Characterization of polymorphic microsatellite loci in Yucca filamentosa

Yuccas and their pollinator moths are a textbook example of mutualism, yet we lack sufficiently variable markers to properly study the population genetics of the plants. We characterized 13 polymorphic microsatellite loci for Yucca filamentosa by screening primers derived from an expressed sequence tag database. We found four to 13 alleles per locus and the observed heterozygosity ranged from 0.31 to 1. These markers will be useful in future ecological studies of Y. filamentosa.     

Characterization of 16 polymorphic microsatellite loci in weathervane scallop Patinopecten caurinus

Discrete and commercially important patches of weathervane scallops (Patinopecten caurinus) are found in the northeastern Pacific Ocean. Little is known about weathervane scallop life history and population structure, but the species is vulnerable to overexploitation because of their large size and long lifespan. Here we describe 16 polymorphic microsatellite loci developed to study the relatedness of these discrete patches. All loci were polymorphic in the 32 individuals tested; the number of alleles range from four to 26 and heterozygosities ranged from 0.437 to 1.000.     

Characterization of nine polymorphic microsatellite loci from the alpine accentor Prunella collaris

Nine polymorphic microsatellite loci were isolated and characterized from the alpine accentor Prunella collaris. In analyses of 50 unrelated individuals, allelic diversity ranged from 2 to 7, and observed heterozygosity ranged from 0.08 to 0.70. Except for one locus (Pco2), variability was relatively low even in long repeat loci. This result may be due to the high return rate to the natal population. Primer sets were also tested in Japanese accentor Prunella rubida, and seven out of nine loci were successfully amplified.     

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

A total of 10 882 porcine microsatellite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium (http://www.piggenome.dk). Of these, 4528 microsatellites were placed on a pig-human comparative map by blast analysis of porcine sequences against the human genome (blast cut-off threshold =1 x 10(-5)). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html. These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude. They are a new resource of microsatellite sequences for generating markers to be used in linkage studies and in fine mapping and positional cloning of quantitative trait loci.     

海南五指山猪遗传多样性的微卫星分析

海南五指山猪(Wuzhishan pig)是我国珍稀的小型猪品种。它的解剖学、生理学、疾病发生机理等都与人类极其相似,具有重要的应用价值,可用于心血管病、皮肤烧伤和新药评价等许多方面的研究。作者利用多重PCR和基因扫描技术对五指山猪32个微卫星基因座进行了遗传检测。统计了全群、核心群和近交群的等位基因组成,并计算了它们的平均纯合率、多态信息含量(PIC)和平均杂合度。结果显示,全群、核心群和近交群32个基因座的平均等位基因数分别为14.590个、9.410个、13.660个,平均基因纯合率分别为44%、44.3%、44%,平均PIC分别为0.742、0.708、0.731,平均杂合度分别为0.560、0.558、0.559。这表明海南五指山猪虽然遗传基础比较稳定,但仍具有较大的遗传变异。上述结果对于海南五指山猪的保种、定向选育、开发利用都具有重要的指导意义。     

Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss)

Thirty‐eight new microsatellite markers were developed for genome mapping and population genetics studies in rainbow trout (Oncorhynchus mykiss). The amount of polymorphism, percentage of heterozygosity and ability of each marker to amplify genomic DNA from other salmonids were recorded. Five markers were observed to be duplicated in the rainbow trout genome by containing more than one allele in homozygous (clonal) fish.     

Isolation of 12 polymorphic microsatellite loci in the phytopathogenic fungus Alternaria brassicicola

Twelve polymorphic microsatellite markers were isolated from the phytopathogenic fungus Alternaria brassicicola, the causal agent of black spot of crucifers. An enrichment protocol was used to isolate microsatellite loci, which were then analysed in a collection of 46 isolates sampled from seven different countries. The number of alleles detected in 12 loci ranged from two to 10 (mean 3.5). Investigation of cross‐species amplifications showed that the designed primers were specific to A. brassicicola.     

Characterization of 11 polymorphic microsatellite loci in the yellowfin seabream Acanthopagrus latus

The development and characterization of polymorphic microsatellite loci in the yellowfin seabream Acanthopagrus latus are presented. Allelic diversity was estimated in 50 samples collected from southeastern China. Eleven loci displayed polymorphism that ranged from 10 to 25 alleles per locus and the observed heterozygosity ranged from 0.48 to 0.91. These markers could be very useful for the study of population genetics of the yellowfin seabream.     

Isolation and characterization of polymorphic microsatellite loci from Brandt's voles (Lasiopodomys brandtii)

Ten polymorphic microsatellite loci from Lasiopodomys brandtii have been isolated and characterized. Two to 11 alleles per locus were detected from 52 Brandt's voles samples collected from a single population. Expected heterozygosities ranged from 0.406 to 0.840. For the majority of loci observed heterozygosities were similar to or greater than the expected heterozygosity. One locus pair appeared to be in linkage disequilibrium. The microsatellite markers will enable the studies of genetic diversity, population structure and relatedness in this species, and perhaps in closely related species of vole.     

Characterization of nine microsatellite loci in impala (Aepyceros melampus)

Nine microsatellite loci were isolated from a genomic DNA library created from impala (Aepyceros melampus). Observed and expected levels of heterozygosity were computed utilizing 25 individuals from a population in central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that three of the nine loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.     

Characterization of 12 polymorphic microsatellite loci in the Japanese bush warbler Cettia diphone

Japanese bush warblers, Cettia diphone, are a common species in Japan and have a polygynous breeding system. In the breeding ground some males have their own territories with more than one female. Male floaters are also not uncommon in the breeding ground. To understand breeding strategy in this species, exact parentage should be elucidated. In order to obtain a tool for this purpose, we isolated 34 microsatellite loci from a genomic library in this species and developed primers for 12 loci. These primers were tested in the Japanese bush warbler and successfully amplified. In analyses of 49 unrelated individuals, allelic numbers ranged from two to 22, and observed heterozygosity (H_O) ranged from 0.27 to 0.854 except for two loci (Cdi29 and Cdi35a) with H_O < 0.1.     

Characterization of 12 polymorphic microsatellite loci for eastern chipmunks (Tamias striatus)

Eastern chipmunks are small forest rodents for which ecological data at multiple spatial scales exist, but no molecular markers have been developed that provide adequate resolution to examine genetic structure at fine scales in this species. Thus, we developed 12 variable microsatellite loci, which amplified in three multiplexed reactions, and screened them in 27 individuals from northern Indiana, USA. Observed heterozygosities across loci ranged from 0.26 to 0.91 and number of alleles per locus ranged from three to 10. We will use these markers along with ecological data to understand population dynamics of eastern chipmunks at small spatial scales.     

Characterization of polymorphic microsatellite loci in the invasive Brazilian pepper,Schinus terebinthifolius

Brazilian pepper trees (Schinus terebinthifolius) pose a significant threat to south Florida ecosystems. To identify the source population of this exotic species we developed eight trinucleotide (AAT) microsatellite loci. Polymorphism ranged from two to six alleles and heterozygosity from 30 to 100% in a sample of 10 individuals from across south Florida. Cross‐species amplification indicated that these loci may be useful in some members of the Anacardiaceae.     

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.     

Characterization of polymorphic tetranucleotide microsatellite loci from the Siberian weasel (Mustela sibirica)

Nine tetrarepeat microsatellite loci for Siberian weasel (Mustela sibirica) were characterized. By using 35 individuals of unknown relationship collected from Taiwan, we evaluated the polymorphism of these loci. The number of alleles for each locus ranged from five to 12 (mean = 8.78 alleles) and the observed heterozygosity from 0.429 to 0.962 (mean = 0.688) and all loci conformed to Hardy–Weinberg expectation.     

Characterization of polymorphic microsatellite loci in a traditional Chinese medicinal plant,Gastrodia elata

Genetic characterization of germplasm resource is essential for the conservation and efficient utilization of a traditional Chinese medicinal plant, Gastrodia elata. Thirty‐two primer pairs flanking microsatellite repeats were designed and tested using 32 individuals from eight wild populations. A total of 13 microsatellite loci were found highly polymorphic, with three to 10 alleles per locus and gene diversity ranging from 0.400 to 0.841. These microsatellites have been directly applied to the ongoing population and conservation genetics studies.     

Characterization of 13 polymorphic microsatellite loci for an evergreen tree,Myrica rubra

We developed 13 microsatellite markers from a genomic library enriched for dinucleotide (CT) repeats in a dioecious evergreen tree, Myrica rubra. We screened loci from 32 adult trees. The number of alleles ranged from two to 14, and the expected heterozygosity ranged from 0.324 to 0.884. The total paternity exclusionary power where the mother was known equalled 0.99965. These loci are of clear value in studying mating system and parentage analysis of this species.     

Eleven polymorphic microsatellite loci in Lindera benzoin,Lauraceae

Microsatellite markers were developed for studies of the genetic diversity and population substructure of Lindera benzoin, Lauraceae (spicebush). Nuclear microsatellite sequences were obtained from DNA libraries that were enriched for (CA), (GA), (AAG) and (ATG) repeat motifs. From 69 microsatellite sequences, 20 primer sets were developed. Of these, 11 primer pairs resulted in amplified polymorphic loci. In 29 samples of eastern Pennsylvania spicebush plants, the number of microsatellite alleles ranged from two to 16 per locus with observed heterozygosity values ranging from 0.10 to 0.82.     

Development and mapping of ten porcine microsatellite markers

Thirty (TG)_n microsatellite clones were isolated from a pig genomic library, sequenced, and tested for their suitability to detect polymorphism on a panel of animals by means of the polymerase chain reaction. Ten of these clones were developed into suitable markers and subsequently segregation of these markers was determined in the five PiGMaP reference pedigrees. A linkage analysis was performed on these 10 microsatellites together with 365 other loci that have been typed on these reference families. Eight of the microsatellites have been mapped to eight different linkage groups that have been previously assigned to different chromosomes (chromosomes 1, 6, 7, 9, 14, 15, 17 and 18). Of the remaining two markers, one is X-linked and the other shows no linkage. The number of alleles detected by these microsatellites, in the reference pedigrees, varied from six to sixteen and the heterozygosity varied from 42 to 85% in the 26 unrelated founder animals of these reference pedigrees.     

Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius

Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci.