Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.)

Cultivated tomato (L. esculentum L.) germplasm exhibits limited genetic variation compared with wild Lycopersicon species. Amplified fragment length polymorphism (AFLP) markers were used to evaluate genetic variation among 74 cultivars, primarily from California, and to fingerprint germplasm to determine if cultivar-specific patterns could be obtained. All 74 cultivars were genotyped using 26 AFLP primer combinations; of the 1092 bands scored, 102 AFLP bands (9.3%) were polymorphic. Pair-wise genetic similarity coefficients (Jaccard and Nei–Li) were calculated. Jaccard coefficients varied from 0.16 to 0.98 among cultivar pairs, and 72% of pair-wise comparisons exceeded 0.5. UPGMA (unweighted pair-group method with arithmetic averaging) clustering and principle component analysis revealed four main clusters, I–IV; most modern hybrid cultivars grouped in II, whereas most vintage cultivars grouped in I. Clusters III and IV contained three and two cultivars, respectively. Some groups of cultivars closely related by pedigree exhibited high bootstrap values, but lower values (<50%) were obtained for cluster II and its four subgroups. Unique fingerprints for all 74 cultivars were obtained by a minimum of seven AFLP primer pairs, despite inclusion of some closely related cultivars. This study demonstrated that AFLP markers are effective for obtaining unique fingerprints of, and assessing genetic diversity among, tomato cultivars.Key words: Lycopersicon esculentum, AFLPs, DNA fingerprinting, genetic diversity, phenetic relationships.

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Genetic Diversity and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.2.242 ◽

2006 ◽

Vol 131 (2) ◽

pp. 242-249 ◽

Cited By ~ 21

Author(s):

Jelka Šustar-Vozlič ◽

Marko Maras ◽

Branka Javornik ◽

Vladimir Meglič

Keyword(s):

Genetic Diversity ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Seed Protein ◽

Fragment Length Polymorphism ◽

Aflp Markers ◽

Group Method ◽

Phaseolus Vulgaris L ◽

Pair Group ◽

High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

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Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.5.0690 ◽

2004 ◽

Vol 129 (5) ◽

pp. 690-697 ◽

Cited By ~ 4

Author(s):

Pachanoor S. Devanand ◽

Jianjun Chen ◽

Richard J. Henny ◽

Chih-Cheng T. Chao

Keyword(s):

Genetic Similarity ◽

Near Infrared ◽

Genetic Relationships ◽

Aflp Markers ◽

Group Method ◽

Limited Information ◽

Similarity Coefficients ◽

Arithmetic Average ◽

Ornamental Foliage Plants ◽

Pair Group

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.

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

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

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.

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

Canadian Journal of Plant Science ◽

10.4141/cjps2013-062 ◽

2013 ◽

Vol 93 (6) ◽

pp. 1089-1096 ◽

Cited By ~ 13

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.

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

Genome ◽

10.1139/g02-093 ◽

2002 ◽

Vol 45 (6) ◽

pp. 1175-1180 ◽

Cited By ~ 29

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.

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Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽

10.1094/pdis-91-12-1556 ◽

2007 ◽

Vol 91 (12) ◽

pp. 1556-1563 ◽

Cited By ~ 11

Author(s):

R. G. Bhat ◽

G. T. Browne

Keyword(s):

Genetic Diversity ◽

Fragment Length Polymorphism ◽

Group Method ◽

Aflp Data ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Horticultural Crops ◽

Pair Group ◽

Phytophthora Citricola ◽

High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

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Genetic Diversity and Population Structure of Sardinian Myrtle (Myrtus communis L.) Selections as Obtained by AFLP Markers

HortScience ◽

10.21273/hortsci.49.5.531 ◽

2014 ◽

Vol 49 (5) ◽

pp. 531-537 ◽

Cited By ~ 8

Author(s):

Sara Melito ◽

Angela Fadda ◽

Emma Rapposelli ◽

Maurizio Mulas

Keyword(s):

Genetic Diversity ◽

Structure Analysis ◽

Aflp Markers ◽

Group Method ◽

Myrtus Communis ◽

Food Industries ◽

Pair Group ◽

Genetic Groups ◽

Cultivar Selection ◽

Mediterranean Maquis

Myrtle is an aromatic plant typical of the Mediterranean maquis. It is widely exploited in pharmaceutical, cosmetic, and food industries, whereas in Italy, it is mainly used for the production of the typical liqueur. Amplified fragment length polymorphism (AFLP) markers were used to evaluate the genetic variability of some Sardinian Myrtus communis L. candidate cultivars. The AFLP selective amplification produced 138 reproducible AFLP fragments, 96% of which were polymorphic. STRUCTURE analysis divided the myrtle accessions into two main genetic groups (K = 2). The two clusters showed different numbers of individuals. Most of the individuals belonged to Cluster B, whereas only eight genotypes were attributed to Cluster A. Unweighted pair group method with Arithmetic Mean (UPGMA) dendrogram segregated all the myrtle cultivars into five main groups, displaying a partial congruence with the division observed by STRUCTURE analysis. The analysis of the genetic diversity distribution in a candidate cultivar selection displayed a geographical gradient of myrtle from north to south, which reflects the Sardinian shape, and from west to east, which reflects the Sardinian mountain distribution.

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Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers

Jurnal AgroBiogen ◽

10.21082/jbio.v7n1.2011.p47-55 ◽

2011 ◽

Vol 7 (1) ◽

pp. 47 ◽

Cited By ~ 4

Author(s):

Dani Satyawan ◽

I Made Tasma

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Jatropha Curcas ◽

Group Method ◽

Diversity Analysis ◽

Similarity Coefficients ◽

Improvement Program ◽

Genetic Diversity Analysis ◽

Chain Reactions ◽

Pair Group

Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers. Dani Satyawan and I Made Tasma. Jatropha curcas nuts are rich in oil that is higly suitable for Hak Cipta © 2011, BB-Biogen the production of bio-diesel or to be used directly in modified diesel engines. The objective of this study was to assess the extent of genetic diversity among 50 J. curcas provenances and one accession of J. integerrima using RAPD markers. The fifty J. curcas provenances were collected from ecologically diverse regions of Indonesia, and planted in the Pakuwon Experimental Station (Sukabumi, West Java). Fourteen RAPD primers with 60-80% G+C content were used in this genetic diversity analysis and produced 64 bands with 95.7% polymorphism level. The Polymerase Chain Reactions used to generate the RAPD bands sometimes produced inconsistent and nonreproducible results, necessitating the duplication of each reaction to prevent scoring errors. Sixty one validated bands were subsequently used for genetic diversity analysis using Unweighted Pair Group Method Arithmetic (UPGMA) method and Dice coefficients. It was shown that the similarity coefficients among the provenances ranged from 0.2 to 0.98 with an average similarity of 0.75. Dendrogram analysis produced two major groups of provenances, with one outlier from South Lampung. There was no tendency for provenances originated from nearby regions to cluster together in each group, and several provenances showed more similarities with provenances originated from distant regions. This pattern lent credence to reports that Jatropha was introduced to Indonesia around four centuries ago and was mainly spread by humans. Based on the mean similarities among the accessions and their clustering pattern, the genetic diversity of the Jatropha collection appeared to be fairly low. Future additions of genetic materials from more diverse genetic background will be necessary to maintain the current progress of Jatropha improvement program.

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Genetic variation and relationship among and within Withania species as revealed by AFLP markers

Genome ◽

10.1139/g00-073 ◽

2000 ◽

Vol 43 (6) ◽

pp. 975-980 ◽

Cited By ~ 7

Author(s):

M S Negi ◽

A Singh ◽

M Lakshmikumaran

Keyword(s):

Genetic Variation ◽

Medicinal Plant ◽

Genetic Relationships ◽

Similarity Coefficient ◽

Aflp Markers ◽

Group Method ◽

Intermediate Type ◽

Aflp Data ◽

Pair Group ◽

High Level

Withania somnifera is an important medicinal plant, and its anticancerous properties have been attributed to various classes of withanolide compounds. The objective of the present study was to investigate the inter- and intraspecific genetic variation present in 35 individuals of W. somnifera and 5 individuals of W. coagulans using AFLP (amplified fragment length polymorphism) marker technique. The information about genetic variation determined from AFLP data for 40 individuals was employed to estimate similarity matrix value based on Jaccard's coefficient. The similarity values were further used to construct a phenetic dendrogram revealing the genetic relationships. The dendrogram generated by UPGMA (unweighted pair group method of arithmetic averages) distinguished W. somnifera from W. coagulans and formed two major clusters. These two main clusters shared a similarity coefficient of 0.3, correlating with the high level of polymorphism detected. The dendrogram further separated W. somnifera into three subclasses corresponding to Kashmiri and Nagori groups and an intermediate type. The AFLP profile of Kashmiri individuals was distinct from that of the Nagori group of plants. The intermediate genotype was distinct as it shared bands with both the Kashmiri and Nagori individuals, even though it was identified as a Kashmiri morphotype. Furthermore, the intermediate type shared a similarity coefficient of 0.8 with the Kashmiri individuals. The present work revealed low levels of variation within a population though high levels of polymorphism were detected between Nagori and Kashmiri populations. The ability of AFLP markers for efficient and rapid detection of genetic variations at the species as well as intraspecific level qualifies it as an efficient tool for estimating genetic similarity in plant species and effective management of genetic resources.Key words: Withania, AFLP, genetic variation, phenetic relationships, medicinal plant.

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Analysis of Genetic Relationships of Calathea Species and Cultivars by AFLP Markers

HortScience ◽

10.21273/hortsci.39.4.888a ◽

2004 ◽

Vol 39 (4) ◽

pp. 888A-888

Author(s):

Jianjun Chen* ◽

Richard Henny ◽

C. Thomas Chao ◽

Pachanoor Devanand

Keyword(s):

Genetic Relationships ◽

Aflp Markers ◽

Group Method ◽

Similarity Coefficients ◽

Low Light ◽

Ornamental Foliage Plants ◽

Pair Group ◽

Light Levels ◽

The Family ◽

Tropical America

Calathea, the largest genus in the family Marantaceae, is composed of 100 species native to tropical America in moist or swampy forest habitats. Because of their brilliant patterns of leaf color and different textures plus ability to tolerate low light levels, calatheas have been widely produced as ornamental foliage plants for interiorscaping. Thus far, genetic relationships among its species and cultivars have not been documented. This study analyzed the relationships of 34 cultivars across 14 species using amplified fragment length polymorphism (AFLP) markers. Six EcoR I + 2/Mse I + 3 primer set combinations were used in this investigation. Each selected primer set generated 105 to 136 scorable fragments. A total of 733 AFLP fragments were detected of which 497 were polymorphic (68%). A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UP-GMA) technique and a principal coordinated analysis (PCOA) was used to analyze the relationships. The 34 cultivars were divided into four clusters. Cluster I had 19 cultivars derived from C. roseo-picta and C. loesnerii with Jaccard's similarity coefficients from 0.74 to 0.97, of which six are somaclonal variants or sports and two cultivars are genetic identical. Only C. kennedeae `Helen' is positioned in cluster II. Cluster III had 10 cultivars across seven species; Jaccard's similarity coefficients among them varied from 0.41 to 0.63. Four species were situated in cluster IV with Jaccard's similarity between 0.27 to 0.41. Results from this study indicate that broadening of genetic diversity is needed for cultivars in cluster I as they are the most commonly grown calatheas but genetically are very close.

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