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.

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.

scholarly journals Genetic Diversity and the Presence of Two Distinct Groups in Ophiostoma clavigerum Associated with Dendroctonus ponderosae in British Columbia and the Northern Rocky Mountains

2007 ◽  
Vol 97 (9) ◽  
pp. 1177-1185 ◽  
Author(s):  
S. Lee ◽  
R. C. Hamelin ◽  
D. L. Six ◽  
C. Breuil
Keyword(s):  
Genetic Diversity ◽  
Mountain Pine Beetle ◽  
Dendroctonus Ponderosae ◽  
Geographic Distance ◽  
The United States ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Northern Rocky Mountains ◽  
Pair Group

The sapstaining fungal pathogen Ophiostoma clavigerum is associated with the mountain pine beetle (Dendroctonus ponderosae), which is currently the most destructive forest pest in North America. The genetic diversity of O. clavigerum populations collected from five sites in Canada and two sites in the United States was estimated with amplified fragment length polymorphism (AFLP) analysis. Genomic DNA from 170 O. clavigerum isolates was digested with EcoRI and PstI and amplified with six primer sets. A total of 469 AFLP markers consisting of 243 monomorphic and 226 polymorphic loci were scored. The overall genetic diversity of the O. clavigerum population was low (Hs = 0.0531) and the differentiation of the seven O. clavigerum populations was moderate (Φ = 0.143). Genetic distances among the populations were not significantly correlated with geographic distance (r = 0.3235, P = 0.074). Two genetically distinct groups in the O. clavigerum populations were shown by unique AFLP profiles and the unweighted pair group method with arithmetic averages. Further work to characterize biological differences between the two groups will be needed to confirm whether cryptic species are present in the O. clavigerum population.

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.

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1175-1180 ◽  
Author(s):  
F J Massawe ◽  
M Dickinson ◽  
J A Roberts ◽  
S N Azam-Ali
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Geographic Origin ◽  
Bambara Groundnut ◽  
Aflp Markers ◽  
Group Method ◽  
Aflp Analysis ◽  
Vigna Subterranea ◽  
Marker Assisted Breeding ◽  
Pair Group

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.Key words: under-utilized, African legume, molecular markers.

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

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.

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

scholarly journals Genetic Diversity of Seven Deciduous Azalea Species (Rhododendron spp. section Pentanthera) Native to the Eastern United States

2008 ◽  
Vol 133 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Matthew Chappell ◽  
Carol Robacker ◽  
Tracie M. Jenkins
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Diversity ◽  
Interspecific Variation ◽  
Genetic Distances ◽  
Anthropogenic Activity ◽  
Group Method ◽  
Aflp Analysis ◽  
Eastern United States

Despite the ecologic and economic importance of native deciduous azaleas (Rhododendron L. section Pentanthera G. Don), our understanding of interspecific variation of North American deciduous azalea species comes principally from morphologic studies. Furthermore, little is known concerning intraspecific or interpopulation genetic variation. With ever-increasing loss and fragmentation of native azalea habitat in the eastern United States due to anthropogenic activity, it is imperative that an understanding of natural genetic variation among and within species and populations is acquired. The present study addresses questions of genetic diversity through the use of amplified fragment length polymorphism (AFLP) analysis. Twenty-five populations of seven species of native azalea were analyzed using three primer pairs that amplified a total of 417 bands. Based on analysis of molecular variance (AMOVA) and estimates of Nei's coefficients of gene diversity (H S, H T, and G ST), the majority of variation found in deciduous azalea occurs within populations. Variation both among species and among population was low, likely the effect of common ancestry as well as frequent introgression among members (and populations) of section Pentanthera. The latter was evident in four populations of R. prunifolium (Small) Millais and R. canescens (Michaux) Sweet that were highly related to R. austrinum (Small) Rehder and R. viscosum (L.) Torrey, respectively. Despite these outliers, most populations were grouped into species based on Nei's unbiased genetic distances viewed as an unweighted pair group method with arithmetic mean (UPGMA) phenogram. The significance of these results is discussed in relation to breeding in section Pentanthera.

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