No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Evaluation of the Genetic Diversity of Bauhinia winitii, an Endemic Plant of Thailand, Using Microsatellite Markers
Abstract
Bauhinia winitii Craib is an endemic species native to Thailand. Genetic diversity was assessed using microsatellite markers developed from a library enriched using (AG)20/(CAG)20 oligonucleotide probes. Eight polymorphic loci produced a total of 28 alleles with a mean number of 3.5 alleles per locus from 33 specimens of B. winitii. The averages of the expected (He) and observed (Ho) heterozygosity were 0.418 and 0.394, respectively. The average value of polymorphic information content (PIC) was 0.364, and two SSR loci were highly informative. Significant linkage disequilibrium (LD) was observed between one pair of loci and a significant deviation from Hardy-Weinberg equilibrium (HWE) (P < 0.05) was detected at three loci. The B. winitii population in Thailand has a moderate level of genetic diversity and a low level of inbreeding. The cross-species transferability success rate among Bauhinia species of the SSRs derived from B. winitii was 75% (B. acuminata), 100% (B. aureifolia), and 100% (B. strychnifolia). These newly developed SSR primers provide a useful genetic tool for analyzing the population structure of B. winitii and the genetic diversity of the related species – B. acuminata, B. aureifolia, and B. strychnifolia. Information from this study can be useful for developing conservation and protection plans as well as management of the genetic resources of B. winitii, an endemic plant in Thailand. © 2021, Department of Science and Technology. All rights reserved.
... Bauhinia winitii Craib is a woody climber of the Fabaceae family, subfamily Caesalpinioideae and synonym of Lysiphyllum winitii (Craib) de Witt. It is distributed in the tropics and is an endemic plant from Thailand (Sraphet et al., 2021). Based on an assessment conducted by the Botanic Gardens Conservation International database for threatened tree species, B. winitii is classified as an endangered species (Rivers et al., 2015) which is given to taxons facing a high risk of extinction (Dublin, 2019). ...
Bauhinia winitii Craib (Fabaceae, Caesalpinioideae) is a woody climber which is currently included in endangered species list. B. winitii seeds are orthodox seeds in which it has hard coat morphologically. Therefore, B. winitii seeds often undergo physical dormancy which can be broken through immersion in certain liquid media. This study aimed to characterize the morphology of B. winitii seeds and determine the pre-sowing treatment method to accelerate the seeds germination of B. winitii. External morphological characterization was carried out by observing the seeds quantitative and qualitative parameters. Characterization of seeds internal morphology was conducted using a digital microscope. Physical dormancy breaking was carried out by immersion in warm and cold water for 24 hours. Morphological characterization data were analyzed descriptively, while seed germination data were analyzed quantitatively by using one-way ANOVA followed by LSD test (with confidence level of 95%). B. winitii has pod-shaped fruits with 2-6 seeds per pod, the seeds are 1.36 cm x 1 cm in size, 0.47 cm thick and weighed 0.5 g, oblong to conical in shape, smooth and shine surface, with light to dark brown in color. Seeds immersion treatment in warm water could break the physical dormancy of B. winitii seeds thus 63% of the seeds were able to germinate and it was significantly different compared to control and cold water immersion treatment. Technical to germinate B. winitii seed can be known from pre-sowing treatment. This study can be used as a reference for seed identification and germination technical of B. winitii seed.
Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces, China. We used one chloroplast DNA (cpDNA) fragment and 12 pairs of microsatellite (simple sequence repeat; SSR) markers to assess the genetic diversity and structure of 12 C. huana populations. A total of 99 alleles were detected for 12 polymorphic loci, and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA. C. huana populations showed a low level of genetic diversity (n = 8, Hd = 0.759, Pi = 0.00042 for cpDNA, N
A
= 3.931, H
E
= 0.466 for SSRs), but high genetic differentiation between populations (F
ST
= 0.2159 for SSRs, F
ST
= 0.9318 for cpDNA). This can be attributed to the narrow distribution and limestone habitat of C. huana. STRUCTURE analysis divided natural C. huana populations into two groups, consistent with their geographical distribution. Thus, we suggest that five natural C. huana populations should be split into two units to be managed effectively.
Genetic diversity is fundamentally important in crop improvement and provides plants with the capacity to meet the demands of changing environments. This work was carried out to assess the diversity and the extent of genetic relatedness among a number of assembled cassava (Manihot esculenta Crantz) accessions. We conducted a microsatellite marker analysis of 89 cassava accessions collected from Ghanaian and exotic sources. These accessions were assayed using 35 simple sequence repeat (SSR) markers. A total of 167 alleles were detected from 35 polymorphic markers with an average of 4.77 alleles per locus. High allelic frequency was detected across the accessions, ranging from 0.32 to 0.99 with an average of 0.62 per marker. Observed heterozygosity ranged from 0.03 - 0.97 across the accessions. Polymorphism information content (PIC) ranged from 0.03 to 0.78 with a mean of 0.45, indicating high level of polymorphism across the accessions. Comparatively, higher number of alleles, gene diversity and observed heterozygosity were detected among the local accessions compared with the exotic accessions indicating rich genetic diversity among them. Population structure analysis based on STRUCTURE identified two subpopulations and a large number of admixtures. Cluster analysis based on the neighbour joining algorithim further separated the collection into seven sub-groupings irrespective of geographical origin. This indicates the possible sharing of common genomic regions occurring across the accessions. High allelic frequency differences and levels of heterozygosity were observed among the germplasm. These findings indicated significant genetic variability in the germplasm to warrant selection.
Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.
Evolutionary analyses have been widely used for evaluation of genetic diversity of natural populations and correlate these data to the fitness of the species, especially in the case of threatened species. Calydorea crocoides occurs in a restricted area at altitudes from 800 to 1500 m in southern Brazil and is considered endangered. A study assessing genetic diversity, cytogenetic features and ecological niche was performed aiming to characterize C. crocoides by multidisciplinary approaches. Molecular data highlighted that most of the total variation (76%; p < 0.001) was found within populations and the parameters of genetic diversity were high at the species level (PPB = 98.97%; I = 0.4319; h = 0.2821). Gene flow (Nm) was estimated in 0.97 individuals per generation. Cytogenetically, C. crocoides presents a bimodal karyotype and low asymmetry. DAPI banding pattern was uniform, but the CMA-signal evidenced a pericentric inversion in the population ESC688. The species presents high pollen viability and two different morphologies of pollen grains. Our data showed high levels of polymorphism maintained in this species that could ensure conservationist practices in which the main goal is to preserve the evolutionary potential of the species through the maintenance of genetic diversity.
The aim of this study was to characterise the genetic diversity, genetic relationship and population structure within local Turkish Denizli chicken subpopulations in rural areas using 19 microsatellite markers. To assess the uniqueness and relations of the Denizli subpopulations we used six local Italian chicken breeds’ samples, which were genotyped in the same laboratory with the same molecular markers. In total, 105 alleles were found across 19 microsatellite loci with a mean number of 5.53 alleles per locus. Considering all subpopulations and loci, genetic differentiation based on global FST was 0.030 (p < .01). Global FIS values (0.200) indicated that non-random mating occurred in all subpopulations of Denizli fowl and all subpopulations deviated significantly (p < .01) from HWE. Over all subpopulations, the mean observed heterozygosity was 0.473, ranging from 0.399 to 0.562. Genetic differentiations between pairs of subpopulations based on the proportion of shared alleles ranged 0.140–0.297. The neighbour-net tree, based on marker estimated kinship distances, separated Denizli subpopulations and Italian breeds into two main clusters. The most likely number of different populations was estimated using the clustering procedure implemented in STRUCTURE. Structure analysis showed a clear separation of the Denizli fowl subpopulations from the Italian populations. A second step sub-clustering allowed discriminating among the six subpopulations of Denizli breed. The results of this study can be used as baseline genetic information to place breeders’ flocks in conservation programmes, controlling inbreeding and safeguarding the genetic variability of the populations.
Premise of the study
Microsatellite or simple sequence repeat (SSR) markers were developed to investigate the influence of ecological factors on gene flow and spatial genetic structuring of the submerged plant Ranunculus bungei (Ranunculaceae), which is regarded as an important species for understanding how plants adapt to an aquatic environment.
Methods and Results
Twenty-two microsatellite loci were identified from an expressed sequence tag (EST) library. The number of alleles per locus ranged from one to five, and the expected heterozygosity varied from 0.0 to 0.5 in four Chinese populations of R. bungei. Fourteen loci were polymorphic and significantly deviated from Hardy–Weinberg equilibrium. All of the loci were found to be amplifiable in two other species of Ranunculus section Batrachium, and cross-amplification in six riparian and aquatic species of Ranunculaceae was also partially successful.
Conclusions
These novel EST-SSR markers will be useful for ecological and evolutionary studies of R. bungei as well as related species.
Background
The Mount Huang eastern honey bees (Apis cerana) are an endemic population, which is well adapted to the local agricultural and ecological environment. In this study, the genetic structure of seven eastern honey bees (A. cerana) populations from Mount Huang in China were analyzed by SSR (simple sequence repeat) markers.
Results
The results revealed that 16 pairs of primers used amplified a total of 143 alleles. The number of alleles per locus ranged from 6 to 13, with a mean value of 8.94 alleles per locus. Observed and expected heterozygosities showed mean values of 0.446 and 0.831 respectively. UPGMA cluster analysis grouped seven eastern honey bees in three groups.
Conclusion
The results obtained show a high genetic diversity in the honey bee populations studied in Mount Huang, and high differentiation among all the populations, suggesting that scarce exchange of honey bee species happened in Mount Huang. Our study demonstrated that the Mount Huang honey bee populations still have a natural genome worth being protected for conservation.
Electronic supplementary material
The online version of this article (doi:10.1186/s41065-016-0010-4) contains supplementary material, which is available to authorized users.
Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, and high repeatability. However, microsatellites are not always available for the species to be studied and their isolation could be time- and cost-consuming. To investigate transferability in cross-species applications, 102 primer pairs previously developed in ryegrass and tall fescue were amplified across three allogamous ryegrass species including Lolium rigidum, Lolium perenne and Lolium multiflorum. Their highly transferability (100%) were evidenced. While, most of these markers were multiple loci, only 17 loci were selected for a robust, single-locus pattern, which may be due to the recentness of the genome duplication or duplicated genomic regions, as well as speciation. A total of 87 alleles were generated with an average of 5.1 per locus. The mean polymorphism information content (PIC) and observed heterozygosity (Ho) values at genus was 0.5532 and 0.5423, respectively. Besides, analysis of molecular variance (AMOVA) revealed that all three levels contributed significantly to the overall genetic variation, with the species level contributing the least (P<0.001). Also, the unweighted pair group method with arithmetic averaging dendrogram (UPGMA), Bayesian model-based STRUCTURE analysis and the principal coordinate analysis (PCoA) showed that accessions within species always tended to the same cluster firstly and then to related species. The results showed that these markers developed in related species are transferable efficiently across species, and likely to be useful in analyzing genetic diversity.
Aloe peglerae Schönland is a rare succulent plant species, which is endemic to South Africa. The species is currently listed as Endangered and is threatened mainly by illegal collection. The aim of this study was to determine the population status of Aloe peglerae in the Magaliesberg Mountain Range, that is, whether the population is declining, stable or increasing. Key population parameters assessed for this study included plant density, population structure, area of occupancy, population size, and rate of past population decline. Nine subpopulations were surveyed in 2009 and 2010 using a distance sampling technique. Also, these data were compared to data collected in 1999 by the Gauteng Department of Agriculture, Conservation and Environment, so as to determine possible population trends. The results showed a decline of 43% in mean population density between 1999 and 2010, suggesting that the population of Aloe peglerae in the Magaliesberg is in a state of decline. The application of this technique to plant populations is relatively novel and key recommendations are provided to improve survey design.
The evolutionary forces that drive recent population genetic changes include migration, mating strategy, genetic drift, and selection. However, the strength of these forces varies depending on population size. The purpose of this article is to review genetic issues associated with small forest populations and to provide perspectives from fish and wildlife genetics through case studies. Small populations are often fragmented, potentially preventing migration. In forest trees, long-distance pollen dispersal and highly mobile, generalist pollinators can help maintain connectivity. A landscape and community approach to understanding connectivity is critical (case study: mussels). Outbreeding depression can also be a concern in forest restoration. This becomes a greater risk when mixing populations that are highly diverged and when the species is polyploid. Management units should be designated that mimic natural gene flow (case study: lake sturgeon). At the other extreme, inbreeding depression can result in reduced fitness. When inbreeding depression is a concern, genetic rescue may be necessary (case study: Florida panther). Loss of diversity through genetic drift can occur with small effective population sizes (Ne) and a small number of founders (case study: salmonids). Selection is most likely to occur through adaptation to captivity or introduction of resistant/tolerant strains (case study: amphibians).
The aim of this study was to evaluate the selected 41 SSR markers developed for yellow passion fruit (Passiflora edulis f. flavicarpa Sims.) for their transferability to 11 different Passiflora species. Twenty-one SSR were successfully amplified in 10 wild species of passion fruit producing 101 bands. All the markers were amplifiable for at least one species. The mean transferability was 68,8%, ranging from 15,4% (primer PE11) to 100 % (PE13, PE18, PE37, PE41 and PE88). Transferability was higher for the species from the Passiflora subgenus than for those from the Decaloba and Dysosmia subgenus. The results indicated a high level of nucleotide sequence conservation of the primer regions in the species evaluated, and consequently, they could potentially be used for the establishment of molecular strategies for use in passion fruit breeding and genetics.
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheettype data entry with univariate and multivariate statistics, curve fitting, time-series analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
A new liana species of the subfamily Caesalpinioideae (Leguminosae), namely Bauhinia nakhonphanomensis, collected from the Phulangkha National Park, Nakhon Pranom Province, Thailand, is described and illustrated. It is easily recognized by the following combination of characters: tendrilled liana, entire leaves, acuminate or caudate leaf apices, oblong or elliptic floral bud, floral bud 25-35 mm long, raceme or panicle inflorescence, 10-13 mm long hypanthium, anther opening by longitudinal slits. Important comparative morphological characters with some closely related species are discussed.
In this study, we compared the genotypes obtained at a microsatellite locus using two methods of amplification and detection of variation in a set of individuals belonging to the red alga haplo-diploid species, Gracilaria gracilis. The methods varied in their capacity to detect longer alleles in heterozygotes, resulting in an apparent heterozygote deficiency. We attributed this bias in favour of short alleles to competition leading to the preferential amplification of shorter alleles (short allele dominance). To test this hypothesis, we created artificial heterozygotes (mixtures of two haploid DNA samples) and showed that long alleles already less intense than short alleles, ‘suffer’ more from being in association.
Abstract: A species is considered to be “rare” if it exhibits any one of the following attributes: (1) naturally occurs in a narrow geographical area, (2) occupies only one or a few specialised habitats, (3) forms only small population(s) in its range. An “endemic” species, however, grows naturally in a single geographical area, the size of which could be either narrow or relatively large. Not all endemic species are rare, just as not all rare species must necessarily be endemic. Many rare and/or endemic species exhibit one or more of the following attributes which make them especially prone to extinction: (1) narrow (and single) geographical range, (2) only one or a few populations, (3) small population size and little genetic variability, (4) over-exploitation by people, (5) declining population sizes, (6) low reproductive potential,
(7) the need for specialised ecological niches, (8) growth that requires stable and nearly constant environments. When habitats of a rare and/or endemic species are damaged and/or fragmented by various human activities, the distribution
ranges and population sizes of the species will be reduced, leaving them vulnerable to extinction at a much higher rate than other comparable species. Species that experience any of the above attributes must be given priority and monitored
and managed carefully in an eff ort to promote genetic conservation.
This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.
A reliable, fast, cheap and sensitive silver staining method to detect nucleic acids in polyacrylamide gels was developed from two standard stain procedures. The main differences between the three methods concerned (i) the preexposure with formaldehyde during silver nitrate impregnation, (ii) the addition of sodium thiosulfate and sodium carbonate instead of sodium hydroxide during development; (iii) the removal of the stop reaction or the inclusion of absolute ethanol with acetic acid in the stop solution and (iv) the duration of the different reaction steps. All methods allowed the detection of similar polymorphisms for single sequence repeats with different cotton genotypes but important differences regarding the contrast, background and conservation duration of the gels were observed. Two methods gave superior sensitivity. The improved method was sensitive, fast (20 min), gave lower backgrounds, produced gels with long-term conservation ability, and allowed a reutilization of all the solutions used in the staining procedure from fi ve to seven times, making it quite cheap.
Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their
abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite
molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation.
Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the
submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The
program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of
microsatellite markers.
Availability
The web tool may be accessed at
http://purl.oclc.org/NET/websat/
Glycosyl hydrolase (GH) genes from Escherichia coli and Bacillus subtilis were used to search for cases of horizontal gene transfer. Such an event was inferred by G + C content, codon usage analysis, and a phylogenetic congruency test. The codon usage analysis used is a procedure based on a distance derived from a Pearson linear correlation coefficient determined from a pairwise codon usage comparison. The distances are then used to generate a distance-based tree with which we can define clusters and rapidly compare codon usage. Three genes (yagH from E. coli and xynA and xynB from B. subtilis) were determined to have arrived by horizontal gene transfer and were located in E. coli CP4-6 prophage, and B. subtilis prophages 6 and 5, respectively. In this study, we demonstrate that with codon usage analysis, the proposed horizontally transferred genes can be distinguished from highly expressed genes.
Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.
Euryodendron excelsum is a critically endangered tertiary relict plant endemic to China. It has only one population remaining in Ba Jia Zhen of Yangchun, Guangdong. In this study, we discovered 25 microsatellite markers from E. excelsumusing a Fast Isolation by Amplified Fragment Length Polymorphism of Sequences COntaining Repeats (FIASCO) protocol. Thirteen loci demonstrated polymorphisms, with the number of alleles per locus ranging from 2 to 13. Values for observed and expected heterozygosity ranged from 0.176 to 1.000 and from 0.261 to 0.889, respectively. Three loci (ZXM-17, ZXM-54, and ZXM-92) were found to significantly deviate from Hardy-Weinberg equilibrium. In addition, five of 13 loci could be successfully cross-amplified in Ternstroemia gymnanthera. These microsatellite loci may help to further survey the adaptive evolution and genetic variation of E. excelsum for guiding its conservation.
A new species of Bauhinia from Peninsular Thailand is described as B. chrysophylla. It appears to be endemic to an isolated mountain and must be regarded as a rare and endangered species. Its pollen morphology is studied and its relationships discussed.
Several methods based on population biology, biogeography, ecology, and genetics have been traditionally used for the identification of units for conservation below the species level. We use a combination of two methods based on population genetic structure estimators and on probabilities of loss of rare alleles to identify the Relevant Genetic Units for Conservation (RGUCs). The aims were to assess the genetic diversity and population structure of the endemic steppe plant Boleum asperum (Brassicaceae), and to determine how many and which populations significantly represent the total genetic diversity and the rarest allelic variation. Despite the high amplified fragment length polymorphism genetic diversity values detected in B. asperum (hT = 0.744), caused probably by its hexaploidy and allogamy, moderate spatial genetic differentiation was detected among populations (< 20%) and geographical ranges (> 13%), suggesting the existence of an ancestral continuous distribution range that was fragmented into separate ‘islands’ in more recent historical times. Five RGUCs, accounting for the 85.10% of the total genetic variation and representative of the entire geographical distribution of the species, were selected for in situ conservation. Ex situ conservation is proposed to complement the preservation of B. asperum. This method of objective selection of populations may be applied to other candidate taxa for conservation with prior adjustment of the threshold values of diversity required for effective protection of each particular species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 341–354.
An improved protocol for constructing microsatellite-enriched libraries was developed. The procedure depends on digesting
genomic DNA with a restriction enzyme that generates blunt-ends, and on ligating linkers that, when dimerized, create a restriction
site for a different blunt-end producing restriction enzyme. Efficient ligation of linkers to the genomic DNA fragments is
achieved by including restriction enzymes in the ligation reaction that eliminate unwanted ligation products. After ligation,
the reaction mixture is subjected to subtractive hybridization without purification. DNA fragments containing microsatellites
are captured by biotin-labeled oligonucleotide repeats and recovered using streptavidin-coated beads. The recovered fragments
are amplified by PCR using the linker sequence as primer, and cloned directly into a plasmid vector. The linker has the sequence
GTTT on the 5′ end, which promotes efficient adenylation of the 3′ ends of the PCR products. Consequently, the amplified fragments
could be cloned into vectors without purification. This procedure enables efficient enrichment and cloning of microsatellite
sequences, resulting in a library with a low level of redundancy.
Simple sequence repeats (SSRs) are a group of repetitive DNA sequences that represent a significant portion of higher eukaryote genomes. They can serve as highly informative genetic markers, and in conjunction with the use of polymerase chain reaction (PCR) technology enable the detection of length variation. This novel means of detecting polymorphism targets highly variable regions of the genome, and has revolutionized human and mammalian research. It is now poised to have a significant impact in plant science.
A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.
We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.
In order to assess the feasibility of using microsatellites as markers in plant genetics, a survey of published DNA sequence data for presence, abundance and ubiquity in higher plants of all types of dinucleotide and trinucleotide repeats with a minimum number of 10 and 7 units, respectively, was conducted. This search revealed that such microsatellites are frequent and widely distributed; they were uncovered in 34 species, with a frequency of one every 50 kb. AT repeats were by far the most frequently observed class of dinucleotide microsatellites, whereas AC/TG repeats, which are common in animals, were observed only once. TAT repeats prevailed among trinucleotides. Polymerase chain reaction amplification of (AT)n and (TAT)n microsatellites in soybean (Glycine max (L.) Merr.) revealed that they are highly polymorphic, as a consequence of length variation, somatically stable and inherited in a co-dominant Mendelian manner. The abundance and amount of information derived from such markers, together with the ease by which they can be identified, make them ideal markers for plant genetic linkage and physical mapping, population studies and varietal identification.
We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.
An update on ayurvedic herb kachhnar (Bauhinia purpurea Linn.) -a review
- Chanchal Dk
- Niranjan Ps
- Alok S Singh S
CHANCHAL DK, NIRANJAN PS, ALOK S, SINGH
S, SAURABH. 2015. An update on ayurvedic herb
kachhnar (Bauhinia purpurea Linn.) -a review. Int J
Pharm 2(8): 381-390.
Impact of climate change on biodiversity loss and extinction of endemic plants of arid land mountains
- El-Keblawy A
EL-KEBLAWY A. 2014. Impact of climate change on
biodiversity loss and extinction of endemic plants of
arid land mountains. J Biodivers Endanger Species
2: 120.
Secondary metabolites and pharmacological activities of Bauhinia genus plants
- Kaewamatawong R
KAEWAMATAWONG R. 2008. Secondary metabolites
and pharmacological activities of Bauhinia genus
plants. J of Ubon Ratchathani University 10(3):
116-130.
Isolation, characterization, and crossamplification of microsatellite markers for the Petunia integrifolia (Solanaceae) complex
- Beheregaray K R I E D T R A , R A M O S -F R E G O N E Z I A M C
- Bonatto Lb
- Freitas Sl
- Lb
K R I E D T R A, R A M O S -F R E G O N E Z I A M C,
BEHEREGARAY LB, BONATTO SL, FREITAS
LB. 2011. Isolation, characterization, and crossamplification of microsatellite markers for the Petunia
integrifolia (Solanaceae) complex. Am J Bot 98(10):
e277-e279.
The genus Bauhinia in Thailand
- Larsen Larsen K
- Ss
LARSEN K, LARSEN SS. 1973. The genus Bauhinia in
Thailand. Nat Hist Bull Siam Soc 25: 1-22.
Addition to the Leguminosae of Thailand
- Larsen Larsen K
- Ss
LARSEN K, LARSEN SS. 1995. Addition to the
Leguminosae of Thailand. Thai For Bull 23: 43-49.
Bauhinia sirindhorniae sp. nov. (Leguminosa Caesalpinioideae) a remarkable new species from Thailand
- Larsen Larsen K
- Ss
LARSEN K, LARSEN SS. 1997. Bauhinia sirindhorniae
sp. nov. (Leguminosa Caesalpinioideae) a remarkable
new species from Thailand. Nord J Bot 17(2): 113-118.
Bauhinia siamensis (Leguminosae-Caesalpinoideae), an extraordinary new species from Thailand
- Larsen Larsen K
- Ss
LARSEN K, LARSEN SS. 2002. Bauhinia siamensis
(Leguminosae-Caesalpinoideae), an extraordinary
new species from Thailand. Nat Hist Bull Siam Soc
50: 99-104.
Leguminosae-Caesalpinioideae
- Larsen Larsen K
- Ss
- Vidal Je
LARSEN K, LARSEN SS, VIDAL JE. 1984.
Leguminosae-Caesalpinioideae. In: Flora of Thailand,
Vol. 4. Smitinand T, Larsen K ed. Bangkok: The Royal
Forest Department.
Leguminosae-Caesalpinioideae), a species new to Thailand
- Larsen Ss
LARSEN SS. 1999. Bauhinia wallichii J.F. Macbr.
(Leguminosae-Caesalpinioideae), a species new to
Thailand. Thai For Bull 27: 25-29.
Genetic diversity and population structure of Ottelia acuminata var. jingxiensis, an endangered endemic aquatic plant from southwest China
- L I Zz
- L U Mx
- Gichira Aw
- Islam Mr
- Wang Qf
- Chen Jm
LI ZZ, LU MX, GICHIRA AW, ISLAM MR, WANG QF,
CHEN JM. 2019. Genetic diversity and population
structure of Ottelia acuminata var. jingxiensis, an
endangered endemic aquatic plant from southwest
China. Aquat Bot 152: 20-26.
Tools for population genetic analysis (TFPGA) 1.3. A windows program for the analysis of allozyme and molecular population genetic data
- Miller Mp
MILLER MP. 1997. Tools for population genetic analysis
(TFPGA) 1.3. A windows program for the analysis
of allozyme and molecular population genetic data.
Computer software distributed by the author.
Rakta Kanchan (Bauhinia variegata): chemistry, traditional and medicinal uses-a review
- G M Ravindra
- G M Shailaja
- Anita Am
RAVINDRA GM, SHAILAJA GM, ANITA AM. 2007.
Rakta Kanchan (Bauhinia variegata): chemistry,
traditional and medicinal uses-a review. Pharmacogn
Rev 1(2): 314-319.
Conserving the world's most threatened trees: a global survey of ex situ collections
- Rivers M
- Shaw K
- E Beech
- Jones M
RIVERS M, SHAW K, BEECH E, JONES M. 2015.
Conserving the world's most threatened trees: a
global survey of ex situ collections. Botanic Gardens
Conservation International, Surrey, UK.
Isolation and characterization of polymorphic microsatellite loci in Camellia nitidissima Chi (Theaceae)
- Wei Jq
- Chen Zy
- Wang Zf
- H Tang
- Jiang Ys
- L I Xy
- Q I Xx
WEI JQ, CHEN ZY, WANG ZF, TANG H, JIANG
YS, WEI X, LI XY, QI XX. 2010. Isolation and
characterization of polymorphic microsatellite loci
in Camellia nitidissima Chi (Theaceae). Am J Bot
97(10): e89-e90.