scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

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.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers

2021 ◽  
Author(s):  
Harun Karcı ◽  
Aibibula Paizila ◽  
Murat Güney ◽  
Mederbek Zhaanbaev ◽  
Salih Kafkas
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Large Scale ◽  
Germplasm Collection ◽  
Mean Value ◽  
Group Method ◽  
Arithmetic Average ◽  
Genic Ssr ◽  
Pair Group ◽  
Average Analysis

Abstract Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and one of the most important nut crop in terms of production. Pistachio cultivars have significant level of variation in their phenotypic appearance and productivity. Understanding the genetic diversity between pistachio cultivars could facilitate breeding programs. Simple sequence repeat (SSR) markers are powerful tools in genetic diversity and germplasm collection studies. However, published information about the characterization of large scale pistachio cultivar germplasm with adequate number of SSR markers is limited. In this study, sixty-six pistachio cultivars and genotypes originated from six different countries were characterized and fingerprinted by 74 genomic and 18 genic SSR markers. SSR analysis identified 576 alleles for all 66 cultivars and genotypes. The number of alleles per locus ranged from 2 to 20 (CUPOhBa1592) alleles with a mean value of six alleles per locus. The polymorphism information content (PIC) values ranged from 0.07 (CUPVEST2939) to 0.87 (CUPSiOh2460) with a mean PIC value of 0.58. The pistachio cultivars and genotypes were divided into five clusters according to Structure and UPGMA (Unweighted Pair Group Method with Arithmetic Average) analysis. Total of 61 cultivar specific alleles were detected in 34 cultivars, among them three primers (CUPOhBa1592, CUPBaPa1606 and CUPOhBa2127) produced more than four cultivar-specific loci therefore very promising for cultivar identification, fingerprinting and breeding studies in pistachio.

scholarly journals Genetic Diversity and Structure of Walnut Populations in Central and Southwestern China Revealed by Microsatellite Markers

2008 ◽  
Vol 133 (2) ◽  
pp. 197-203 ◽  
Author(s):  
Hua Wang ◽  
Dong Pei ◽  
Rui-sheng Gu ◽  
Bao-qing Wang
Keyword(s):  
Genetic Diversity ◽  
Juglans Regia ◽  
Central Area ◽  
Population Level ◽  
Genetic Distances ◽  
Mantel Test ◽  
Southwestern China ◽  
Group Method ◽  
Pair Group ◽  
Genetic Diversity And Structure

Molecular markers were used to study the genetic diversity, structure, and relationship of Juglans L. with nine populations (five from Juglans regia L. and four from Juglans sigillata Dode) in central and southwestern China. A moderate level of genetic diversity was observed at the population level with the number of effect alleles per locus (A E) ranging from 1.75 to 3.35 (average 2.39) and the proportion of polymorphic loci (P) equaling 100.0%. The expected heterozygosity (H E) within populations ranged from 0.389 to 0.687, and the average was 0.525. The proportion of genetic variation presented among populations accounted for 18.6% of the total genetic diversity. The overall gene flow (N m) among populations equaled 1.10. The unweighted pair-group method using arithmetic averages (UPGMA) clustering and the Mantel test showed that genetic distances among the nine populations are in a good agreement with their geographic distribution, supporting the viewpoint that J. regia and J. sigillata belong to one species. We suggest that the central area of the southwestern mountain regions of China could be considered as a priority for walnut genetic resource conservation.

scholarly journals Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 671
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
Sezai Ercisli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
In Silico ◽  
Germplasm Collection ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Average ◽  
Principal Coordinates ◽  
Two Samples ◽  
Pistacia Terebinthus

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

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.

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

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.

Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Tibet Plateau ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Elymus Nutans ◽  
Qinghai Tibet Plateau ◽  
Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

scholarly journals Genetic Diversity in Aus Rice Genotypes using ILP Markers

2017 ◽  
Vol 20 (2) ◽  
pp. 13-19
Author(s):  
MA Siddique ◽  
M Khalequzzaman ◽  
MZ Islam ◽  
ESMH Rashid ◽  
MHK Baktiar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Distance Matrix ◽  
Group Method ◽  
Intron Length Polymorphism ◽  
Arithmetic Average ◽  
Pair Group ◽  
Conservation Genetic ◽  
Breeding Programmes ◽  
Rice Genotypes ◽  
Selection Of

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice genotypes of Bangladesh was assessed using 11 ILP (intron length polymorphism) markers. A total of 28 alleles were detected and the number of alleles per locus varied from 2 (RI01779, RI05751, RI05304, RI03205, RI00299, RI05407) to 4 (RI05559). The PIC values ranged from 0.06 (RI05407) to 0.57 (RI05559) with an average of 0.33. PIC value revealed that RI05559 was the best ILP markers for the studied 31 Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering classified the genotypes into five groups at a coefficient of 0.57. Two dimensional graphical views of Principal Coordinate Analysis (PCoA) revealed that the genotypes Kuchmuch, Kalo dhan, Aus dhan, Sadey aus, Chaina and Dighi bawalia were found far away from the centroid of the cluster and can be seslected as parents for further breeding programmes. Parangi and V3, Adubali and H1-2, Begunbichi and Hashikalmi had closest distance (0.000) in the distance matrix might have same genetic background. This information will be useful for the selection of genetically diversed parents and assist in trait development using genotypes in rice breeding programmes in future. The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. It was also suggested that ILP markers could be very useful for the genetic study and breeding in rice.Bangladesh Rice j. 2016, 20(2): 13-19

Identification and structure analysis of three tilapia species using microsatellite markers

2009 ◽  
Vol 6 (2) ◽  
pp. 119-125
Author(s):  
Song Hong-Mei ◽  
Bai Jun-Jie ◽  
Quan Ying-Chun ◽  
Li Sheng-Jie
Keyword(s):  
Microsatellite Markers ◽  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Mean Value ◽  
Group Method ◽  
Oreochromis Aureus ◽  
Arithmetic Average ◽  
Pair Group ◽  
Expected Heterozygosity ◽  
The Mean

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

scholarly journals GENETIC DIVERSITY INAUS RICE LANDRACES OF BANGLADESH USING SSR MARKERS

2017 ◽  
Vol 30 (1) ◽  
pp. 11-20 ◽  
Author(s):  
M. Khalequzzaman ◽  
M. Z. Islam ◽  
M. A. Siddique ◽  
M. F. R. K. Prince ◽  
E. S. M. H. Rashid ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Three Dimensional ◽  
Group Method ◽  
Breeding Programs ◽  
Arithmetic Average ◽  
Pair Group ◽  
Rice Landraces ◽  
Conservation Genetic ◽  
Maximum Selection

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice landraces of Bangladesh was assessed using 36 SSR (simple sequence repeats) markers. A total of 141 alleles were detectedand the number of alleles per locus ranged from two (RM1216, RM145, RM282, RM293, RM567and RM496) to 10 alleles (RM304), with an average of 3.92. The gene diversity varied from 0.06 (RM145) to 0.80 (RM304) with an average of 0.54 and the PIC values ranged from 0.06 (RM145) to 0.78 (RM304), with an average of 0.48.PIC value revealed that RM304 was the best marker for characterizing the studied Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering of markers classified the genotypes into five major groups with a coefficient of 0.49. Two and three-dimensional graphical views of Principal Coordinate Analysis (PCA) revealed that the genotypes Hashikalmi, Chaina, Puitraaijang, Saithsail, Kuchmuch, Kalodhan, Ausdhan and Itcriewere found far away from the centroid of the cluster and can be selected as parents for further breeding programs.The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. This information will provide maximum selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in future.

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