scholarly journals Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

Author(s):  
Ha Buer ◽  
Sa Rula ◽  
Zi Yuan Wang ◽  
Shu Fang ◽  
Yu´e Bai

AbstractPopulation genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

2021 ◽  
Author(s):  
Habuer ◽  
Sarula ◽  
Wang Zi Yuan ◽  
ShuFang ◽  
Bai Yu'e

Abstract Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 97.94% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT3 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of Prunus sibirica in Inner Mongolia. The analysis of molecular variance (AMOVA) showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic (UPGMA) cluster analysis, principal coordinate analysis (PCoA) and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of Prunus sibirica in Inner Mongolia can provide a reference for Prunus sibirica variety breeding and resource development.


2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.


1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba

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.


2020 ◽  
pp. 1-10
Author(s):  
Shaoyu Chen ◽  
Tao Wu ◽  
Liangjun Xiao ◽  
Delu Ning ◽  
Li Pan

Abstract Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.


2015 ◽  
Vol 7 (2) ◽  
pp. 997-1000
Author(s):  
T. N. Ranjini ◽  
K. Bhanuprakash ◽  
M. A. Suryanarayana ◽  
B. G. Yamuna

Terminalia chebula is an important medicinal plant, extensively used in Ayurveda, Unani and Homoeopathic medicines. The present study was aimed to reveal its genetic diversity based on molecular markers from twelve T. chebula accessions. Molecular diversity was studied using RAPD markers. A total of 8 polymorphic primers produced 314 polymorphic bands and 195 monomorphic bands. Unweighted Pair Group Method with Arithmetic Mean (UPMGA) dendrogram divided the accessions into 2 major clusters. Accession IIHRTc2 and IIHRTc10 showed maximum genetic diversity with 55% similarity. This characterization based on molecular markers will help in identification of economically useful accessions for further crop improvement programme.


Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 167-174
Author(s):  
Lin Meng ◽  
Xiaoyan Zhang ◽  
Peichun Mao ◽  
Xiaoxia Tian

The genetic diversity among 30 accessions of Elytrigia repens (L.) Nevski was analyzed using 100 intersimple sequence repeat (ISSR) primers, 12 of which generated distinct amplification products. Out of the 132 repeatable bands detected, 100 bands were polymorphic. The percentage of polymorphic bands was 70.66%, with a mean of 8.33 percentage of polymorphic bands per primer. The ISSR-based genetic similarity coefficients among the 30 accessions ranged from 0.509 to 0.873, revealing high genetic diversity. The 30 E. repens accessions were divided into eight groups based on an unweighted pair-group method with arithmetic mean cluster analysis and a principal components analysis. We found that genetic distance is correlated with geographical distance among the 30 E. repens accessions studied (r = 0.812, p < 0.05) using Mantel’s test. Our results confirm the potential value of genetic diversity preservation for future breeding programs.


2021 ◽  
Author(s):  
Shi dong Cao ◽  
Senmiao Chen ◽  
Shuyu Cao ◽  
Nipi Chen ◽  
Bo Jin

Abstract Background: As a traditional Chinese medicine, Polygonatum has been demonstrated to have immunomodulatory, antibacterial, anti-inflammatory, anti-aging, anti-cancer, hypoglycemic and other pharmacological effects. However, the germplasm resources of Polygonatum have been destroyed in recent years and the research on its genetic diversity is extremely scarce. In this study, the genetic diversity of 28 Polygonatum germplasms from 11 different provinces in China was evaluated by Start codon targeted (SCoT) marker. Results: A total of 365 bands were generated by 15 SCoT primers, of which 355 were polymorphic, with a high polymorphism of 97.3%. And the genetic similarity coefficient is between 0.59 and 0.75, indicating a high genetic diversity. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram, PCoA (Principal Coordinate Analysis) and Structure analysis have similar results in grouping Polygonatum germplasm and they are all divided into two populations. We found that there was a certain correlation between the genetic distance and geographical distance of Polygonatum germplasm. By analyzing other valid genetic diversity parameters (Na, Ne, H, I), it is clarified that Polygonatum has abundant alleles and abundant genetic diversity among populations. Conclusions: This study suggests that Polygonatum germplasm resources from different provenances have rich genetic diversity. The SCoT molecular marker is a valuable marker system and can be used for genetic analysis of Polygonatum resources. This will be helpful to further study the preservation and genetic improvement of Polygonatum germplasm.


Author(s):  
Mehfuz Hasan ◽  
Mohammad Sharif Raihan

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.


2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.


2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.


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