Polymorphic microsatellite loci for the Japanese anchovy Engraulis japonicus (Engraulidae)

We isolated and characterized 14 polymorphic microsatellite loci in the Japanese anchovy (Engraulis japonicus) using a (GT)(13)-enriched genomic library. The numbers of alleles per locus ranged from 6 to 31, with a mean of 17.8. The observed and expected heterozygosities ranged from 0.180 to 0.949 and from 0.172 to 0.966, with means of 0.731 and 0.825, respectively. All 14 loci were in Hardy-Weinberg equilibrium and no significant linkage disequilibrium between loci pairs was detected. These microsatellite markers will be useful for analyzing the population genetic structure and gene flow of E. japonicus.     

Development and characterization of 70 novel microsatellite markers for the sea cucumber (Apostichopus japonicus)

The sea cucumber (Apostichopus japonicus) is an important item in Asian cuisine. It is currently produced through aquaculture, especially in China, after being overexploited in the wild in the 1990s. We isolated 70 novel polymorphic microsatellite loci using an enrichment-colony hybridization protocol. All loci were characterized in 48 individuals from a natural population in Rongcheng (Shandong, China) using genomic DNA isolated from muscle tissue. The number of alleles ranged from 2 to 17 (mean 7.0), and the observed and expected heterozygosities varied from 0.0010 to 1.0000 and from 0.2125 to 0.9477, respectively. Thirty-one of the 70 loci exhibited departure from Hardy-Weinberg equilibrium. These microsatellite markers should be useful resources for population genetic studies and for molecular marker-assisted breeding of A. japonicus.     

利用SLAF-seq技术开发带鱼(Trichiurus japonicus)微卫星标记以及跨物种扩增检测

带鱼(Trichiurus japonicus)是广泛分布于东亚大陆架海域的暖温性近底层鱼类,长期位居我国单鱼种渔获量第一位。自上世纪70年代以来,持续过度捕捞和海洋环境变化导致中国近海带鱼资源基础和遗传多样性受到严重影响,但有关带鱼种群的微卫星DNA标记研究却较为缺乏,不利于该物种遗传资源评估和保护。为此,本研究采用基于高通量测序平台的SLAF-seq技术,从带鱼的195 308个SLAF标签中识别出25 704个二至六碱基重复微卫星位点。经过引物扩增验证,最终筛选出36个具有多态性的微卫星标记。各位点等位基因数4～35,均值14.47。观测杂合度0.214～1.000,期望杂合度0.456～0.979,均值分别为0.620和0.803。所有位点的多态信息含量值均大于0.25。经Bonferroni校正,21个位点符合哈迪-温伯格平衡,且各位点间不存在连锁不平衡。这21个多态性微卫星标记可为带鱼的种群遗传资源研究提供新的有效分子标记和技术支撑。Bottleneck分析结果表明,宁波近海带鱼群体未检测到近期的遗传瓶颈效应,这可能与目前东海区带鱼野生群体数量还比较庞大、遗传变异仍然较为丰富有关。跨物种扩增结果显示,分别有12、16、4和3个带鱼微卫星标记在带鱼属(Trichiurus)、沙带鱼(Lepturacanthus savala)、窄颅带鱼(Tentoriceps cristatus)及小带鱼(Eupleurogrammus muticus)中具有较好的通用性,这些微卫星标记为今后带鱼科相应属、种的系统进化关系研究提供新的分析手段和契机。     

Isolation and characterization of 15 polymorphic microsatellite DNA loci from Argyrosomus japonicus (mulloway), a new aquaculture species in Australia

Fifteen microsatellite loci were isolated for population genetic studies of mulloway (Argyrosomus japonicus), a commercial/recreational fish species in Southern Australia. A genomic library was screened randomly for di- tri- and tetranucleotide repeats. Fifteen microsatellite marker loci were developed that were highly polymorphic (allele number ranged from four to 18). Observed and expected heterozygosities ranged from 0.17 to 1 and from 0.27 to 0.91, respectively. These markers have proven useful for estimating genetic variation and for evaluating population structure across the species' natural distribution. They also provide powerful tools for optimizing hatchery practices to conserve genetic diversity.     

Characterization of highly polymorphic nuclear microsatellite loci from the ascidian Ciona intestinalis

Eight nuclear polymorphic microsatellite markers were characterized from the ascidian Ciona intestinalis whole genome sequence. The behaviour of these loci was investigated against two geographically distinct populations: one from Plymouth, UK the other from the Fusaro Lagoon, Italy, both belonging to the type A Ciona cryptic species. The markers exhibited six to 29 alleles and average observed heterozygosity ranging from 0.06 to 0.73. These new microsatellite loci demonstrated to be valuable tools for both population genetic analysis at different scales and genetic identification of mutant phenotypes frequently encountered in Mediterranean populations of C. intestinalis.     

PERMANENT GENETIC RESOURCES: Development and characterization of 14 polymorphic microsatellite loci in the endangered tree Euptelea pleiospermum (Eupteleaceae)

Fourteen polymorphic microsatellite loci were developed and characterized for the endangered and tertiary relict tree, Euptelea pleiospermum. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 32 individuals from one natural population. The observed number of alleles ranged from two to nine. The ranges of observed and expected heterozygosities were 0.25-1.00 and 0.22-0.85, respectively. These microsatellite markers provide powerful tools for the ongoing conservation genetic studies of E. pleiospermum.     

Characterization of microsatellite markers in the shea tree (Vitellaria paradoxa C. F Gaertn) in Mali

In order to study the genetic diversity and structure in the population of Vitellaria paradoxa, we characterized eight polymorphic microsatellite loci. Primers to amplify these loci were tested on 169 individual trees representing a sample of the population of shea tree in Mali. The loci were all polymorphic with a number of alleles between three to nine and with observed level of heterozygosity ranging from 0.035 to 0.507. These markers will be useful for genetic and ecological studies of this species.     

Novel polymorphic microsatellite DNA markers from Malaysian giant freshwater prawn, Macrobrachium rosenbergii

Seven single locus microsatellite markers were characterized in Malaysian giant freshwater prawn, Macrobrachium rosenbergii from an enriched genomic library Primer pairs were designed to flank the repeat sequences and the loci characterized for this species. The bands resulting from the PCR amplifications of these eight microsatellite loci were polymorphic with the number of alleles ranging from 8 to 26 alleles per locus, whereas the observed heterozygosity ranged from 0.0641 to 0.6564. These newly developed microsatellite markers should prove to be useful for population studies and in the management of genetic variations in broodstocks of freshwater prawn, M. rosenbergii.     

Characterization of 11 novel polymorphic microsatellite loci in the threatened Korean loach,Iksookimia koreensis,isolated using a next-generation sequencing method

To investigate the genetic diversity and population structure of Iksookimia koreensis, we characterized 11 novel polymorphic microsatellite markers developed using next-generation sequencing. The number of alleles per locus ranged from 4 to 10 (average = 6.26). Observed and expected heterozygosities ranged from 0.333 to 0.866 and from 0.375 to 0.866, respectively. No loci showed significant deviation from Hardy–Weinberg equilibrium (HWE). These loci were also used successfully to study the genetic diversity of a closely related species, Iksookimia longicorpa. Four of the 11 loci amplified in the two species showed different allele frequency and distribution, indicating deep genetic divergence between I. koreensis and I. longicorpa. The newly developed microsatellite markers reported here will provide a useful tool for examining gene flow, population genetic structure, and genetic diversity of these species.     

Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish,Arctoscopus japonicus

We developed 12 polymorphic microsatellite markers from Arctoscopus japonicus by screening an enriched genomic library using polymerase chain reaction (PCR) techniques. The average of alleles size was 16.2, and the average observed and expected heterozygosities were 0.59 and 0.78, respectively. The observed genotypic frequencies in five loci were significantly deviated from Hardy–Weinberg expectations. The high variability revealed in this study suggested that these microsatellite loci should provide useful markers for population genetics of A. japonicus.     

Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817)

We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.     

花鲈微卫星标记分离及其多态性分析

该文利用FIASCO法(fast isolation by AFLP of sequences containing repeats)和GenBank数据库搜索法开发花鲈微卫星标记,并对筛选的标记进行多态性检测.两种方法共获得54条能够设计引物的序列,扩增结果显示15对引物具有多态性,多态性微卫星位点的等位基因数为2～10个.15个多态性位点中,4个位点偏离了Hardy-Weinberg平衡;各位点间没有连锁不平衡现象;仅位点SP52可能存在无效等位基因;除SP17和SP468外,其余引物的P1C值均在0.5以上,可用于花鲈群体遗传分析等研究.     

Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae)

Sebastiscus marmoratus is a typical sedentary fish and usually lives at the bottom of the coastal zone from Japan to the East China Sea. Next-generation sequencing platform was used to obtain microsatellite loci sequences of S. marmoratus, among which forty-eight perfect microsatellite repeats were suitable for primer design. Nine polymorphic microsatellite markers were exploited and characterized for it. The allele number of all polymorphic microsatellite markers ranged from 4 to 12. Expected and observed heterozygosity varied from 0.302 to 0.909 and from 0.190 to 0.625, respectively. In further studies, the genetic variation and population structure of this species would be investigated using these microsatellite loci.     

Novel polymorphic microsatellite DNA markers from Malaysian giant freshwater prawn, <Emphasis Type="Italic">Macrobrachium rosenbergii</Emphasis>

Seven single locus microsatellite markers were characterized in Malaysian giant freshwater prawn, Macrobrachium rosenbergii from an enriched genomic library Primer pairs were designed to flank the repeat sequences and the loci characterized for this species. The bands resulting from the PCR amplifications of these eight microsatellite loci were polymorphic with the number of alleles ranging from 8 to 26 alleles per locus, whereas the observed heterozygosity ranged from 0.0641 to 0.6564. These newly developed microsatellite markers should prove to be useful for population studies and in the management of genetic variations in broodstocks of freshwater prawn, M. rosenbergii.     

Microsatellite DNA primers for the endangered vermilion darter,Etheostoma chermocki,and cross‐species amplification in other darters (Percidae: Etheostoma)

The endangered vermilion darter (Etheostoma chermocki) is endemic to the Black Warrior River system in the Mobile Basin in Alabama. Restoration and conservation of this species require an understanding of its population genetic structure, which can be characterized using microsatellite DNA. Nine microsatellite loci were developed; eight loci were polymorphic. Although observed heterozygosity was lower than expected heterozygosity in most polymorphic loci, only one locus showed significant deviation from Hardy–Weinberg equilibrium. These nine markers were tested in an additional 24 species of Etheostoma and appear to have sufficient allelic variation to be useful in studies of population genetic structure.     

Isolation and characterization of new microsatellite markers in shea tree (Vitellaria paradoxa C. F. Gaertn)

Vitellaria paradoxa is one of the major components of African parkland agroforestry systems. In order to assess the genetic diversity and population structure of this species, we isolated and characterized 14 polymorphic nuclear microsatellite loci. Primers developed to amplify these loci were used to analyse 200 individuals of a shea tree population in Mali. Loci have shown a high number of alleles ranging from four to 26, and display an observed level of heterozygosity between 0.37 and 0.85. These new very polymorphic microsatellite markers will be useful for genetic and ecological studies of V. paradoxa.     

Polymorphic microsatellite loci for population studies of <Emphasis Type="Italic">Bullacta exarata</Emphasis>

Nine polymorphic microsatellite loci were isolated and characterized from an AC-enriched genomic library of Bullacta exarata. They were polymorphic in 30 individuals from Qidong in Jiangsu Province, China. The number of alleles per polymorphic loci varied from 7 to 14 and the values of observed heterozygosity and expected heterozygosity ranged from 0.2593 to 0.9667 and from 0.7090 to 0.9164, respectively. Six of the nine microsatellites conformed to Hardy–Weinberg equilibrium, and inherited independently. These informative microsatellite markers will be useful in studies of population genetic structure for this species.     

Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand

Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306?bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.     

Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis

Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean polymorphic information content was 0.62. Among these, three loci deviated from the Hardy-Weinberg equilibrium. However, no significant genotypic disequilibrium was detected between any pair of loci. These microsatellite markers are useful for the population genetic study of the great hornbill.     

Isolation and characterization of a first set of polymorphic microsatellite markers in saffron, Crocus sativus (Iridaceae)

? Premise of the study: Twelve novel polymorphic microsatellite loci were developed and characterized from a repeat-enriched genomic library of Crocus sativus to study population and conservation genetics of this economically and medically important species. ? Methods and Results: The microsatellite loci were isolated using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method. The average number of alleles per locus was 2.6. The observed and expected heterozygosities varied from 0.07 to 0.92 and 0.1 to 0.58, respectively. Polymorphic information content value ranged from 0.09 to 0.55 with an average of 0.34. Four out of twelve loci showed significant departures from Hardy-Weinberg equilibrium. ? Conclusions: The microsatellite markers reported here will be useful for evaluating genetic diversity and will likely serve as an ideal resource for use in marker-assisted breeding programs, germplasm analysis, and varietal identification.