Characterization of polymorphic microsatellite DNA markers in Banksia nivea, formerly Dryandra nivea

A genomic library was constructed and 10 novel polymorphic microsatellite markers were developed for Banksia nivea subsp. uliginosa, a woody shrub endemic to the southwest of Western Australia. Polymorphism was investigated for these markers in 30 individuals from one population located in restricted habitat at the base of the Whicher Range east of Busselton. Expected heterozygosity ranged from 0.124 to 0.898 and averaged 0.570. Observed heterozygosity ranged from 0.133 to 0.933 and averaged 0.544. The number of alleles per locus ranged from 2.0 to 16.0 and averaged 7.3. These markers also produced amplification products in three other Banksia species and will be used to assay genetic diversity in these species.     

Characterisation of microsatellite markers isolated from Bossiaea ornata (Lindl.) Benth. (Papilionaceae)

Bossiaea ornata is a member of the pea family that occurs in the forest understorey of south-western Australia. We constructed a genomic library and developed eight polymorphic loci to assess genetic variability and structure within the species. Polymorphism was investigated for these markers in 20 individuals from a single population located in the jarrah forest. Expected heterozygosity ranged from 0.765 to 0.889 with a mean of 0.842, and observed heterozygosity ranged from 0.550 to 0.900 with a mean of 0.742. The number of alleles per locus ranged from 7 to 16 and averaged 11.9.     

Microsatellite DNA markers for American shad (Alosa sapidissima) and cross‐species amplification within the family Clupeidae

Sixteen microsatellite loci were identified and characterized for American shad (Alosa sapidissima). The number of alleles per locus observed ranged from eight to 32 and averaged 15.4 alleles. Average observed heterozygosity was 81.1%. The markers were screened using four other species from the family Clupeidae. Amplification success among Alosa species was 79.2% with 81.6% polymorphism among those markers that amplified successfully. Amplification success was poor in Dorosoma (31.3%). Due to allelic diversity and estimates of heterozygosity, these markers can be useful in A. sapidissima for population level analyses, parentage assignment and broodstock management.     

广西药用野生稻遗传多样性分析及SSR引物数量对遗传多样性结果的影响研究

采用25对SSR分子标记,对广西境内采集的1610份药用野生稻材料进行遗传多样性和聚类分析,其中检测到等位变异181个,有效等位基因数Ae范围为1.0094(RM240)~2.2674(RM488),平均值为1.3568;期望杂合度He范围为0.0093(RM240)~0.5591(RM448),平均值为0.2112;Shannon多样性指数I在0.0393~0.9296之间变动,平均值为0.3624。数据表明,广西药用野生稻遗传多样性较为丰富,12个药用野生稻地理居群按遗传多样性指数大小排序为:梧州-3南宁-1梧州-2梧州-1南宁-2玉林-2贵港-2梧州-4玉林-3玉林-1贺州贵港-1,其中指数高的居群均分布于梧州市和南宁市两地,因此确定了这两地为广西药用野生稻的遗传多样性中心。通过不同数量的SSR引物对药用野生稻材料间相似系数矩阵进行相关性测验,结果显示当引物按照PIC值降序排列时,10对引物即达到较好聚类效果,升序排列时,21对引物即达到较好聚类效果。研究表明,在进行药用野生稻大居群聚类分析时,SSR引物适宜数量应多于21对,最低不得少于10对。     

Isolation and characterization of microsatellite loci in Lampsilis abrupta (Bivalvia: Unionidae) and cross‐species amplification within the genus

We have documented the first microsatellites isolated from a unionid and demonstrated that these markers can be useful for surveys of neutral genetic variation in several Lampsilis species. We describe the isolation and characterization of 15 polymorphic microsatellite DNA loci for the endangered unionid Lampsilis abrupta. Among individuals from five collections, allelic diversity ranged from six to 17 alleles and averaged 10.4 alleles per locus. Individual heterozygosity was observed to range from 20.0% to 86.7% and averaged 46.9%. Cross‐species amplification was investigated in nine additional Lampsilis species. A high level of flanking sequence similarity was inferred as 13 of 15 loci amplified in at least seven species.     

核桃种质资源遗传多样性的SSR分析

应用16对SSR引物对国内不同地理生态型的44个核桃样品、8个铁核桃样品和7个美国核桃样品进行了分析。结果显示,在16个SSR位点上共获得87个等位基因,每个位点扩增等位基因4～9个,平均5.4个。各SSR位点的观察杂合度为0～0.931 0,平均为0.389 4。各位点PIC值在0.376 2～0.786 3之间,平均为0.663 2。59个核桃样品的杂合度在0.133～0.813之间,平均0.387。聚类分析表明,来自秦岭山地的核桃样品与华北核桃属于同一生态类型;巩留的野核桃属于与新疆生态型和华北生态型不同的一个独立的生态型;美国核桃和铁核桃属于核桃种下不同的生态类型。     

Development of microsatellite markers for the endangered freshwater pearl mussel Margaritifera margaritifera L. (Bivalvia: Unionoidea)

Freshwater pearl mussels (Margaritifera margaritifera L.) are among the most critically endangered freshwater invertebrates. We describe the isolation and characterization of the first microsatellite markers for this species, which were obtained by screening 4900 recombinant clones from two genomic libraries. Thirteen loci revealed polymorphisms as demonstrated on 42 tested individuals from four river drainages. Allelic richness ranged from two to 12 alleles and averaged 6.8 alleles per locus with heterozygosity levels varying from 0 to 0.850 for observed heterozygosity (H_O) and from 0.174 to 0.850 for expected heterozygosity (H_E). Deficiency of heterozygous genotypes was observed in eight of 13 loci.     

Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker)

We developed and characterized 31 microsatellite markers from expressed sequence tags of Pinctada martensii (Dunker). The number of alleles per locus ranged from 4 to 18 as determined in 44 individuals from a wild population. The expected heterozygosity ranged from 0.4121 to 0.9436, while the observed heterozygosity ranged from 0.4054 to 0.7273. Most of the loci are in Hardy-Weinberg equilibrium. These markers should be useful for population genetics studies, parentage and genome mapping in this species.     

Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.     

Isolation and characterization of microsatellites in a marine food fish species,golden trevally Gnathanodon specious

The first set of six polymorphic microsatellites was isolated from a partial genomic DNA library of an important marine food fish Gnathanodon specious, and was characterized in 28 unrelated individuals. The allele number ranged from three to 12 with an average of seven/locus; average expected heterozygosity was 0.57 ranging from 0.10 to 0.87, whereas the observed heterozygosity ranged from 0.11 to 0.96 (average: 0.57). All six markers conform to Hardy–Weinberg and linkage equilibria. These markers will be useful for accessing genetic population structure of wild populations and for selective breeding program in fish farms.     

Isolation and characterization of eleven polymorphic microsatellite markers of sand lance (Ammodytes personatus)

Eleven polymorphic microsatellite markers were developed to delineate population structure of Ammodytes personatus. These markers had between 8 and 27 alleles. Expected heterozygosity ranged from 0.818 to 0.965, whereas the observed heterozygosity ranged from 0.441 to 0.886. Five of the eleven markers conformed to Hardy–Weinberg equilibrium. We believe the markers will be useful for genetic diversity study of A. personatus.     

Isolation and characterization of microsatellite loci in Alasmidonta heterodon (Bivalvia: Unionidae)

We developed 13 species‐specific microsatellite markers for the federally endangered Atlantic slope unionid Alasmidonta heterodon. Four to 18 alleles per locus were observed among 30 individuals. Observed heterozygosity throughout the loci ranged from 26.9 to 86.2% and averaged 63.6%. Estimates of individual pairwise genetic distances indicated that levels of genetic diversity among loci were sufficient to produce unique multilocus genotypes for all animals surveyed. Randomization tests showed that genotypes for this collection were consistent with Hardy–Weinberg expectations, and no significant linkage disequilibrium was observed between loci. These loci therefore appear suitable for population surveys, kinship assessment and other such applications.     

Eight microsatellite markers for the San Esteban chuckwalla,Sauromalus varius

We characterize eight polymorphic microsatellite loci for the San Esteban chuckwalla, Sauromalus varius, which are being used as markers in a study of the genetic results from a decade of captive breeding in this endangered species. Observed heterozygosity estimates for S. varius ranged from 0.00 to 0.30, whereas expected heterozygosity estimates ranged from 0.06 to 0.58.     

Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel, <Emphasis Type="Italic">Perna viridis</Emphasis>

We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species. This article was submitted by the authors in English.     

Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel Perna viridis

We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species.     

Isolation and characterization of 14 polymorphic microsatellite loci in the ringneck snake <Emphasis Type="Italic">Diadophis punctatus</Emphasis> (Colubridae: Dipsadinae)

We constructed a genomic library and developed 14 polymorphic loci to assess species boundaries between previously described mtDNA lineages and to examine the genetic variability between populations of the ringneck snake Diadophis punctatus species complex. Polymorphism was investigated for these markers in 34 individuals from populations in southeastern Louisiana and southern Florida. The number of alleles ranged from 5 to 29, expected heterozygosity ranged from 0.816 to 0.962 and observed heterozygosity ranged from 0.452 to 0.889. These new loci provide the tools necessary to examine species boundaries, population genetics within species and to determine the conservation status of imperiled populations.     

Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)

? Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. ? Methods and Results: A microsatellite-enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci amplified perfect and imperfect repeats with three to seven alleles per locus. Observed heterozygosity ranged from 0.05 to 0.80 and expected heterozygosity ranged from 0.23 to 0.75. ? Conclusions: These microsatellite loci provide a sufficient set of markers for further investigation of population genetics of P. ruthii.     

Isolation and characterization of 10 microsatellite DNA markers in the oriental honey buzzard (Pernis ptilorhyncus)

We designed 10 new microsatellite markers for the oriental honey buzzard (Pernis ptilorhyncus) and tested them on 44 individuals. The number of alleles ranged from two to 12 with an average of five, while the observed heterozygosity ranged from 0.273 to 1.0. Linkage disequilibrium was not found. These markers are being used in a study of the ecology of this species in Taiwan. We also tested their utility on eight other raptor species.     

Sixteen new polymorphic microsatellite markers isolated for red‐legged partridge (Alectoris rufa) and related species

We developed and tested 16 new polymorphic microsatellite markers for the red‐legged partridge (Alectoris rufa): four dinucleotide, two trinucleotide, eight tetranucleotide and two pentanucleotide repeat loci. The number of alleles per locus ranged from two to 21, observed heterozygosity was from 0.03 to 1.00 and expected heterozygosity was comprised between 0.18 and 0.91. Cross‐specific amplification in others members of the Phasianidae family highlighted the potential usefulness of these molecular markers for the study of related species.     

Polymorphic markers for the sea cucumber Parastichopus californicus

Five polymorphic markers were isolated from a Parastichopus californicus genomic DNA library. In addition, a method was developed to extract DNA from both muscle and skin tissue. The number of alleles at these loci ranged from three to 14. Observed heterozygosity ranged from 0.2 to 0.9. These markers, the first of their type for a sea cucumber species, will prove useful for exploration of the population structure of P. californicus.