scholarly journals Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

2020 ◽  
Author(s):  
Tianxu Cao ◽  
Jingyu Sun ◽  
Nan Shan ◽  
Xin Chen ◽  
Putao Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differences ◽  
The Other ◽  
Group Method ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Srap Marker ◽  
Arithmetic Means ◽  
Local Varieties ◽  
Pair Group

China is one of the native places of yams with abundant representative local varieties. However, the genetic differences between these local varieties remains unclear, thus considerably inhibiting their utilization and development. In this study, 26 phenotypic traits of 112 accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. A total of 56 variations of 20 quality traits were detected in 112 accessions, and the most diverse phenotypic trait was stem color. Meanwhile, seven principal components were obtained from 26 phenotypic traits, with a cumulative contribution rate of 69.39%, and all the accessions were divided into six groups by clustering the phenotypic traits. Unweighted pair-group method with arithmetic means and principal coordinate analysis based on SSR-SRAP marker data showed that 112 accessions were also divided into six groups, similar to the result of phenotypic traits but with a slight difference among few accessions. Results of genetic structure analysis showed that 112 accessions could be divided into two groups; one group composed of the accessions of D. opposita, the most abundant resource in China, and the other group was a collection of the other accessions. In addition, the analysis of the origin and genetic relationship of yam also indicated that the specie of D. opposita may have originated in China. These results clarified the genetic differences in yam in China, thereby providing a basis for the identification, evaluation, and conservation of yam resource.

scholarly journals Morphologic and molecular assessments of cucumber (Cucumis sativus L.) landraces

2020 ◽  
Vol 48 (2) ◽  
pp. 604-614
Author(s):  
Esra CEBECI ◽  
Volkan GOZEN ◽  
Levent KESKIN ◽  
Aytul YILDIRIM
Keyword(s):  
Genetic Diversity ◽  
Cucumis Sativus ◽  
Polymorphic Marker ◽  
Morphological Data ◽  
Group Method ◽  
Srap Marker ◽  
Discrimination Power ◽  
Cucumis Sativus L ◽  
Pair Group ◽  
Morphologic Data

In this study, 90 locally grown cucumber (Cucumis sativus L.) landraces were collected and morphologically characterized using 20 descriptors derived from UPOV (International Union for the Protection of New Varieties of Plants). Genetic diversity and relationships of the genotypes were revealed using 20 sequence-related amplified polymorphism (SRAP) marker combinations. The discrimination power of each polymorphic marker (estimated by the polymorphism information content) ranged from 0.15 to 0.99 with an average of 0.73. Dice's similarity coefficient ranged between 0.00-1.00. The cluster analysis that was conducted using the unweighted pair group method of arithmetic averages (UPGMA) for both molecular and morphologic data showed that all of the genotypes fell into two main groups and many subdivisions. According to morphological data, fruit length, diameter and weight of the genotypes were determined between 6.5 - 32.5 cm, 25 - 52 mm and, 28 - 625 g respectively. It is clear from the results, a moderate level of genetic diversity, which has the potential for broadening the genetic base, was observed among the Turkish cucumber landraces.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 278 ◽  
Author(s):  
Hong-Ying Guo ◽  
Ze-Liang Wang ◽  
Zhen Huang ◽  
Zhi Chen ◽  
Han-Bo Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographical Distribution ◽  
Mantel Test ◽  
Group Method ◽  
Arithmetic Means ◽  
Mountain Area ◽  
Pair Group ◽  
Hill Area ◽  
Population Genetic Variation ◽  
High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

scholarly journals Genetic DiversityAssessment in Ten Aromatic Rice Varieties of Bangladesh

2017 ◽  
Vol 27 (2) ◽  
pp. 217-225 ◽  
Author(s):  
Tahmina Islam ◽  
Shinthia Rahman ◽  
M Imdadul Hoque ◽  
RH Sarker
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa L ◽  
Group Method ◽  
Aromatic Rice ◽  
Arithmetic Means ◽  
Rice Varieties ◽  
Center Of Origin ◽  
Pair Group ◽  
Relationship Of ◽  
Selection Of

The availability of molecular marker systems allowed estimating the relationships among various taxa. This study was aimed at assessing the genetic diversity among ten aromatic rice (Oryza sativa L.) pools from Bangladesh by means of randomly amplified polymorphic DNA (RAPD) markers. These varieties were evaluated for polymorphisms after amplification with 10 decamer primers. A total of 60 RAPD fragments were generated among the assessed varieties with a polymorphism percentage of 80. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that these 10 varieties could be placed into two groups with a similarity ranging from 65 to 86% depicting adjacent association between Rajbhog and Kalijira‐12, whereas Maloti belongs to a separate group maintaining maximum distance from rest of the varieties. The analysis revealed that the intervarietal genetic relationship of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The present results could be used for the selection of possible parents to generate a mapping population and utilized by the breeders for assessing the genetic diversity of rice genotypes.Plant Tissue Cult. & Biotech. 27(2): 217-225, 2017 (December)

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 731-737 ◽  
Author(s):  
N A Barkley ◽  
M L Newman ◽  
M L Wang ◽  
M W Hotchkiss ◽  
G A Pederson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Expressed Sequence Tag ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Expressed Sequence ◽  
Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

scholarly journals Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (6) ◽  
pp. 797-800
Author(s):  
Xiaoli Wang ◽  
Zhiyong Wang ◽  
Li Liao ◽  
Xinyi Zhang ◽  
Changjun Bai
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Warm Season ◽  
Group Method ◽  
Sequence Repeat ◽  
Marker Assisted Breeding ◽  
Arithmetic Means ◽  
Pair Group ◽  
Simple Sequence

Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

scholarly journals Genetic diversity analysis of thirteen mungbean (Vigna radiata (L.) Wilczek) cultivars using RAPD markers

2013 ◽  
Vol 41 (2) ◽  
pp. 169-175 ◽  
Author(s):  
Sonia Khan Sony ◽  
Md Ahashan Habib ◽  
Mohammad Nurul Islam
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Distances ◽  
Polymorphic Band ◽  
Group Method ◽  
Diversity Analysis ◽  
Arithmetic Means ◽  
Genetic Diversity Analysis ◽  
Pair Group ◽  
Band Size

Genetic diversity analysis among 13 mungbean cultivars from Bangladesh was performed through polymerase chain reaction (PCR) based random amplification of polymorphic DNA (RAPD). Out of 20 arbitrary decamer oligonucleotide primers used, 10 produced a total of 379 different bands with an average of 37.9 bands per primer. Based on the observed banding pattern all the primers were found to be 100% polymorphic. Band size of the amplicons ranged from 250 - 5000 bp. A total of 10 unique DNA fragments was amplified from the 13 mungbean cultivars genome. The values of pair-wise genetic distances ranged from 0.0700 - 1.0852, indicating the presence of wide genetic diversity. The highest genetic distance (1.0852) was found between cultivar BARI Mung-2 and 6 while the lowest (0.0700) between cultivar BINA Mung-2 and 7. Dendogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) has segregated the 13 mungbean cultivars into two major clusters. BARI Mung-1, 2, 3, 4 and 5 formed cluster 1 and BARI Mung-6, BINA Mung-1, 2, 7, 6, 4, 5 and 8 have made cluster 2. DOI: http://dx.doi.org/10.3329/bjb.v41i2.13444 Bangladesh J. Bot. 41(2): 169-175, 2012 (December)

scholarly journals Estimation of Genetic Diversity in Genus Mentha Collected From Azad Jammu And Kashmir, Pakistan

2019 ◽  
Author(s):  
Fozia Abasi ◽  
Israr Ahmad ◽  
Sami Ullah khan ◽  
Khawaja Shafique Ahmad ◽  
Aneela Ulfat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Means ◽  
Jammu And Kashmir ◽  
Pair Group ◽  
High Level

ABSTRACTMints are perennial aromatic herbs used both for medicinal and aromatic purposes. Flora of Pakistan has reported six species of genus Mentha. Taxonomy of genus Mentha is more complex and confusing due to inter specific hybridization. The present research is the first documented report from Pakistan for the purpose to dissect Mentha specimens using molecular tools. A total of 17 SCoT and SSR markers used to dissect genetic diversity among 41 Mentha specimens. The results revealed substantial variation among Mentha specimens. The molecular data analyzed through NTSYS and Power marker software’s. Dendrogram constructed on the base of similarity coefficients generated using weighted pair group method of arithmetic means (UPGMA) recorded high level of polymorphism. Polymorphic Information Content (PIC) for molecular markers recorded in the range of 5-8. Mean genetic distance (GD) was estimated in the range from 0.35% to 100%. The minimum and maximum GD recorded in one combination each as P2-P4 and M41-P10. The present study was explored the efficiency of SCoT and SSR markers for evaluating the genetic diversity of medicinal plants. The present research was concluded that both morphological and molecular dendrogram determined considerable level of diversity among Mentha species. Furthermore, specific primers and DNA chloroplast technology could be needed for further molecular analysis to refine the data more up to varietal level.

scholarly journals Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

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