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Journal of Ocean University of China 2017年第3期16卷 509-516页

作者： TENG Shuangshuang FANG Jun CAI Yilong CHAI Xueliang XIAO Guoqiang Zhejiang Mariculture Research Institute Wenzhou 325005 P. R. China Engineering Research Center for Marine Bivalves Chinese Academy of Fishery Sciences Wenzhou 325005 P. R China Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource Wenzhou 325005 P. R. China

Blood clam, Tegillarca granosa, is an important shellfish in Chinese mariculture industry. Investigative research in this species, such as genetic linkage mapping, requires a large panel of molecular markers. In present study, a total of 89 polymorphic microsatellite markers were developed in T. granosa using the sequence database of Life Sciences Technology 454 next generation sequencing technology. All 89 loci were characterized in 20 individual clams from a natural population inhabiting Yueqing Gulf, Zhejiang Province, China. The number of alleles per polymorphic locus varied between 2 and 15, while the observed heterozygosity, expected heterozygosity and polymorphic information content varied between 0.000 and 1.000, 0.102 and 0.921, and 0.048 and 0.886, respectively. Of the 89 loci identified, 32 loci deviated significantly from Hardy-Weinberg equilibrium following Bonferroni correction. Thirty nine markers, which were shown to be polymorphic in a full-sibling family, were tested in Mendelian segregations. As expected, 32 loci were co-dominantly segregated in a Mendelian fashion. These novel developed microsatellite markers represent useful research tools for investigation of population genetic structure and genetic diversity in this species.

关键词： Tegillarca granosa 表示顺序标签 microsatellite

BanSatDB, a whole-genome-based database of putative and experimentally validated microsatellite markers of three Musa species

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The Crop Journal 2018年第6期6卷 642-650页

作者： Vasu Arora Neera Kapoor Samar Fatma Sarika Jaiswal Mir Asif Iquebal Anil Rai Dinesh Kumar Center for Agricultural Bioinformatics ICAR-Indian Agricultural Statistics Research Institute School of Sciences Indira Gandhi National Open University

The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%–32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB(http://***/bansatdb/) having the highest number(>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata(110,000), M. balbisiana(107,000), and M. itinerans(124,000)from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types(simple or compound),repeat nucleotides(1–6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability(DUS) tests of variety identification and for marker assisted selection(MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity.

关键词： Musaceae Musa Banana microsatellite Short tandem repeat(STR) Primers

Genetic Diversity and Population Structure for the Conservation of Giant Spiny Frog(Quasipaa spinosa)Using microsatellite Loci and Mitochondrial DNA

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Asian Herpetological Research 2016年第2期7卷 75-86页

作者： Danna YU Rongquan ZHENG Qinfang LU Guang YANG Yao FU Yun ZHANG Institute of Ecology Zhejiang Normal UniversityJinhua 321004ZhejiangChina Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province JinhuaZhejiang 321004China Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing 210046JiangsuChina

The giant spiny frog （Quasipaa spinosa） is an endangered species with a relatively small distribution limited to southern China and Northern Vietnam. This species is becoming increasingly threatened because of over-exploitation and habitat degradation. This study provides data on the genetic diversity and population genetic structure of the giant spiny frog to facilitate the further development of effective conservation recommendations for this economically important but threatened species. We examined 10 species-specific microsatellite loci and Cyt b genes （562 bp） collected from 13 wild populations across the entire range of this species. Results of 10 microsatellite loci analysis showed a generally high level of genetic diversity. Moreover, the genetic differentiation among all 12 populations was moderate to large （overall Fs7= 0.1057）. A total of 51 haplotypes were identified for Cyt b, which suggests high haplotype nucleotide diversities. Phylogeographic and population structure analyses using both DNA markers suggested that the wild giant spiny frog can be divided into four distinct major clades, i.e., Northern Vietnam, Western China, Central China, and Eastern China. The clades with significant genetic divergence are reproductively isolated, as evidenced by a high number of private alleles and strong incidence of failed amplification in microsatellite loci. Our research, coupled with other studies, suggests that Q. spinosa might be a species complex within which no detectable morphological variation has been revealed. The four phylogenetic clades and some subclades with distinct geographical distribution should be regarded as independent management units for conservation purposes.

关键词： Cyt b Conservation Giant spiny frog microsatellite Phylogeography Quasipaa spinosa

Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes)

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Chinese Birds 2015年第4期6卷 276-284页

作者： Yufei Dai Qingxian Lin Wenzhen Fang Xiaoping Zhou Xiaolin Chen Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems School of Life SciencesCollege of the Environment and EcologyXiamen University

Background: Noninvasive and nondestructive DNA sampling techniques are becoming more important in genetic studies because they can provide genetic material from wild animals with less or even without disturbance,which is particularly useful for the study of endangered species,i.e.,***,nondestructively and noninvasively sampled DNA may,in some cases,be inadequate in the amount and quality of the material collected,which can lead to low amplification success rates and high genotyping ***: In this study,noninvasive(eggshell swab,shed feather and feces),nondestructive(plucked feather and buccal swab) and invasive(blood) DNA samples were collected from the vulnerable Chinese Egret(Egretta eulophotes).DNA concentrations,PCR amplification success and microsatellite genotyping errors of different sample types were evaluated and compared to determine whether noninvasive and nondestructive samples performed as well as invasive samples in our experimental ***: A total of 159 samples were collected in the *** the different sample types,the highest DNA concentrations(154.0–385.5 ng/μL) were obtained from *** extracted from fecal samples were the lowest,ranging from 1.25 to 27.5 ng/μ*** all of the DNA samples,i.e.,95.59 %,were successfully amplified for mt DNA(n = 152) and 92.76 % of mt DNA samples were successfully genotyped for at least five of the nine microsatellite loci tested(n = 141).Blood samples and buccal swabs produced reliable genotypes with no genotyping errors,but in feces,allelic dropouts and false alleles occurred in all nine loci,with error rates ranging from 6.67 to 38.10 % for the dropouts and from 6.06 to 15.15 % for the false ***: These results indicate that both nondestructive and noninvasive samplings are suitable for avian microsatellite genotyping,save for fecal ***,we should remain cautious of the appearance of genotyping errors,especially when using noninvasive material.

关键词： Genotyping Noninvasive sampling Nondestructive sampling microsatellite PCR Avian genetics Chinese Egret

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of microsatellite Instability

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Genomics, Proteomics & Bioinformatics 2020年第1期18卷 65-71页

作者： Peng Jia Xiaofei Yang Li Guo Bowen Liu Jiadong Lin Hao Liang Jianyong Sun Chengsheng Zhang Kai Ye School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Laboratory for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Leiden Institute of Advanced Computer Science Leiden UniversityLeiden 2311 ZENetherlands School of Mathematics and Statistics Xi’an Jiaotong UniversityXi’an 710049China Precision Medicine Center the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China

microsatellite instability(MSI)is a key biomarker for cancer therapy and *** experimental assays are laborious and time-consuming,and next-generation sequencingbased computational methods do not work on leukemia samples,paraffin-embedded samples,or patient-derived xenografts/organoids,due to the requirement of matched normal ***,we developed MSIsensor-pro,an open-source single sample MSI scoring method for research and clinical ***-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative site selection method to enable MSI detection without matched normal *** demonstrate that MSIsensor-pro is an ultrafast,accurate,and robust MSI calling *** samples with various sequencing depths and tumor purities,MSIsensor-pro significantly outperformed the current leading methods in both accuracy and computational ***-pro is available at https://***/xjtu-omics/msisensor-pro and free for non-commercial use,while a commercial license is provided upon request.

关键词： microsatellite Polymerase slippage Multinomial distribution microsatellite instability Tumor

Establishment of microsatellite-based triplex PCR for parentage analysis of Chinese shrimp Fenneropenaeus chinensis

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Acta Oceanologica Sinica 2007年第2期26卷 65-74页

作者： GAO Huan KONG Jie HU Ping MENG Xianhong LUAN Sheng ZHANG Tianshi Jiangsu Key Laboratory of Marine Biotechnology Huaihai Institute of Technology Lianyungang 222005 China Key Laboratory for Sustainable Utilization of Marine Fisheries Resources of Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Qingdao 266071 China

Through exploring the microsatellite primers from the random genome sequences of Chinese shrimp （Fenneropenaeus chinensis）, some microsatellite primers were obtained with rich polymorphic genetic information, and a triplex PCR was established using three primers （RS1101, RS0683 and H081 primers）. By adjusting the final concentration of Mg^2＋, dNTP and primers, and using a touch-town PCR program, the optimum amplification parameters of PCR system were obtained, which could successfully amplify the three primers in a PCR reaction. In the denatured PAGE gel, the amplified DNA fragments of three primers RS1 101,RS0683 and H081 could be easily identified each other. For the triplex PCR system, the PPE （probabilities of paternity exclusion） is 0.967 9,and the DP （discrimination power） is 0.999 *** the triplex PCR to test ten individuals of a parentage and their parents, an individual was excluded from the parentage in all of the three microsatellite loci, which might be mixed into the parentage for some unknown reason such as factitious misplay. The triplex PCR will be of great practical value in identifying the parentages of F. chinensis.

关键词： multiplex PCR touch-down PCR microsatellite parentage analysis Fenneropenaeus chinensis

Using microsatellite markers to identify heritability of Pacific whiteleg shrimp Litopenaeus vannamei

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Acta Oceanologica Sinica 2015年第6期34卷 59-65页

作者： ANDRIANTAHINA Farafidy LIU Xiaolin HUANG Hao College of Animal Science and Technology Northwest A&F University Shaanxi Key Laboratory of Molecular Biology for Agriculture Hainan Guangtai Ocean Breeding Company Limite

Pacific whiteleg shrimp （Litopenaeus vannamei） is an economically relevant shrimp species in many Asian countries. The specific objective of the current research was to assess microsatellite markers in screening the fast- growth of domesticated L. vannamei stocks to establish a founder population for breeding-selection plans. The *** produced by the reproduction of second generation broodstock were cultured in the same conditions throughout a five months growing period. Ninety juvenile shrimp were selected from the slow-, medium- and the fast-growth groups, and ten microsatellite markers were used to investigate their genetic diversity, and to understand the improvement of a breeding-selection scheme. Ten polymorphic loci （markers）（M1-M10） were produced at ten loci in this sample, among them Primer M8 was the highest polymorphic locus and M7 was the lowest one. A specific locus was found in the fast-growth group using Primer M5. The longest genetic distance （0.481） was determined between the fast- and medium-growth groups and the shortest （0.098） was between the slow- and medium-growth groups; therefore, the largest genetic identity （0.946） was observed between the slow- and medium-growth groups and the smallest （0.667） was observed between the medium- and fast-growth groups. The Unweighted Paired Group with Arithmetic Average （UPGMA） dendrogram based on Nei＇s genetic distances provided two different groups; the first consist of the slow- and medium-growth groups and the second the fast- growth group. Selection response and realized heritability for growth were 11.55% and 31.26%, respectively. Therefore, this set of microsatellite markers would provide a useful tool in shrimp breeding schemes.

关键词： genetic parameters growth heritability microsatellite molecular markers

Analysis of novel immune-related genes and microsatellite markers in the transcriptome of Paphia undulata

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Journal of Oceanology and Limnology 2019年第4期37卷 1301-1316页

作者： WU Xiangwei LIU Xiande YU Ziniu Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Provincial Key Laboratory of Applied Marine Biology South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China Animal Science and Technology College Yunnan Agricultural University Kunming 650201 China Key Laboratory of Healthy Mariculture for the East China Sea Ministry of Agriculture of ChinaFisheries College Jimei University Xiamen 361021 China University of Chinese Academy of Sciences Beijing 100049 China

Increasingly,exogenous stressors such as pathogen infections,variable water conditions,and pollution are resulting in high mortality of Paphia undulata,deleteriously affecting the quality of clam *** foot is a burrowing organ in *** damage and constant contact with the external environment cause the foot to be highly sensitive to pathogen invasion and water condition *** the present study,the foot tissue transcriptome was analyzed to identify genes involved in immune and stress *** *** transcriptome included 5 286 668 078 bp reads generated by Illumina Hiseq 2000 sequencing and were assembled into 1 785 226 contigs by de novo *** contigs were clustered into 99 339 transcripts and further grouped into 60 201 *** them,22 260 unigenes were successfully annotated using public *** genes that were response to immune and stress were identified with abundant expression levels,including heat shock protein 70,cold shock protein,complement C3,cathepsin L,ubiquitin carboxyl-terminal hydrolase L5,and translationally controlled tumor ***,566 unigenes were found homologous to genes involved in the immune response systems of pathogen discrimination,signal transduction,and immune effector,such as lectins,toll-like receptors,complement pathway,toll-like receptor signaling pathway,heat shock proteins,antioxidant enzymes,lysozymes,and mucins,indicating that *** could have a complete set of innate immune *** addition,4 270 microsatellite markers(SSRs)were identified from 60 201 unigenes,of which trinucleotide repeats were most abundant and 16 SSRs were tested to be *** present study provides a new insight into innate immunity and stress response mechanisms in ***.

关键词： Paphia undulata foot tissue transcriptome innate immunity unigene microsatellite

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

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Journal of Oceanology and Limnology 2020年第6期38卷 1880-1890页

作者： SONG Chenyu FENG Ziyi LI Chunhou SUN Zhicheng GAO Tianxiang SONG Na LIU Lu Fisheries College Ocean University of ChinaQingdao 266003China South China Sea Fisheries Research Institute Chinese Academy of Fishery SciencesGuangzhou 510300China National Engineering Research Center for Marine Aquaculture Zhejiang Ocean UniversityZhoushan 316022China

Acanthogobius ommaturus,a fish species of the Family Gobiidae,is a marine commercial fish perched on the bottom of *** this study,Illumina high-throughput sequencing technology was applied to obtain the candidate microsatellite markers of ***.A total of 4746 microsatellite-rich fragments were found,of which 4542 microsatellites are with primer fragments,containing 971 dinucleotide sequences,2643 trinucleotide sequences,569 tetranucleotide sequences,406 pentanucleotide sequences,and 212 hexanucleotide *** on the results of high-throughput sequencing,a total of 141 pairs of the microsatellite primers were designed and *** then 24 polymorphic primers were finally obtained by polyacrylamide gel *** total,271 alleles were detected in the 24 pairs of *** number of alleles for different primers ranged from 5 to *** average number of effective alleles(Na)was 11.292;the average observed heterozygosity(Ho)of the 24 pairs of primers was 0.665,the average expected heterozygosity(He)was 0.880,and the average polymorphic information content was *** sites were highly polymorphic(PIC>0.50).

关键词： microsatellite Acanthogobius ommaturus high-throughput sequencing polymorphic sites

Risks involved in fecal DNA-based genotyping of microsatellite loci in the Amur tiger Panthera tigris altaica:a pilot study

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Journal of Forestry Research 2018年第2期29卷 517-523页

作者： Xue Zhang Yanchun Xu Hui Liu Guangshun Jiang Feline Research Center of Chinese State Forestry Administration College of Wildlife ResourcesNortheast Forestry UniversityHarbin 150040HeilongjiangPeople’s Republic of China Ocean and Fishery Bureau of Weifang Binhai Economic and Technological Development Zone Weifang 261108ShandongPeople’s Republic of China

In modern wildlife ecological research,feces is the most common non-invasive source of DNA obtained in the field and polymerase chain reaction(PCR) technology based on microsatellite markers is used to mine genetic information contained *** is especially the case for endangered ***,there are risks associated with this genotyping method because of the poor quality of fecal *** this study,we assessed genotyping risk across 12 microsatellite loci commonly used in previous tiger studies using blood and fecal DNA from captive Amur tigers(Panthera tigris altaica).To begin,we developed an index termed the accumulated matching rate of genotypes(R)between positive DNA(blood samples) and fecal DNA to explore the correct genotyping probability of a certain microsatellite *** found that different microsatelliteloci had different genotyping risks and required different PCR amplification *** genotyping errors we detected altered population genetic parameters and potentially impact subsequent *** on these findings,we recommend that:(1) four loci(E7,Fca094,Pti007 and Pti010) of 12 loci are not suitable for Amur tiger genetic research because of a low Rand difficulty reaching a stable status;(2) the Rof the 12 microsatellite loci plateaued differently,and considering limited budgets,amplification times of some loci could be increased when using fecal samples; and(3) future genetic analysis of wild Amur tigers should be corrected by genotyping error rates(1-R).

关键词： Amur tiger Genotyping risk microsatellite Non-invasive sample