In vitro propagation and assessment of genetic stability of micropropagated Samanea saman (rain tree) using microsatellite markers

An efficient in vitro propagation of Samanea saman (rain tree) protocol has been successfully developed using nodal explants from a 20-year-old tree. Higher percentage (76 %) of explants produced up to five shoots per explant on Murashige and Skoog (MS) medium supplemented with 2 mg L^?1 6-benzyladenine (BA), 0.1 mg L^?1 gibberellic acid (GA₃) and 100 mg L^?1 casein hydrolysate after 3 weeks of culture. When explants were subcultured to fresh medium after harvesting first batch of shoots, more shoots could be generated (another eight shoots per explant). Shoot elongation was achieved (3 cm) when shoots were cultured on MS medium supplemented with 0.25 mg L^?1 BA and 0.75 mg L^?1 GA₃. In vitro generated shoots rooted on MS medium fortified with 0.75 mg L^?1 indole-3-butyric acid plus 0.1 % of activated charcoal. A higher percentage of explant response and shoots per explant were obtained on MS medium with BA and GA₃. Each responsive nodal explant yields an average of 15 rooted plants within a period of 10 weeks. Rooted plantlets were successfully acclimatized in green house with a survival rate of 90 %. Micropropagated plants were tested for genetic stability using simple sequence repeats (SSR) markers. Use of the 12 high-resolution SSR markers revealed the exact same genetic profile between the mother tree (donor) and micropropagated plants, suggesting the genetic fidelity of our micropropagation protocol. The same protocol was also used successfully in propagating a “Golden Rain Tree” although response of explant and efficiency of propagation was much lower. This protocol will be useful for germplasm preservation/large scale production of true-to-type clones of desirable genotypes.     

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.     

Genetic characterization of four wild species of Chinese marmots using microsatellite markers

Marmots are large ground squirrels, and 14 species have been reported in the world, including four species of marmots (Himalayan marmot, Tarbagan marmot, gray marmot and long-tailed marmot) living in China. Although these biological resources are abundant in China, information regarding their genetic features is lacking, hampering further study regarding them. The aims of this research were to evaluate genetic variations of four species of Chinese wild marmots, and analyzed kinship of these marmot populations. In the current study, we collected samples of four species of Chinese wild marmot and analyzed the effective allele number, gene diversity, the Shannon index, and polymorphism information to evaluate genetic variations using 13 microsatellite loci. Based on Nei’s genetic distance using the unweighted pair group method, we constructed a dendrogram to analyze the population kinship. We determined that all four Chinese marmot species had high genetic polymorphisms and departure from Hardy-Weinberg equilibrium. The Chinese marmots to be divided into two large groups: Himalayan marmot was independent group. Tarbagan marmot, gray marmot and long-tailed marmot were others; Tarbagan marmot and gray marmot showed a close kinship with each other, but long-tailed marmot did not have a close relationship with the other species. The high polymorphisms and the kinship of Chinese marmot populations were correlated with geographical terrain of their habitat. Himalayan marmot was characterized as living in unique alpine meadows in Qinghai-Tibet plateau and was affected by terrain; however, Tarbagan marmot, gray marmot and long-tailed marmot were characterized as living in grassland or alpine grassland and were not affected by terrain. Genetic features of Chinese wild marmots were investigated in this study. This may give using information regarding protection of Chinese wild marmot resource and further application of biomedical research.     

Monitoring of cultivar identity in micropropagated olive plants using RAPD and ISR markers

Randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers were applied to assess the genetic stability of micropropagated olive (Olea europaea L. cv. Maurino) plants regenerated by axillary buds. Initial olive explants, isolated from one donor tree, were multiplied on Murashige and Skoog medium for 12 repeated subcultures. A total of 40 RAPD and 10 ISSR markers resulted in 301 distinct and reproducible band classes showing homogeneous RAPD and ISSR patterns. The amplification products revealed genetic stability among the micropropagated plants and between them and the donor plant. The results demonstrate the genetic stability of nine year old mature micropropagated olive plants cultured in field, and corroborated the fact that axillary multiplication is the safest mode for multiplication of true to type plants.     

Assessment of genetic diversity of Czech sweet cherry cultivars using microsatellite markers

We analyzed 24 sweet and wild cherry genotypes collected in Czech Republic to determine genetic variation, using previously described 16 SSR primers to adapt a fast, reliable method for preliminary screening and comparison of sweet cherry germplasm collections. All SSRs were polymorphic and they were able all together to distinguish unambiguously the genotypes. These SSR primers generated 70 alleles; the number of alleles per primer ranged from 2 to 7, with a mean of 4.4 putative alleles per primer combination. The primer UDP-98-412 gave the highest number of polymorphic bands (totally 7), while Empa2 and Empa3 gave the lowest number (2). The allele frequency varied from 2.1% to 87.5%. We observed 10% of unique alleles at different loci. The observed heterozygosity value ranged from 0.25 to 0.96 with an average of 0.72 while expected heterozygosity value varied from 0.22 to 0.75 with an average of 0.59. The PIC value ranged from 0.21 to 0.71 with a mean value of 0.523. Cluster analysis separated the investigated cultivars in two groups. High level of genetic diversity obtained in the collection and proved to be sufficiently genetically diverse and therefore these genotypes would be useful to breeders for the development of new cherry cultivars.     

Determination of genetic stability of long-term micropropagated plantlets of Platanus acerifolia using ISSR markers

Inter-simple sequence repeat (ISSR) markers were used to assess the genetic stability of long-term micropropagated plantlets of London plane tree (Platanus acerifolia Willd.). Twenty micropropagated plantlets were chosen from a clonal collection of shoots that originated from a single mother shoot. This clonal collection had been maintained under in vitro culture conditions for at least 8 years, as achieved by axillary branch multiplication. Out of 38 ISSR primers screened, 16 primers were found to produce clear reproducible bands resulting in a total of 103 distinct bands with an average of 6.44 scorable bands per primer. Of these 103 bands, 86 were monomorphic across all 20 of the plants tested and 17 showed polymorphisms (16.5 % polymorphism). Based on the ISSR band data, similarity indices between the plantlets ranged from 0.92 to 1.00. These similarity indices were used to construct an UPGMA dendrogram and demonstrated that all 20 micropropagated plants grouped together in one major cluster with a similarity level of 91 %. A total of 1771 scorable bands were obtained from the full combination of primers and plantlets and only 51 (2.88 %) were polymorphic across the plantlets which indicates that this micropropagated line of P. acerifolia is genetically stable.     

An improved micropropagation and assessment of genetic stability of micropropagated Salvadora oleoides using RAPD and ISSR markers

An improved micropropagation method has been developed for Salvadora oleoides, a valuable tree species of alkaline and arid regions. Nodal explant obtained from a mature tree (30- to 35-year-old) responded optimally (80.0 %) on BAP (2.0 mg l^?1) and produced (4.56 ± 0.52) shoots. Shoots were further multiplied by subculturing the in vitro excised shoots and transferring them to MS medium containing either BAP (0.0–2.0 mg l^?1) alone or in combination with lower concentrations of an auxin (IAA or NAA 0.05–0.4 mg l^?1). Among all the PGRs combination tested, MS medium supplemented with BAP (0.5 mg l^?1) and IAA (0.1 mg l^?1) formed the maximum number of shoots (68.40 ± 2.74 per culture bottle) with an average height (6.59 ± 0.30 cm), after 6 weeks of culture. Rooting in regenerated shoots was achieved by ex vitro methods and about 92.5 % of shoots were rooted with 5.25 ± 0.64 roots per shoot and an average length of 2.76 ± 0.53 cm after 3 weeks of incubation in the green house. More than (80 %) of hardened plantlets survived in the field conditions. Genetic stability of the discussed protocol was confirmed by two DNA-based fingerprinting techniques i.e. RAPD and ISSR. Of the 10 RAPD primers finally selected, a total of 42 bands (out of 43) were monomorphic and one polymorphic, whereas from 10 ISSR primers selected, all the 43 bands were monomorphic revealing a high level of genetic homogeneity in the regenerated plants and the donor plant. In the present investigation, we achieved significantly more number of shoots during multiplication, which are higher than all previous reports and further evaluated the genetic fidelity of protocol for the first time in S. oleoides, which concludes the clonal (true-to-type) nature of micropropagated plantlets.     

Determination of genetic stability in long-term micropropagated shoots of Pinus thunbergii Parl. using RAPD markers

Random amplified polymorphic DNA (RAPD) markers were used to determine the genetic stability of long-term (more than 10 years) micropropagated shoots of Japanese black pine (Pinus thunbergii Parl.). Thirty-six shoots consisting of three morphotypes (short, medium, and long needles) were randomly chosen from about 4,000 micropropagated shoots regenerated from the explants of a single nematode-resistant mother plant. Out of 126 primers screened, 30 gave 134 clear reproducible bands. A total of 4,824 bands obtained from these studies exhibited no aberration in RAPD banding patterns among the tested shoots. Our results show that regenerants from our plant micropropagation system are genetically stable. Received: 5 December 1997 / Revision received: 17 May 1998 / Accepted: 1 June 1998     

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker‐based analysis reveals cattle‐specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY_cattle = 2.66 ± 0.53% and Q_cattle = 0.69 ± 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai‐Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak‐cattle hybridization is primarily driven to produce F₁ hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make‐up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.     

Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Microsatellite markers are increasingly being used in crop plants to discriminate among genotypes and as tools in marker-assisted selection. Here we evaluated the use of microsatellite markers to quantify the genetic diversity within as well as among accessions sampled from the world germplasm collection of sorghum. Considerable variation was found at the five microsatellite loci analysed, with an average number of alleles per locus equal to 2.4 within accessions and 19.2 in the overall sample of 25 accessions. The collection of sorghum appeared highly structured genetically with about 70% of the total genetic diversity occurring among accessions. However, differentiation among morphologically defined races of sorghum, or among geographic origins, accounted for less than 15% of the total genetic diversity. Our results are in global agreement with those obtained previously with allozyme markers. We were also able to show that microsatellite data are useful in identifying individual accessions with a high relative contribution to the overall allelic diversity of the collection. Received: 10 August 1999 / Accepted: 27 August 1999     

Construction of two genetic linkage maps of taro using single nucleotide polymorphism and microsatellite markers

Linkage maps are needed for genetic studies and molecular breeding of taro (Colocasia esculenta). In this study, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) loci on two mapping populations: F31 (HLB11 × VU006) composed of 266 progenies and F32 [HLB01 × (VU370×ID316)] composed of 292 progenies. SNP calling generated an initial set of 22,734 SNPs for F31 and 16,744 for F32. A large proportion of individuals and loci were later removed by filtering on the proportion of missing data and segregation distortions. Linkage maps were constructed with filtered SNPs in association with 14 simple sequence repeat (SSR) markers, using the maximum likelihood method. In both populations, loci were successfully grouped into 14 linkage groups (LGs) with an independence logarithm of odds (LOD) threshold of 11.0 and 8.0 for F31 and F32, respectively. LGs ranged in size from 90 to 15 markers for F31 and from 92 to 12 markers for F32. Bridge markers (459 SNPs and 9 SSRs) were identified and revealed homologous groups between families. Although our maps presented unprecedented chromosome coverage, the colinearity between homologous groups was low (except for LG07), and map lengths were globally inflated. Putative effects of missing data, segregation distortion, and genotyping errors on map accuracy are discussed. This research work led to the identification of a reliable set of SNPs potentially useful as a tool for a wide range of genetic studies in taro.     

Comparative genetic diversity of wild and hachery populations of Korean threadsail filefish Stephanolepis cirrhifer using cross-species microsatellite markers

The threadsail filefish Stephanolepis cirrhifer is a highly commercial fisheries resource in Korea that suffers intensive anthropogenic pressure across much of its range. For basic information about its current genetic status in relation to stock enhancement, the level and distribution of genetic variation between a wild and a hatchery-bred population were investigated using 10 microsatellite markers developed for Thamnaconus modestus. High levels of polymorphism were observed between the two populations. A total of 95 different alleles were found at all loci, with some alleles being unique. The allelic variability ranged from six to 13 in the wild population and from five to 13 in the hatchery one. The average observed and expected heterozygosities were estimated to be 0.72 and 0.80 in the wild sample and 0.70 and 0.79 in the hatchery one, respectively. These results showed similar genetic variability in the hatchery population, as compared with the wild population and significant genetic differentiation between the wild population and the hatchery samples (F _ST = 0.016, P < 0.05). Genetic drift in the intensive breeding practices for stock enhancement has probably promoted differentiation between populations. Significant deviations from Hardy-Weinberg equilibrium were detected in both populations. Our results indicate that further studies using species-specific microsatellite markers will be necessary for a more reliable assessment of genetic diversity of the species.     

Development and characterization of microsatellite markers for two dioecious Ficus species

Microsatellite markers for Ficus montana and Ficus septica were developed using genomic libraries enriched for di‐, tri‐ and tetranucleotide repeats. The subsets of five and three best scorable primer pairs were characterized on 24 F. montana and 36 F. septica individuals, respectively. For F. montana, loci showed five to 14 alleles per locus and expected heterozygosities ranged between 0.23 and 0.87. For F. septica, loci showed three to five alleles per locus and expected heterozygosities ranged between 0.36 and 0.49. Four primer pairs (two from each subset) cross‐amplified in the other species, indicating transportability of the markers within the genus Ficus.     

Transferability and characterization of microsatellite markers in two Neotropical Ficus species

Microsatellite markers were transferred and characterized for two Neotropical fig tree species, Ficus citrifolia and Ficus eximia. Our study demonstrated that microsatellite markers developed from different subgenera of Ficus can be transferred to related species. In the present case, 12 of the 15 primer pairs tested (80%) were successfully transferred to both of the above species. Eleven loci were polymorphic when tested across 60 F. citrifolia and 60 F. eximia individuals. For F. citrifolia, there were 4 to 15 alleles per locus, whereas expected heterozygosities ranged from 0.31 to 0.91. In the case of F. eximia, this was 2 to 12 alleles per locus and expected heterozygosities from 0.42 to 0.87.     

Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers.

An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results.     

Population genetic structure of wild and hatchery black rockfish Sebastes inermis in Korea, assessed using cross-species microsatellite markers

The population structure of the black rockfish, Sebastes inermis (Sebastidae), was estimated using 10 microsatellite loci developed for S. schlegeli on samples of 174 individuals collected from three wild and three hatchery populations in Korea. Reduced genetic variation was detected in hatchery strains [overall number of alleles (N(A)) = 8.07; allelic richness (A(R)) = 7.37; observed heterozygosity (H(O)) = 0.641] compared with the wild samples (overall N(A) = 8.43; A(R) = 7.83; H(O) = 0.670), but the difference was not significant. Genetic differentiation among the populations was significant (overall F(ST) = 0.0237, P < 0.05). Pairwise F(ST) tests, neighbor-joining tree, and principal component analyses showed significant genetic heterogeneity among the hatchery strains and between wild and hatchery strains, but not among the wild populations, indicating high levels of gene flow along the southern coast of Korea, even though the black rockfish is a benthic, non-migratory marine species. Genetic differentiation among the hatchery strains could reflect genetic drift due to intensive breeding practices. Thus, in the interests of optimal resource management, genetic variation should be monitored and inbreeding controlled within stocks in commercial breeding programs. Information on genetic population structure based on cross-species microsatellite markers can aid in the proper management of S. inermis populations.     

应用微卫星标记研究Dunkin Hartley豚鼠封闭群的遗传背景

目的检测我国现有Dunkin Hartley豚鼠封闭的遗传背景,分析评估其遗传多样性水平和遗传分离情况,为建立标准化的豚鼠封闭群监测方法提供基础资料。方法应用筛选获得的8个微卫星位点,从一个数量为1000的豚鼠封闭群中随机选择72个个体,通过PCR扩增和聚丙烯酰胺凝胶电泳的方法,进行等位基因检测。并根据检测结果分析评估了该豚鼠封闭群的遗传现状。结果共检测到28个等位基因,每个座位的等位基因数为2～5个,有效等位基因数为1.5191～3.4422,平均2.3093。平均期望杂合度为0.5294。各位点多态信息含量在0.3154～0.6545之间,平均值为0.4687。有5个位点显著偏离Hardy-Weinberg平衡。结论豚鼠封闭群的遗传多态性处于中等水平,遗传平衡检测结果提示种群的繁殖过程未能实现完全随机交配,近交现象一定程度上存在。本研究的结果将为豚鼠封闭群遗传监测方法和标准的建立提供基础。     

Analysis of genetic diversity among persimmon cultivars using microsatellite markers

In the Mediterranean area, the production of persimmon (Diospyros kaki Thumb) [2n = 6x = 90] has increased recently as an alternative to the major fruit crops. In Spain, production relies almost exclusively on the cultivar “Rojo Brillante” which accounts for 83% of the crop. A crop based on a monovarietal culture implies several commercial risks that can compromise the future of the crop. Although the species was introduced in Europe very recently, it is well adapted to the climate of southern Europe. However, the recent introduction from Japan, the mistakes on the identity of varieties in the collections due to a bad translation of variety names from Japanese, and the lack of genetic characterization of many varieties have caused difficulties for effective management of the available genetic resources. The present paper was aimed at exploring the genetic diversity among different persimmon cultivars, including those collected in the European survey as well as Japanese cultivars. Seventy-one persimmon cultivars coming from two European collections that included accessions from Japan, Italy, and Spain were analyzed using 19 polymorphic microsatellite markers. A total of 206 alleles were obtained, with a mean value of 10.8 alleles per locus. A neighbor joining dendrogram and a principal coordinate analysis arranged the cultivars according to their genetic relationships. Analysis of molecular variance revealed significant genetic variability between and within groups, 73.3% and 85.2% for astringent-type and country origin, respectively. The simple sequence repeat markers classified the persimmon cultivars according to their genetic relationship.     

Assessment of multidrug resistance reversal using dielectrophoresis and flow cytometry

In cancer, multidrug resistance (MDR) is the simultaneous resistance of tumor cells to different natural product anticancer drugs that have no common structure. This is an impediment to the successful treatment of many human cancers. A common correlate of MDR is the overexpression of a membrane protein, P-glycoprotein. Many studies have shown that MDR can be reversed after the use of substrate analogs, called MDR modulators. However, our understanding of MDR modulation is incomplete. In this article, we examine the electrical properties of the human leukemic cells (K562) and its MDR counterpart (K562AR) using dielectrophoresis and flow cytometry (with a membrane potential sensitive dye, DIOC5), both before and after treatment with XR9576 (a P-glycoprotein-specific MDR-reversal agent). The results show significant differences in the cytoplasmic conductivity between the cell lines themselves, but indicate no significant changes after modulation therapy. We conclude that the process of MDR modulation is not associated with changes in the electrical properties of cancer cells. Moreover, the results demonstrate that using the flow cytometry method alone, with MDR cells, may produce artifactual results--whereas in combination with dielectrophoresis, the results show the role of MDR modulators in preventing drug efflux in MDR cells.     

Assessment of genetic diversity and relationships of Krachaai Sayam,an endemic plant in Thailand using microsatellite markers

Nineteen microsatellite markers were developed from Boesenbergia siamensis (Gagnep.) P. Sirirugsa, an endemic plant of Kanchanaburi Province, Thailand and used to determine genetic diversity of this plant. The number of alleles of each locus varied from 4 to 16 in 25 individual samples. The average values of observed and expected heterozygosities were 0.577 and 0.804, respectively. The polymorphic information content value ranged between 0.486 and 0.912. Ten loci significantly deviated from Hardy–Weinberg equilibrium, and eight pairs of loci showed significant evidence of linkage disequilibrium. Moreover, these newly developed microsatellite markers were used to determine cross-species amplification with three samples each of B. thorelii (Gagnep.) Loes., B. rotunda (L.) Mansf. and Kaempferia parviflora Wall. Of the 19 markers developed, 13 (68.42%) primer pairs were able to be used with B. thorelii (Gagnep.) Loes. and K. parviflora Wall., while 12 (63.16%) primer pairs were able to be used with B. rotunda (L.) Mansf. These microsatellite markers will be useful for further genetic analysis of this endemic plant as well as related species.