鱼类,传统养殖过程中使用大量的冰鲜鱼为饵料,冰鲜鱼的使用不仅增加了养殖成本,而且多余的冰鲜鱼残饵还会给环境带来严重的污染。为了保护环境并降低养殖成本必须减少冰鲜鱼的使用量,本实验以选育适合人工配合饲料饲喂大口黑鲈为研究目标,用人工配合饲料作为饵料驯化大口黑鲈幼鱼,在驯食后14和16 d,测定其体质量、全长、体高等生长指标。同时在大口黑鲈转录组测序分析获得的SNP位点中,选择其所在序列的基因功能与能量代谢有相关性的7个SNP位点进行SNaPshot分型,用SPSS 19.0进行卡方分析标记与生长性状的相关性。结果发现,序列Unigene031044中的C1332G位点、Unigene085384中的A741G位点和Unigene022319中的A284G位点在体质量、全长及体高性状上存在显著差异。这3个SNP位点所在的基因经预测分别与雌二醇17β脱氢酶12B (hsd17b12b)基因、长链酰基辅酶A合成酶家族成员1(acsl1)基因和琥珀酸脱氢酶组装因子2(sdhaf2)基因具有很高的同源性,推测上述3个SNP位点的变异可能影响了基因表达产物对脂肪酸代谢或三羧酸循环的调节功能,与大口黑鲈对人工配合饲料的利用能力存在密切的相关性。本研究筛选得到的与驯食相关的SNP位点为大口黑鲈功能基因多态性的进一步研究,及加快大口黑鲈食性改良与驯化育种的遗传研究提供了科学的参考依据。
Micropterus salmoides is a species of carnivorous teleost. Annually, a large amount of forage fish were used as food for M. salmoides. The residual forage fish not only increase the culture costs, but also pollute environment seriously. In order to protect the environment and cut down culture costs, it is necessary to breed the strain which can digest and absorb formulated feed efficiently to reduce the utilization of forage fish. In this study, for promoting selective breeding of the M. salmoides strain suitable for formulated feeds, bait domestication was carried out in juvenile M. salmoides of breeding group and non-breeding guoup. On the 14 th day and the 16 th day after bait domestication, the growth traits including body weight, total length and body height were measured. At the same time, seven candidate Unigenes related to energy metabolism with SNPs were selected from the transcriptome of M. salmoides. The SNP sites were genotyped by using of SNaPshot in a bulked segregate analysis(BSA)population with 129 minimax individuals, and the association analysis between genotypes and growth traits were detected. After analysis by using of SPSS 19.0 software, the results showed that, among the seven SNP sites,C1332 G in Unigene031044, A741 G in Unigene085384, A284 G in Unigene022319, were significantly associated with body weight, full length and body height. By BLAST analysis, Unigene031044, Unigene085384 and Unigene022319 were predicted as hydroxysteroid 17-beta dehydrogenase 12-B(hsd17 b12 b), Acyl-CoA synthetase long-chain family member 1(acsl1) and Succinate dehydrogenase complex assembly factor 2(sdhaf2). The results indicated that the SNP sites in above three genes probably play the roles of regulating lipid metabolism and three carboxylic acid cycle, and help M. salmoides to improve the capacity to digest, absorb and utilize formulated feed.The current three SNPs can be used as candidate markers for breeding M. salmoides suitable for formulated feeds.
Micropterus salmoides is a species of carnivorous teleost. Annually, a large amount of forage fish were used as food for M. salmoides. The residual forage fish not only increase the culture costs, but also pollute environment seriously. In order to protect the environment and cut down culture costs, it is necessary to breed the strain which can digest and absorb formulated feed efficiently to reduce the utilization of forage fish. In this study, for promoting selective breeding of the M. salmoides strain suitable for formulated feeds, bait domestication was carried out in juvenile M. salmoides of breeding group and non-breeding guoup. On the 14 th day and the 16 th day after bait domestication, the growth traits including body weight, total length and body height were measured. At the same time, seven candidate Unigenes related to energy metabolism with SNPs were selected from the transcriptome of M. salmoides. The SNP sites were genotyped by using of SNaPshot in a bulked segregate analysis(BSA)population with 129 minimax individuals, and the association analysis between genotypes and growth traits were detected. After analysis by using of SPSS 19.0 software, the results showed that, among the seven SNP sites,C1332 G in Unigene031044, A741 G in Unigene085384, A284 G in Unigene022319, were significantly associated with body weight, full length and body height. By BLAST analysis, Unigene031044, Unigene085384 and Unigene022319 were predicted as hydroxysteroid 17-beta dehydrogenase 12-B(hsd17 b12 b), Acyl-CoA synthetase long-chain family member 1(acsl1) and Succinate dehydrogenase complex assembly factor 2(sdhaf2). The results indicated that the SNP sites in above three genes probably play the roles of regulating lipid metabolism and three carboxylic acid cycle, and help M. salmoides to improve the capacity to digest, absorb and utilize formulated feed.The current three SNPs can be used as candidate markers for breeding M. salmoides suitable for formulated feeds.
引文
[1]农业部渔业渔政管理局.中国渔业统计年鉴2014[M].北京:中国农业出版社,2014.Fisheries and Fisheries Administration Bureau of the Ministry of Agriculture. Chinese fishery statistical year-book 2014[M]. Beijing:China Agriculture Press,2014(in Chinese).
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[9]李延恩,周艳红.SNP功能分析的生物信息学方法及其资源[J].计算机仿真,2007, 24(4):297-300.Li Y E, Zhou Y H. Bioinformatics methods and resources for SNP functional analysis[J]. Computer Simulation, 2007, 24(4):297-300(in Chinese).
[10] Luu-The V, Tremblay P, Labrie F. Characterization oftype 1217 beta-hydroxysteroid dehydrogenase, an isoform of type 317β-hydroxysteroid dehydrogenase responsible for estradiol formation in women[J]. Molecular Endocrinology, 2006, 20(2):437-443.
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[12] Tsuchiya M, Nakao H, Katoh T, et al. Association between endometriosis and genetic polymorphisms of the estradiol-synthesizing enzyme genes HSD17B1 and CYP19[J]. Human Reproduction, 2005, 20(4):974-978.
[13] Plourde M, Ferland A, Soucy P, et al. Analysis of 17β-hydroxysteroid dehydrogenase types 5,7, and 12 genetic sequence variants in breast cancer cases from French Canadian Families with high risk of breast and ovarian cancer[J]. The Journal of Steroid Biochemistry and Molecular Biology, 2009, 116(3):134-153.
[14] Su W, Wang Y, Jia X, et al. Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein in nonalcoholic fatty liver disease[J]. Proceedings of the National Academy of Science of the United States of America,2014, 111(31):11437-11442.
[15] Soupene E, Kuypers F A. Multiple erythroid isoforms of human long-chain acyl-CoA synthetases are produced by switch of the fatty acid gate domains[J]. BMC Molecular Biology, 2006, 7:21.
[16]李庆岗,陶著,杨玉增,等.长链脂酰CoA合成酶(ACSL)的研究进展[J].中国畜牧兽医,2012, 39(6):137-140.Li Q G, Tao Z, Yang Y Z, et al. Research progress of long chain Acyl-CoA synthetase[J]. China Animal Husbandry&Veterinary Medicine, 2012, 39(6):137-140(in Chinese).
[17] Manichaikul A, Wang X Q, Zhao W, et al. Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis[J]. Journal of Lipid Research, 2016, 57(3):433-442.
[18] Li Q G, Tao Z, Shi L H, et al. Expression and genome polymorphism of ACSL1 gene in different pig breeds[J].Molecular Biology Reports, 2012, 39(9):8787-8792.
[19] Lopes-Marques M, Cunha I, Reis-Henriques M A, et al.Diversity and history of the long-chain acyl-CoA synthetase(Acsl)gene family in vertebrates[J]. BMC Evolutionary Biology, 2013, 13:271.
[20] Cheng H L, Chen S, Xu J H, et al. Molecular cloning and nutrient regulation analysis of long chain acyl-CoA synthetase 1 gene in grass carp, Ctenopharyngodon idella L[J]. Comparative Biochemistry and PhysiologyPart B:Biochemistry and Molecular Biology, 2017, 204:61-68.
[21] Hao H X, Khalimonchuk O, Schraders M, et al. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma[J]. Science, 2009,325(5944):1139-1142.
[22] Bayley J P, Kunst H P M, Cascon A, et al. SDHAF2mutations in familial and sporadic paraganglioma and phaeochromocytoma[J]. The Lancet Oncology, 2010,11(4):366-372.
[2]雷霁霖.中国海水养殖大产业架构的战略思考[J].中国水产科学,2010, 17(3):600-609.Lei J L. Strategy consideration for industry construction of Chinese marine culture[J]. Journal of Fishery Sciences of China, 2010, 17(3):600-609(in Chinese).
[3] Babji Y,Murthy T R K,Anjaneyulu A S R. Microbial and sensory quality changes in refrigerated minced goat meat stored under vacuum and in air[J]. Small Ruminant Research, 2000, 36(1):75-84.
[4]王广军,吴锐全,谢骏,等.大口黑鲈投喂两种不同饲料对水质指标的影响[J].水产学杂志,2009, 22(1):35-37,46.Wang G J, Wu R Q, Xie J, et al. Effects of feeding two kinds of feed on the water quality in largemouth bass(Micropterus salmoides)aquarium[J]. Chinese Journal of Fisheries, 2009, 22(1):35-37, 46(in Chinese).
[5] Krishnankutty N. Plant proteins in fish feed:An additional analysis[J]. Current Science, 2005, 89(6):934-936.
[6] Overturf K, Bullock D, LaPatra S, et al. Genetic selection and molecular analysis of domesticated rainbow trout for enhanced growth on alternative diet sources[J].Environmental Biology of Fishes, 2004, 69(1-4):409-418.
[7] Al-Shahib A, Underwood A. Snp-search:Simple processing, manipulation and searching of SNPs from highthroughput sequencing[J]. BMC Bioinformatics, 2013,14:326.
[8]全迎春,马冬梅,白俊杰,等.大口黑鲈转录组SNPs筛选及其与生长的关联分析[J].水生生物学报,2016,40(6):1128-1134.Quan Y C, Ma D M, Bai J J, et al. SNPs identification in RNA-SEQ data of largemouth bass(Micropterus salmoides)fed on formulated feed and association analysis with growth trait[J]. Acta Hydrobiologica Sinica, 2016,40(6):1128-1134(in Chinese).
[9]李延恩,周艳红.SNP功能分析的生物信息学方法及其资源[J].计算机仿真,2007, 24(4):297-300.Li Y E, Zhou Y H. Bioinformatics methods and resources for SNP functional analysis[J]. Computer Simulation, 2007, 24(4):297-300(in Chinese).
[10] Luu-The V, Tremblay P, Labrie F. Characterization oftype 1217 beta-hydroxysteroid dehydrogenase, an isoform of type 317β-hydroxysteroid dehydrogenase responsible for estradiol formation in women[J]. Molecular Endocrinology, 2006, 20(2):437-443.
[11] Moon Y A, Horton J D, Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade[J]. Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade[J]. Journal of Biological Chemistry, 2003,278(9):7335-7343.
[12] Tsuchiya M, Nakao H, Katoh T, et al. Association between endometriosis and genetic polymorphisms of the estradiol-synthesizing enzyme genes HSD17B1 and CYP19[J]. Human Reproduction, 2005, 20(4):974-978.
[13] Plourde M, Ferland A, Soucy P, et al. Analysis of 17β-hydroxysteroid dehydrogenase types 5,7, and 12 genetic sequence variants in breast cancer cases from French Canadian Families with high risk of breast and ovarian cancer[J]. The Journal of Steroid Biochemistry and Molecular Biology, 2009, 116(3):134-153.
[14] Su W, Wang Y, Jia X, et al. Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein in nonalcoholic fatty liver disease[J]. Proceedings of the National Academy of Science of the United States of America,2014, 111(31):11437-11442.
[15] Soupene E, Kuypers F A. Multiple erythroid isoforms of human long-chain acyl-CoA synthetases are produced by switch of the fatty acid gate domains[J]. BMC Molecular Biology, 2006, 7:21.
[16]李庆岗,陶著,杨玉增,等.长链脂酰CoA合成酶(ACSL)的研究进展[J].中国畜牧兽医,2012, 39(6):137-140.Li Q G, Tao Z, Yang Y Z, et al. Research progress of long chain Acyl-CoA synthetase[J]. China Animal Husbandry&Veterinary Medicine, 2012, 39(6):137-140(in Chinese).
[17] Manichaikul A, Wang X Q, Zhao W, et al. Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis[J]. Journal of Lipid Research, 2016, 57(3):433-442.
[18] Li Q G, Tao Z, Shi L H, et al. Expression and genome polymorphism of ACSL1 gene in different pig breeds[J].Molecular Biology Reports, 2012, 39(9):8787-8792.
[19] Lopes-Marques M, Cunha I, Reis-Henriques M A, et al.Diversity and history of the long-chain acyl-CoA synthetase(Acsl)gene family in vertebrates[J]. BMC Evolutionary Biology, 2013, 13:271.
[20] Cheng H L, Chen S, Xu J H, et al. Molecular cloning and nutrient regulation analysis of long chain acyl-CoA synthetase 1 gene in grass carp, Ctenopharyngodon idella L[J]. Comparative Biochemistry and PhysiologyPart B:Biochemistry and Molecular Biology, 2017, 204:61-68.
[21] Hao H X, Khalimonchuk O, Schraders M, et al. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma[J]. Science, 2009,325(5944):1139-1142.
[22] Bayley J P, Kunst H P M, Cascon A, et al. SDHAF2mutations in familial and sporadic paraganglioma and phaeochromocytoma[J]. The Lancet Oncology, 2010,11(4):366-372.