Pub Date : 2019-12-02DOI: 10.4194/2459-1831-v3_2_03
Rabeeha Mankhi Jebur
This study was specifically aimed at Genetic Variation Study Within (Ompok bimaculatus & Clupisoma sinensis) Populations, and evaluated partial Cytb gene sequence of mtDNA for determining the genetic variation within Ompok bimaculatus & Clupisoma sinensis populations in Samarra Dam Middle of Iraq and Shatt Al-Arab Southern of Iraq belonging to Tigris River Using Mitochondrial Cytochrome b Gene. DNA extracted from 80 specimens of the two species of interest from two stations were analyzed. The Size of gene was (amplified Cytb gene) 1,118 bp long and 1,138bp long for O. bimaculatus and C. sinensis, respectively. By using Software DnaSP v5.1, the study revealed that there are two individual species in Samarra Dam and 3 in Shatt-AlArab river whereas 2 haplotypes in C. sinensis population in Shatt Al-Arab and only one hap. In Samarra Dam, there is also Sequencing of Cytb fragments. According to the molecular variance analysis, analyzes of nucleotide diversity and haplotypes pattern were performed separately for each community using the DnaSP v5.10 program. The analysis revealed that there are two types of specific haplotypes in (O. bimaculatus) in the Samarra Dam and 3 of the haplotypes patterns observed in the Shatt al-Arab River, while there are two haplotypes patterns in (St. Sinensis) in the Shatt al-Arab and 1 of haplotypes in Samarra Dam. Low range values of nucleotide and haplotype diversity for both species in Shatt Al-Arab river populations were revealed which refer to low genetic variation within each population in Shatt Al-Arab. As well as low range values of π and Hd for (O. bimaculatus) species in Samarra Dam populations which revealed low genetic variation while no genetic variation in (C. sinensis) population.
本研究专门针对中华鳖和中华鳖（Ompok bimaculatus&Clupisoma sinensis）群体的遗传变异研究，利用线粒体细胞色素b基因评价了mtDNA的Cytb基因部分序列，以确定伊拉克萨马拉大坝中部和伊拉克沙特阿拉伯南部属于底格里斯河的中华鳖和双斑鳖群体的遗传变化。分析了从两个站点的两个感兴趣物种的80个样本中提取的DNA。双斑O.bimaculatus和中华绒螯蟹的Cytb基因扩增长度分别为1118bp和1138bp。通过使用DnaSP v5.1软件，研究表明，萨马拉大坝有两个物种，阿拉伯河有3个物种，而阿拉伯河有2个单体型，只有一个单体型。在萨马拉大坝，还有Cytb片段的测序。根据分子方差分析，使用DnaSP v5.10程序分别对每个群落的核苷酸多样性和单倍型模式进行分析。分析表明，在萨马拉大坝的（双斑O.bimaculatus）中有两种类型的特定单倍型，在阿拉伯河中观察到3种单倍型模式，而在阿拉伯河的（St.Sinensis）中有两只单倍型和萨马拉大坝中有1种单倍模型。两个物种在Shatt Al Arab河种群中的核苷酸和单倍型多样性的低范围值被揭示，这是指在Shatt Al-Arab的每个种群中的低遗传变异。以及萨马拉大坝种群中（双斑O.bimaculatus）物种的π和Hd的低范围值，这表明（中华鳖）种群的遗传变异较低，而没有遗传变异。
{"title":"Genetic Variation Study within (Ompok bimaculatus and Clupisoma sinensis) Populations in Samarra Dam Middle of Iraq and Shatt Al-Arab Southern of Iraq belonging to Tigris River Using Mitochondrial Cytochrome b Gene","authors":"Rabeeha Mankhi Jebur","doi":"10.4194/2459-1831-v3_2_03","DOIUrl":"https://doi.org/10.4194/2459-1831-v3_2_03","url":null,"abstract":"This study was specifically aimed at Genetic Variation Study Within (Ompok bimaculatus & Clupisoma sinensis) Populations, and evaluated partial Cytb gene sequence of mtDNA for determining the genetic variation within Ompok bimaculatus & Clupisoma sinensis populations in Samarra Dam Middle of Iraq and Shatt Al-Arab Southern of Iraq belonging to Tigris River Using Mitochondrial Cytochrome b Gene. DNA extracted from 80 specimens of the two species of interest from two stations were analyzed. The Size of gene was (amplified Cytb gene) 1,118 bp long and 1,138bp long for O. bimaculatus and C. sinensis, respectively. By using Software DnaSP v5.1, the study revealed that there are two individual species in Samarra Dam and 3 in Shatt-AlArab river whereas 2 haplotypes in C. sinensis population in Shatt Al-Arab and only one hap. In Samarra Dam, there is also Sequencing of Cytb fragments. According to the molecular variance analysis, analyzes of nucleotide diversity and haplotypes pattern were performed separately for each community using the DnaSP v5.10 program. The analysis revealed that there are two types of specific haplotypes in (O. bimaculatus) in the Samarra Dam and 3 of the haplotypes patterns observed in the Shatt al-Arab River, while there are two haplotypes patterns in (St. Sinensis) in the Shatt al-Arab and 1 of haplotypes in Samarra Dam. Low range values of nucleotide and haplotype diversity for both species in Shatt Al-Arab river populations were revealed which refer to low genetic variation within each population in Shatt Al-Arab. As well as low range values of π and Hd for (O. bimaculatus) species in Samarra Dam populations which revealed low genetic variation while no genetic variation in (C. sinensis) population.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42471754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-02DOI: 10.4194/2459-1831-v3_2_02
Cheryl K. Y. Tan, J. Cowley, D. Jerry
Due to their convenience, magnetic bead-based nucleic acid extraction kits are commonly used in shrimp genotyping and pathogen screening applications. However, in advanced breeding programs requiring the testing of many thousands of shrimp, their cost can be prohibitive. Various permutations of different Proteinase K digestion, tissue lysis and bead washing buffers as well as magnetic bead types were thus evaluated to devise a high-throughput shrimp DNA extraction (SDE) protocol capable of recovering high-purity DNA using a KingFisher™ Flex Magnetic Particle processor. When genotyped using a MassARRAY® platform (Agena Bioscience) requiring 60-61 genome regions to be co-amplified in a single multiplexed PCR, DNA extracted from shrimp muscle tissue using either the SDE protocol or a commercial kit generated comparable single-nucleotide polymorphism (SNP) call data. The SDE protocol also extracted high-purity DNA from salmon fin clips. It thus offers potential to markedly reduce the costs of large-scale genotyping in shrimp and salmon breeding programs.
{"title":"A Magnetic Bead-Based DNA Extraction Protocol Suitable for High-Throughput Genotyping in Shrimp Breeding Programs","authors":"Cheryl K. Y. Tan, J. Cowley, D. Jerry","doi":"10.4194/2459-1831-v3_2_02","DOIUrl":"https://doi.org/10.4194/2459-1831-v3_2_02","url":null,"abstract":"Due to their convenience, magnetic bead-based nucleic acid extraction kits are commonly used in shrimp genotyping and pathogen screening applications. However, in advanced breeding programs requiring the testing of many thousands of shrimp, their cost can be prohibitive. Various permutations of different Proteinase K digestion, tissue lysis and bead washing buffers as well as magnetic bead types were thus evaluated to devise a high-throughput shrimp DNA extraction (SDE) protocol capable of recovering high-purity DNA using a KingFisher™ Flex Magnetic Particle processor. When genotyped using a MassARRAY® platform (Agena Bioscience) requiring 60-61 genome regions to be co-amplified in a single multiplexed PCR, DNA extracted from shrimp muscle tissue using either the SDE protocol or a commercial kit generated comparable single-nucleotide polymorphism (SNP) call data. The SDE protocol also extracted high-purity DNA from salmon fin clips. It thus offers potential to markedly reduce the costs of large-scale genotyping in shrimp and salmon breeding programs.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42409594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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