DNA profiles to identify Dillenia species (Dilleniaceae) in Thailand

Phytotaxa ◽  
2017 ◽  
Vol 296 (3) ◽  
pp. 239
Author(s):  
TIKUMPORN THOOPTIANRAT ◽  
ARUNRAT CHAVEERACH ◽  
RUNGLAWAN SUDMOON ◽  
TAWATCHAI TANEE
Keyword(s):  
Genetic Distance ◽  
Genetic Distances ◽  
Rbcl Gene ◽  
Species Pairs ◽  
Unidentified Species ◽  
Dna Profiles ◽  
Intraspecific Genetic Distance ◽  
Rbcl Gene Sequences ◽  
Paired Species

Surveying of the species throughout Thailand revealed 13 identified and one unidentified species including D. aurea, D. excelsa, D. grandifolia, D. hookeri, D. indica, D. obovata, D. ovata, D. parviflora, D. pentagyna, D. philippinensis, D. pulchella, D. reticulata, D. suffruticosa and Dillenia sp. They were phylogenetically examined based on RAPD profiles of 2,290 discrete characters including a monomorphic and 226 polymorphic characteristics. The phylogenetic relationships calculated from theses banding data show that the intraspecific genetic similarity (S) values ranged from 0.990 to 1.000, and the interspecific S values ranged from 0.520 to 0.790. The RAPD method can be effectively used in Dillenia study. However, its quality of unreproducible method, it cannot be reasonable used in any study on specific genes or areas. In additions, sequences from two molecular regions, rbcL gene and psbA-trnH spacer, were analyzed and determined for genetic distances. The rbcL gene sequences were rather ineffective, as all of the paired species displayed no or low genetic distance values. The psbA-trnH spacer sequences were rather effective, with only one pair (D. reticulata and D. parviflora) showing low genetic distance values. The other species pairs indicated rather far genetic distances, ranging from 0.006 (D. parviflora and D. grandifolia) to 0.376 (Dillenia specie and D. indica). Intraspecific genetic distance values ranged from 0–0.003 and 0–0.013 for rbcL and psbA-trnH spacer regions, respectively. Based on the results from both nucleotide variations and DNA fingerprinting, D. grandifolia and D. ovata were distinct Dillenia species.

scholarly journals DMSO Improves the Ski-Slope Effect in Direct PCR

2021 ◽  
Vol 11 (4) ◽  
pp. 1943
Author(s):  
Joo-Young Kim ◽  
Ju Yeon Jung ◽  
Da-Hye Kim ◽  
Seohyun Moon ◽  
Won-Hae Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Pcr Amplification ◽  
Analytical Techniques ◽  
Direct Pcr ◽  
Dna Profile ◽  
Novel Technologies ◽  
Specific Amplification ◽  
Polymerase Chain ◽  
Dna Profiles

Analytical techniques such as DNA profiling are widely used in various fields, including forensic science, and novel technologies such as direct polymerase chain reaction (PCR) amplification are continuously being developed in order to acquire DNA profiles efficiently. However, non-specific amplification may occur depending on the quality of the crime scene evidence and amplification methods employed. In particular, the ski-slope effect observed in direct PCR amplification has led to inaccurate interpretations of the DNA profile results. In this study, we aimed to reduce the ski-slope effect by using dimethyl sulfoxide (DMSO) in direct PCR. We confirmed that DMSO (3.75%, v/v) increased the amplification yield of large-sized DNA sequences more than that of small-sized ones. Using 50 Korean buccal samples, we further demonstrated that DMSO reduced the ski-slope effect in direct PCR. These results suggest that the experimental method developed in this study is suitable for direct PCR and may help to successfully obtain DNA profiles from various types of evidence at crime scenes.

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

scholarly journals The optimal mating distance resulting from heterosis and genetic incompatibility

2018 ◽  
Vol 4 (11) ◽  
pp. eaau5518 ◽  
Author(s):  
Xinzhu Wei ◽  
Jianzhi Zhang
Keyword(s):  
Animal Model ◽  
Genetic Distance ◽  
Polynomial Function ◽  
Genetic Distances ◽  
Quadratic Polynomial ◽  
Model Organisms ◽  
Genetic Incompatibility ◽  
Large Numbers ◽  
Practical Implications

Theory predicts that the fitness of an individual is maximized when the genetic distance between its parents (i.e., mating distance) is neither too small nor too large. However, decades of research have generally failed to validate this prediction or identify the optimal mating distance (OMD). Respectively analyzing large numbers of crosses of fungal, plant, and animal model organisms, we indeed find the hybrid phenotypic value a humped quadratic polynomial function of the mating distance for the vast majority of fitness-related traits examined, with different traits of the same species exhibiting similar OMDs. OMDs are generally slightly greater than the nucleotide diversities of the species concerned but smaller than the observed maximal intraspecific genetic distances. Hence, the benefit of heterosis is at least partially offset by the harm of genetic incompatibility even within species. These results have multiple theoretical and practical implications for speciation, conservation, and agriculture.

scholarly journals rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

1994 ◽  
Vol 91 (12) ◽  
pp. 5730-5734 ◽  
Author(s):  
M. Hasebe ◽  
T. Omori ◽  
M. Nakazawa ◽  
T. Sano ◽  
M. Kato ◽  
...  
Keyword(s):  
Rbcl Gene ◽  
Gene Sequences ◽  
Evolutionary Lineages ◽  
Rbcl Gene Sequences

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

scholarly journals Генетический полиморфизм редких и малораспространенных аборигенных донских генотипов L

2019 ◽  
pp. 191-197 ◽  
Author(s):  
Elena Ilnitskaya ◽  
Lyudmila Naumova ◽  
Valentina Ganich ◽  
Sergey Tokmakov ◽  
Marina Makarkina
Keyword(s):  
Vitis Vinifera ◽  
Genetic Similarity ◽  
Genetic Distances ◽  
The Other ◽  
Vitis Vinifera L ◽  
Separate Branch ◽  
History Of ◽  
The Difference ◽  
Dna Profiles ◽  
Basic Minimum

История виноградарства на Дону насчитывает несколько веков, местные сорта винограда многообразны и специфичны. Микросателлитные маркеры широко используются для генотипирования сортов и подвоев винограда, при изучении происхождения сортов и анализе их родословной. Целью исследования было изучение выборки редких и малораспространенных автохтонных донских сортов и сравнение их с другими аборигенными донскими генотипами на основе данных ДНК-анализа. В исследования включены 23 стародавних донских сорта. Генотипирование проводили методом микросателлитного профилирования. В исследовании использовали микросателлитные маркеры (SSR), рекомендованные в качестве основного минимального набора для ДНК-паспортизации сортов вида Vitis vinifera L.: VVMD5, VVMD7, VVMD27, VVS2, VrZAG62 и VrZAG79. По результатам проведенного анализа все изученные образцы показали сорт-специфическую комбинацию аллелей в идентифицированных ДНК-профилях. Количество выявленных аллелей составило в среднем 8 аллелей/локус. Наибольший полиморфизм в исследовании этой группы донских сортов был обнаружен в локусе VVMD5: идентифицировано 10 аллелей на локус, наименьшее - в локусе VrZAG62: 6 аллелей/локус. Основываясь на данных SSR-анализа, степень генетического сходства сортов оценивали с использованием метода UPGMA. Кластерный анализ матрицы генетических дистанций, созданный на основе выявленных значений аллелей в шести микросателлитных локусах исследуемых сортов, определил несколько групп генотипов. Сорт Красностоп золотовский выделился в отдельную ветвь, что указывает на различия между этим генотипом и другими сортами исследуемой выборки. Наивысший уровень генетического сходства наблюдался между следующими парами сортов: Крестовский и Бургундский, Шилохвостый и Мушкетный, Кумшацкий черный и Ефремовский.The history of viticulture on the Don goes back several centuries. Local grapevine varieties are diverse and peculiar. Microsatellite markers are widely used in genotyping grapevine cultivars and rootstocks, in grapevine origin and breeding background analysis. Our study aimed to examine samples of rare and less common autochthonous Don varieties, and compare them with the other aboriginal Don genotypes using DNA data. The study involved 23 traditional Don varieties. The genotyping was done by microsatellite profiling. The study used microsatellite (SSR) markers recommended as the basic minimum set for DNA-certification of the genotypes of Vitis vinifera L.: VVMD5, VVMD7, VVMD27, VVS2, VrZAG62 and VrZAG79. Based on the findings, all the studied samples demonstrated variety-specific combination of alleles in the identified DNA profiles. The number of detected alleles on average was 8 alleles/locus. The greatest polymorphism in the studied group of Don varieties was detected in VVMD5 locus: 10 alleles per locus were identified, the smallest in VrZAG62 locus: 6 alleles/locus. UPGMA method was used to assess the extent of genetic similarity of the varieties based on SSR-genotyping data. Based on determined allele values of the studied varieties, cluster analysis of the genetic distances matrix determined several groups of genotypes. ‘Krasnostop zolotovskiy’ variety stood out as a separate branch, which indicates the difference between this genotype and the other varieties of the studied sampling. The highest level of genetic similarity was observed between the following pairs of varieties: ‘Krestovskiy’ and ‘Burgundskiy’, ‘Shilohvostyi’ and ‘Mushketnyi’, ‘Kumshatskiy chornyi’ and ‘Efremovskiy’.

scholarly journals The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. The Genetic Distance Between Population Subdivisions

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 273-283
Author(s):  
Jeffrey C Long ◽  
Peter E Smouse ◽  
James W Wood
Keyword(s):  
Genetic Distance ◽  
Group Size ◽  
Linguistic Diversity ◽  
Genetic Distances ◽  
Demographic Feature ◽  
Distance Methods ◽  
Tribal Populations ◽  
Geographic Differences ◽  
Population Subdivisions ◽  
Theoretical Considerations

ABSTRACT The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.

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