Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding.     

Development of 12 microsatellite markers for Platycrater arguta (Hydrangeaceae) endemic to East Asia

? Premise of the study: Microsatellite markers were characterized in Platycrater arguta, a rare endemic shrub from eastern China and southern Japan, to investigate its population genetic structure, phylogeographic patterns, and breeding system. ? Methods and Results: Using both the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol and the compound microsatellite marker technique, we developed 12 microsatellite markers. All primers showed polymorphism when assessed in 43 individuals from two populations in eastern China and southern Japan. Overall, the number of alleles ranged from five to 21, with an average of 14.91 alleles per locus. ? Conclusions: These markers can be used in further studies on population genetics, phylogeography, and breeding system of P. arguta.     

A high density genetic map of tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis> L.) obtained from large scale microsatellite marker development

Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato.     

Isolation and characterization of 19 highly polymorphic microsatellite markers in the devil stinger, Inimicus japonicus (Synanceiidae)

Inimicus japonicus, the devil stinger, has an extensive distribution along the coast of China, Japan and the Korean Peninsula. Nineteen highly polymorphic microsatellite markers were isolated and characterized in I. japonicus. Twenty-eight individuals from a wild population were tested for polymorphism using this set of polymorphic microsatellite markers. The number of alleles per locus ranged from 4 to 14. The ranges of observed and expected heterozygosity were 0.500-0.892 and 0.521-0.910, respectively. Significant deviations from Hardy-Weinberg equilibrium were detected at two loci. To the best of our knowledge, these were the first microsatellite loci characterized from the Synanceiidae; they can be used for estimating genetic diversity, population structure studies, parentage analysis, genetic linkage map construction, germplasm classification and identification, gene identification, quantitative trait loci mapping, and marker-assisted selection in breeding of I. japonicus and other species of this family.     

Microsatellite markers for the common bean Phaseolus vulgaris

Efforts to develop molecular tools for genetic analysis and breeding of common bean in the tropics are still limited. The number of microsatellite markers available for the crop is small compared to other crops of similar social and economic importance. As part of a project to broaden the use of molecular tools in bean breeding, a genomic library enriched for AG/TC repeat sequences was constructed for Phaseolus vulgaris. Twenty microsatellite markers were initially developed and 10 were characterized using a panel of 85 representative accessions of the bean gene bank. The number of alleles per marker ranged from three to 10. The polymorphism information content (PIC) varied from 0.23 to 0.80. The results indicate that the new markers can be readily used in genetically analysis of common bean.     

Characterization of 12 polymorphic microsatellite loci for the whitespotted bamboo shark (Chiloscyllium plagiosum Bennett)

Twelve polymorphic microsatellite loci without linkage disequilibrium were isolated and characterized from a microsatellite DNA-enriched DNA library for the whitespotted bamboo shark (Chiloscyllium plagiosum Bennett, 1830). These loci show polymorphism information content ranging from 0.384 to 0.885, allele number ranging from 4 to 12, effective allele number ranging from 1.686 to 9.438, and observed and expected heterozygosities from 0.229 to 1.000 and from 0.407 to 0.894 respectively. Four loci show strong Hardy-Weinberg deviations. We expect that these markers would be useful for population genetic and breeding studies of the whitespotted bamboo shark.     

Characterization of eight polymorphic microsatellite loci for the leopard coralgrouper (Plectropomus leopardus Lacepède)

Eight polymorphic microsatellite loci were isolated and characterized from a microsatellite DNA-enriched DNA library for the leopard coralgrouper (Plectropomus leopardus Lacepède, 1802), a popular food fish in the East Indies. These loci showed polymorphism information content ranging from 0.493 to 0.854, allele numbers ranging from 3 to 10, effective allele numbers ranging from 2.2 to 7.6, and observed and expected heterozygosities from 0.375 to 0.906 and 0.544 to 0.868 respectively. Thus, we expect that these markers will be useful for population genetic and breeding studies of the leopard coralgrouper.     

Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers

Quinoa (Chenopodium quinoa Willd.) is a staple seed crop in the Andean region of South America. Improving quinoa productivity is a primary food-security issue for this region, and has been part of the impetus for the establishment of several new quinoa breeding programs throughout the Andean region. Chilean quinoa has been characterized as morphologically diverse and bifurcated into coastal and highland ecotypes. The success of emerging breeding programs will rely heavily on the development of core germplasm collections and germplasm evaluation—especially of the coastal quinoa ecotypes that are often neglected in traditional breeding programs. Thus, the objective of this study was to characterize and quantify the genetic diversity within 28 Altiplano and 31 coastal Chilean accessions of quinoa using microsatellite markers. To facilitate the analysis, we also report the development of seven sets of fluorescent multiplexed microsatellite PCR reactions that result in genetic information for 20 highly polymorphic microsatellite loci. A total of 150 alleles were detected among the quinoa accession, ranging from 2 to 20 alleles per locus and an average 7.5 allele/locus. Both cluster (UPGMA) and principal component analyses separated the accessions into two discrete groups. The first group contained quinoa accessions from the north (Andean highlands) and the second group consisted of accessions from the south (lowland or coastal). Three accessions from Europe were classified into the southern quinoa group. The data obtained in the diversity analyses highlights the relationships within and among northern and southern Chilean quinoa accessions and provides the quinoa scientific community with a new set of easy to use and highly informative genetic markers.     

华南鲤选育群体不同世代遗传多样性与遗传结构的微卫星分析

为了解人工选育对华南鲤(Cyprinus carpio rubrofuscus)选育群体遗传结构的影响, 采用微卫星技术分析了华南鲤4个连续选育世代(F₁、F₂、F₃和F₄)的遗传多样性和遗传结构。结果显示:在4个选育群体中, 16对微卫星引物共扩增得到99个等位基因, 每个微卫星座位检测到的等位基因数为3—10个, 平均为6.1875个。随着人工连续选育的进行, F₁到F₄的平均等位基因数(N_a)从5.6875下降到4.6755, 平均观测杂合度(H_o)从0.7943下降到0.7135, 平均多态信息含量(PIC)从0.6577下降到0.5834。F₁与其后各代的遗传距离逐代增加(从0.1486上升到0.2181), 遗传相似系数逐代减小(从0.8619下降到0.8041), 而相邻世代间的遗传分化指数(F_st)逐代变小(F₁与F₂为0.062, F₂与F₃为0.058, F₃与F₄则为0.051), 遗传相似性逐步升高。世代间F_st值配对比较结果显示4个世代间的遗传分化处于中等水平, 表明人工选育已对华南鲤选育群体的遗传结构产生了影响。实验结果表明, 华南鲤经过4代选育后, 虽然遗传杂合度和遗传多样性存在下降的现象, 但遗传多样性水平依然较高, 还具有进一步选育的潜力。研究结果为下一步制定华南鲤新品种选育计划提供基础遗传数据。     

Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites

Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J. curcas as potential crop with superior agronomical traits.     

Eight polymorphic microsatellite markers for the spotted babylon, Babylonia areolata (Buccinidae)

The spotted babylon, Babylonia areolata, is one of the most extensively cultured marine mollusks in southeast Asia. Eight polymorphic microsatellite markers were developed for this species, from a microsatellite-enriched library. These markers, characterized in 32 individuals from a hatchery population, were polymorphic, with allele numbers ranging from 6 to 18 per locus, expected and observed heterozygosities ranging from 0.68 to 0.94 and 0.56 to 0.81, respectively. One locus (HUBA09) showed significant deviation from Hardy-Weinberg equilibrium, probably due to the presence of null alleles. These microsatellite loci should be useful for future population genetic studies and marker-assisted breeding in this species.     

利用微卫星遗传标记对恒河猴进行遗传同质性分群的探索

目的探索建立利用微卫星遗传标记对中国恒河猴免疫遗传学同质性分群的方法。方法根据已报道的中国恒河猴和印度恒河猴微卫星标记和与MHC基因高度连锁的微卫星遗传标记,对52只恒河猴进行了微卫星检测和遗传同质性分群。结果依据判断标准,可以将检测的恒河猴分为印度恒河猴,中国恒河猴和无法判定来源的恒河猴3个地理类别,并根据MHC附近的微卫星遗传标记将其分为若干MHC基因相同的同质性群体。结论此方法的建立将有利于恒河猴参与的实验分组,也为恒河猴繁殖管理提供了参考。     

Identification and characterization of microsatellites for striped bass from repeat-enriched libraries

Striped bass (Morone saxatilis) is economically important in the US due to its value as an aquaculture species and in supporting commercial and recreational fisheries, especially those off the Atlantic coast and in the Gulf of Mexico. Modern strategies for managing fishery populations and aquaculture broodstocks employ the use of molecular genetic markers to identify individuals, assign parentage, and characterize population genetic structure and levels of inbreeding and migration. As part of a collaborative effort to utilize molecular genetic technologies in striped bass breeding programs we generated microsatellite markers for use in population genetic studies, broodstock selection and management strategies, and the construction of a genetic map. We developed 345 new microsatellite markers for striped bass, a subset (n=71) of which was characterized by genotyping samples from two striped bass broodstock populations to evaluate marker polymorphism, percent heterozygosity, Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD) and utility for population genetic studies.     

Isolation and characterization of microsatellite markers for Acacia senegal (L.) Willd., a multipurpose arid and semi-arid tree

Acacia senegal is a multipurpose African tree that improves the soil fertility of degraded areas. The species is exploited mainly for gum arabic, but it also supplies fuel wood and fodder for animals. Despite its wide distribution in Africa, no microsatellite markers have yet been characterized for this species. In this study, we characterized 11 polymorphic microsatellite loci specifically designed for A. senegal and analysed 247 individuals from three populations from Niger. On average, 10.9 alleles per locus were detected and expected heterozygosity ranged from 0.160 to 0.794, showing the ability of the markers to detect genetic diversity in this species.     

Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.)

Millets such as proso millet have excellent nutritional properties and could become a basic resource for crop breeding programs and food diversification. In this study, 25 polymorphic microsatellite markers were developed and characterized through construction of an SSR-enriched library from genomic DNA of proso millet (Panicum miliaceum L.). In total, 110 alleles were detected, with an average of 4.4 alleles per locus. Values of major allele frequency (M _AF ) and expected heterozygosity (H _E ) ranged from 0.36 to 0.98 (mean = 0.73) and from 0.04 to 0.74 (mean = 0.37), respectively. The mean genetic similarity coefficient was 0.3711, indicating that among 50 accessions of proso millet there was wide genetic variation. The newly developed microsatellite markers should be useful tools for assessing genetic diversity, understanding population structure, and breeding of proso millet.     

Isolation and characterization of microsatellite markers for Thujopsis dolabrata var. hondai (Cupressaceae)1

? Premise of the study: Microsatellite markers were developed for the endemic Japanese species Thujopsis dolabrata var. hondai for studies on forest ecology and tree breeding. ? Methods and Results: We characterized 10 dinucleotide microsatellite loci by screening primers developed using a simple sequence repeat-enriched library. The number of alleles per locus ranged from eight to 44 with an average of 20.3. The observed and expected heterozygosities ranged from 0.326 to 0.854 and from 0.670 to 0.976, respectively. ? Conclusions: The development of these markers can be used to assess useful genetic information for ecological studies and tree breeding in T. dolabrata var. hondai.     

Isolation and characterization of microsatellite loci in tropical forage Stylosanthes capitata Vogel

Stylosanthes capitata is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. capitata populations is of great importance for the conservation and germplasm management of this species. Thus, eight microsatellite markers were developed from an S. capitata-enriched library. They were characterized in 20 accessions from the germplasm collection of the Empresa Brasileira de Pesquisa Agropecuária (Embrapa). The observed and expected heterozygosities ranged from 0.16 to 0.85 and from 0.40 to 0.85, respectively. These microsatellites are the first set of molecular markers from this species and will contribute towards studies of genetic diversity, conservation and breeding of S. capitata.     

利用分子标记分析遗传多样性时的玉米群体取样策略研究

利用分子标记技术对玉米种质资源进行遗传多样性分析对种质资源的保存和利用具有重要的指导意义。但是,在对地方品种和育种群体这些开放授粉群体进行大规模遗传多样性分析时,取样方法将会严重影响到研究结果和工作效率。本研究用2个育种群体和3个地方品种为试材,利用微卫星(SSR)标记对每个群体100个个体及其组成的不同随机混合样品进行了分子检测。结果表明,不同群体的群体内遗传变异大小存在差异;相同数目的个体随机混合的不同样品间的检测结果基本相同;不同数目的个体混合的样品间存在一定程度的差异,并且与材料本身的遗传变异大小有一定关系。考虑到结果的科学性和工作的可行性,建议在利用分子标记(如SSR)进行地方品种和育种群体的遗传多样性评估时,随机选取30个个体组成混合样(或用15个个体组成2个混合样)来代表1个地方品种或育种群体进行分子鉴定。     

Microsatellite markers for Lycium ruthenicum (Solananeae)

We developed microsatellite markers in Lycium ruthenicum, a desert plant widely distributed in northwestern China. In order to investigate its population genetic structure, genetic diversity, and its evolutionary history, we have isolated 11 novel microsatellite loci primers and characterized them in 24 individuals from 3 populations of L. ruthenicum using the combined biotin capture technique. For these microsatellites, one to seven alleles per locus were identified. The observed heterozygosities ranged from 0 to 0.958, meanwhile the expected heterozygosities ranged from 0 to 0.841. These microsatellite markers could be first useful for population level studies like genetic diversity and structure in this species.     

Genetic diversity of Chinese giant salamander (Andrias davidianus) based on the novel microsatellite markers

Chinese giant salamander (Andrias davidianus) is a rare amphibian species in the world. Microsatellite markers are a promising tool for accurate estimation population structure and genetic diversity. In this paper, we isolated novel microsatellite marker for Chinese giant salamander using fast isolation by AFLP of sequences containing repeats (FIASCO) method. More than 50% sequences in 132 clones had repeat number over ten times with di or trinucleeotide repeat except of (GA)₁₂. Seventy pairs of primers were designed and eleven polymorphic microsatellite loci were characterized for wild and cultivated Chinese giant salamander populations. The allele number was from 3 to 9 in different loci. Polymorphism information content was from 0.544 to 0.702 in cultivated population. The results implied more alleles and PIC were in the wild population than cultivated population. The observed heterozygosities in two populations were higher than 0.553. The data analysis suggested that the cultivated population has lower genetic diversity than wild population, which it??s perhaps owing to inbreeding in artificial breeding. To our knowledge, it??s the first time to isolated microsatellite markers for Chinese giant salamander. The result indicated that the markers were suitable for the population genetic analysis of Chinese giant salamander.