Isolation and characterization of 10 microsatellite loci in Callicarpa subpubescens (Verbenaceae), an endemic species of the Bonin Islands

Ten microsatellite loci were isolated and characterized for Callicarpa subpubescens (Verbenaceae), an endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from two to eight with an average of 4.9, and the expected heterozygosity ranged from 0.238 to 0.690 with an average of 0.483. All 10 loci were screened in cross-amplification tests for two other endemic Callicarpa species that also inhabit the Bonin Islands. All loci were successfully amplified in these species.     

Amplification of rainbow trout microsatellites in Brachymystax lenok

Brachymystax lenok is a cold freshwater fish accustomed to inhabit relatively high concentration of dissolved oxygen and clean upper streams. Here we present 13 polymorphic microsatellite primer pairs from rainbow trout to amplify in 32 B. lenok individuals from Ussuri River of China. The number of alleles ranged from two to seven with an average of 3.9 per locus. Observed heterozygosity ranged from 0.0625 to 0.9677. One locus showed significant deviation from Hardy-Weinberg equilibrium. These 13 loci will provide a good basis for investigation of B. lenok population structure and genetic diversity in different distribution region.     

Reproductive Isolation with Little Genetic Divergence in Sympatric Populations of Brown Trout (SALMO TRUTTA)

Two reproductively isolated demes of brown trout coexist in a small Swedish mountain lake, Lake Bunnersj?rna. We electrophoretically examined 102 specimens from that lake for 27 enzymes encoded by 54 loci. The two demes are fixed for different alleles at a lactate dehydrogenase locus (LDH-1); statistically significant allele frequency differences at five other loci further support the complete lack of gene flow between these demes. There are significant differences in growth rates between fish in the two demes, but no further morphological differentiation h-s been detected.--In light of these findings, the genetic distance between these populations is surprisingly small (Nei's I = 0.975). These demes represent one of the least genetically divergent, reproductively isolated sympatric pair of vertebrate populations that have been identified. The results are discussed from both an evolutionary and ecological perspective.     

Identification and characterization of eight microsatellite loci in Machilus pseudokobu (Lauraceae), an endemic species of the Bonin Islands

Eight microsatellite loci were identified and characterized for the endangered Machilus pseudokobu (Lauraceae), an endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from 1 to 20 with an average of 6.2, and the expected heterozygosity ranged from 0.00 to 0.83 with an average of 0.47. All eight loci were screened in cross-amplification tests for two other endemic Machilus species that also inhabit the Bonin Islands. All loci were successfully amplified in these species.     

Development of eighteen tetranucleotide microsatellite markers in Tibetan Macaque (Macaca thibetana) and genetic diversity analysis of captive population

In this study, eighteen tetranucleotide microsatellite loci were isolated from AAAG-enriched and GATA-enriched libraries of the Tibetan macaque, Macaca thibetana. These loci were tested on 53 individuals of M. thibetana, and most loci were proved to be highly polymorphic. A total of 109 alleles were detected with an average of 6.06 alleles per locus. The PIC values of these loci ranged from 0.192 to 0.879, with an average of 0.624. The observed and expected heterozygosities ranged from 0.170 to 0.800 and from 0.217 to 0.898, with an average of 0.583 and 0.675, respectively. 5 loci significantly deviated from Hardy–Weinberg equilibrium (HWE). Significant linkage disequilibrium (LD) was found between 9 pairs of loci. The newly identified polymorphic markers would facilitate the study of M. thibetana on the population structure and genetic diversity.     

Development and characterization of 14 novel microsatellite markers for an invasive goby (Tridentiger bifasciatus) in water transfer system

Genetic patterns observed among populations by neutral molecular markers is a major method used to reconstruct the invasion history of invasive species. The Shimofuri goby (Tridentiger bifasciatus) has invaded several lakes along the East Route of the South-to-North Water Transfer Project, China (ENST). However, neutral molecular markers for this goby are not currently available. In this study, fourteen novel polymorphic microsatellite loci were developed through next generation sequencing technology. These markers were also tested in an invasive population (Nansi Lake, a storage lake of ENST) consisting of 54 individuals. The average number of alleles per locus was 7.6 and ranged from 4 to 13. The average H_o was 0.587 and ranged from 0.404 to 0.852, and the average H_e was 0.733 and ranged from 0.564 to 0.851. The average PIC per locus was 0.689 and ranged from 0.521 to 0.824. Four markers (TB4, TB65, TB66 and TB26) were found to deviate from HWE after correction following the False Discovery Rate method. Null alleles were found in four loci (TB11, TB65, TB66 and TB26). These highly polymorphic microsatellite markers are useful for further study to reconstruct invasion history of Shimofuri goby.     

Isolation and characterization of microsatellite loci in tiger frog (Hoplobatrachus rugulosus)

Nine novel microsatellite loci were developed from the tiger frog (Hoplobatrachus rugulosus) using enrichment methods. The number of alleles ranged from 6 to 11 with an average of 8.56 alleles per locus. The observed and expected heterozygosity ranged from 0.571 to 0.935 (average 0.796) and 0.765 to 0.888 (average 0.837) respectively. These polymorphic loci can be used in population structure, gene flow, and population differentiation.     

Biochemical genetic variation in populations of golden trout, Salmo aguabonita: evidence of the threatened Little Kern River golden trout, S.a. whitei.

Eight wild populations of the High Sierra golden trout, Salmo aguabonita, and one domestic stock of rainbow trout, Salmo gairdneri, were examined for biochemical-genetic variation in eight protein systems. Variation within the eight systems was determined by at least 10 loci in both golden and rainbow trout and all the alleles identified in rainbow trout were observed as electro-phoretically identical phenotypes in golden trout. Variation was observed at an average of 51 percent of the loci in the golden trout samples and for five of the 10 loci in the rainbow trout. Average heterozygosity ranged from 12.6 to 13.9 percent for seven of the golden trout populations with one showing a low value of 5.4 percent. A comparable estimate of 12.1 percent was found for the rainbow stock. On the basis of genetic variation and allele frequencies at three loci, the eight golden trout populations were divided into two distinct groups. Three populations sampled from the Little Kern River basin tended to be genetically distinct from two additional Little Kern River basin populations and from three geographically distinct populations sampled from the eastern Kern River area. The former three populations were hypothesized to be of a recent rainbow-golden hybrid origin. Trout in the other two Little Kern River basin populations, sampled in head-waters of a stream tributary to the Little Kern River, were considered to be the threatened Little Kern golden trout, S. a. whitei Evermann, due to their high degree of genetic similarity to the geographically distinct subspecies S. a. aguabonita sampled from the eastern Kern River area. The finding of substantial genetic variation in the wild golden trout populations indicates that this threatened species is not at present genetically impoverished and thus does not appear to be in immediate danger of extinction through lack of adaptive capability.     

Isolation and characterization of twenty-one polymorphic microsatellite loci in the Tibetan macaque (<Emphasis Type="Italic">Macaca thibetana</Emphasis>)

Twenty-one microsatellite loci were isolated from AC-enriched library of Tibetan macaque (Macaca thibetana). The number of alleles at the 21 microsatellite loci ranged from 8 to 15, with an average of 12.2 per locus. Polymorphism information content (PIC) ranged from 0.805 to 0.910 with an average of 0.873. The observed and expected heterozygosities ranged from 0.208 to 0.792 and from 0.843 to 0.938, respectively. These microsatellite loci will be useful for future studies that relate to the genetic diversity and population structure of Tibetan macaque.     

利用产量位点标记分析中国水稻骨干恢复系与南亚及东南亚恢复系的遗传多样性

利用47个根据已报道的QTL位点或者已被精细定位或克隆的与水稻产量性状基因紧密连锁的产量位点标记,对来自中国、印度和越南等国的58份水稻恢复系进行遗传多样性分析。结果表明:(1)在中国恢复系中,47个产量位点标记中有36个具有多态性,共检测到90个等位基因,每个标记检测到等位基因2~4个,平均为2.500个;有效等位基因共62.905个,平均每个标记1.747个;36个有效标记的Shannon信息指数平均值为0.632,变幅为0.271~1.266。(2)在来自国外的材料中,47个产量位点标记均具有多态性,共检测到131个等位基因,每个标记检测到的等位基因数为2~6个,平均2.787个;有效等位基因数共82.686个,平均1.759个;47个标记的Shannon信息指数平均值为0.649,变幅为0.109~1.110。(3)聚类分析显示,在遗传相似系数为0.73水平上,参试资源聚为三大类群,中国资源多聚在第Ⅰ类群下的第1、2、3亚群,越南资源多聚在第Ⅰ-4亚群,孟加拉资源多聚在第Ⅲ-3亚群。由此表明,中国资源遗传基础较为狭窄,而其他国家的恢复系具有较远的亲缘关系。     

Isolation and characterization of twenty-one polymorphic microsatellite loci in the Tibetan macaque (Macaca thibetana)

Twenty-one microsatellite loci were isolated from AC-enriched library of Tibetan macaque (Macaca thibetana). The number of alleles at the 21 microsatellite loci ranged from 8 to 15, with an average of 12.2 per locus. Polymorphism information content (PIC) ranged from 0.805 to 0.910 with an average of 0.873. The observed and expected heterozygosities ranged from 0.208 to 0.792 and from 0.843 to 0.938, respectively. These microsatellite loci will be useful for future studies that relate to the genetic diversity and population structure of Tibetan macaque.     

New polymorphic microsatellite markers for bluefin leatherjacket (<Emphasis Type="Italic">Navodon septentrionalis</Emphasis> Gunther, 1877)

A microsatellite-enriched genomic DNA library of Navodon septentrionalis was generated and screened by sequencing. Ten dinucleotide microsatellite loci were characterized by genotyping 24 samples. The observed number of alleles ranged from two to seven with an average of 4.40, while the effective number of alleles ranged from 1.49 to 5.70 with an average of 3.31. The observed and expected heterozygosities ranged from 0.2917 to 0.9167 and from 0.3369 to 0.8422, respectively. No significant linkage disequilibrium between pairs of loci was found, but one loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. These polymorphic microsatellite loci would be useful for investigating genetic population structure and molecule-assisted breeding for N. septentrionalis.     

Isolation and characterization of nine polymorphic microsatellite loci in the rock carp, Procypris rabaudi (Tchang)

Nine highly polymorphic microsatellite loci were isolated from AC- and GATA-repeat microsatellite enrichment DNA libraries in the rock carp, Procypris rabaudi (Tchang). The number of alleles for these loci ranged from eight to 18 in tested individuals. Polymorphism information content ranged from 0.712 to 0.908 with an average of 0.837. Average observed and expected heterozygosities were 0.719 and 0.870, respectively. These molecular markers will be useful for the assessment of genetic diversity and analysis of population structure in wild rock carp.     

Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos) genome and cross-amplification in other birds

In order to study duck microsatellites, we constructed a library enriched for (CA)n, (CAG)n, (GCC)n and (TTTC)n. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97) was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04) at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%). The polymorphism information content (PIC) of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose.     

Microsatellite DNA markers in Populus tremuloides.

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars.     

Characterization of 13 microsatellites for Lahontan cutthroat trout (Oncorhynchus clarki henshawi) and cross-amplification in six other salmonids

Thirteen newly developed tri- and tetranucleotide repeat microsatellite markers were developed for Lahontan cutthroat trout (Oncorhynchus clarki henshawi), a threatened subspecies endemic to the Lahontan hydrographic basin in the western USA. These loci are highly polymorphic with five to 30 alleles per locus and observed heterozygosities ranging from 0.4 to 0.7. Cross-species amplification of these markers was most successful in the closely related rainbow trout, Oncorhynchus mykiss, with only three loci amplifying in brown trout, Salmo trutta. Nonoverlapping allelic distributions for many of these loci among the six salmonid species screened suggest these markers may be useful for hybrid determination.     

Polymorphic molecular markers from anonymous nuclear DNA for genetic analysis of populations

A simple method is presented for developing polymorphic, anonymous DNA markers suitable for population genetic studies. Anonymous DNA fragments are screened for sequence variability using a common mutation detection technique (single strand conformation polymorphism analysis; SSCP) and locus-specific PCR primers are designed for polymorphic DNA fragments. Detection of the markers by SSCP analysis coupled with sequence analysis of SSCP variants allows rapid screening while retaining information about the genealogical relationship among alleles. Variability detected for six markers was assessed in rainbow trout Oncorhynchus mykiss and was compared with variability detected by similar analysis of intron loci. Between three and 12 distinct alleles were observed at each marker locus, and average within-population heterozygosity ranged from 0.12 to 0.44. Advantages and limitations of the methodology for population genetic analysis are discussed.     

Characterization of eight polymorphic microsatellite markers in the tarnished plant bug,Lygus lineolaris (Palisot de Beauvois)

A partial genomic library of the tarnished plant bug, Lygus lineolaris, enriched for microsatellite sequences was screened to identify marker loci. Eight polymorphic loci suitable for population genetic studies were identified by screening 192 field‐collected insects. The observed number of alleles ranged from four to 21 with an average of 12.25 (SE ± 1.94) while the effective number of alleles ranged from 1.23 to 11.05 with an average of 4.49 (SE ± 1.15). No linkage disequilibria or significant deviations from Hardy–Weinberg expectations were detected at any of the loci. Seven of the eight L. lineolaris microsatellite loci were transferable to Lygus hesperus.     

Development of microsatellite markers for the bracken fern, Pteridium aquilinum

We isolated eight novel polymorphic microsatellite loci from Pteridium aquilinum. These loci were characterized in 30 individuals, one from Bolivia, two from Peru, one from the USA, one from Japan, and 25 from Northeast China to Southwest China. The number of alleles per locus ranged from two to seven. The observed heterozygosity (H(O) ) ranged from 0.000 to 0.600 with an average of 0.3051, and the expected heterozygosity (H(E) ) ranged from 0.0966 to 0.7780 with an average of 0.4267. One locus deviated from Hardy-Weinberg equilibrium and four pairs of loci were found to be in linkage disequilibrium. These polymorphic loci will be useful in the study of the population genetic structure of Pteridium.     

Parallel introgression and selection on introduced alleles in a native species

As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome‐wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.