Use of AFLP molecular markers for estimating genetic similarity of alfalfa (Medicago sativa L. Sl.)

Use of AFLP molecular markers for estimating genetic similarity of alfalfa (Medicago sativaL. Sl.)The aim of study was to determine genetic similarity among sixteen alfalfa populations using the AFLP technique. Plant material was selected considering the high genotypic variability. It included populations of different origin: native forms of alfalfa (secondary ecotypes), inbred lines, single hybrids, synthetic populations, varieties and mutants. Analysis was carried out using 10 combinations of primers. It was noticed, that in case of the studied alfalfa populations, the highest polymorphism was obtained using primers with three selective nucleotides. The genetic similarity coefficients were calculated by the method of Nei and Li. Those coefficients were used for the hierarchical grouping of objects by the unweighted pair group method of arithmetic means. Results of the grouping were presented in the form of dendrogram. Values of coefficients ranged from 0.3311 (between the inbred F line and the Ulstar variety) to 0.8076 (between ecotype 27 and the synthetic population Syn 7-3). Dendrogram of genetic similarity obtained in this way did not fully correspond with the known data about the studied populations' origin. Considering the genetic similarity, inbreed line F was the most outlying from the studied populations of alfalfa.

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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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RAPD polymorphism in the prebreeding material for cultivation of synthetic variations of lucerne (Medicago sativa L.)

Open Life Sciences ◽

10.2478/s11535-012-0106-4 ◽

2013 ◽

Vol 8 (1) ◽

pp. 38-47 ◽

Cited By ~ 1

Author(s):

Lidia Skuza ◽

Stanisława Rogalska ◽

Stanisław Dyba ◽

Jan Bocianowski

Keyword(s):

Medicago Sativa ◽

Genetic Similarity ◽

Seed Set ◽

Inbred Lines ◽

Specific Yield ◽

Group Method ◽

Green Mass ◽

Molecular Image ◽

Synthetic Population ◽

Medicago Sativa L

AbstractGenetic diversity between synthetic cultivars (Syn5, Syn7), inbred lines (D3, D5, E1/2, G1/1, G1/2) and ecotypes (E16, E51, E182, E231) of lucerne (Medicago sativa L.) was studied using the RAPD-PCR method. The plants differed in the efficiency of seed set and in the yield of green mass. The ecotypes E182 and E231 and the synthetic population Syn5 showed the highest fertility. Additionally, Syn5 also showed the highest efficiency of seed set and the yield of green mass. Among the inbred lines, D3 was characterised by the highest yield of green mass and E1/2 by the highest fertility. An optimal combination of yield and biomass was observed for the synthetic population Syn5, obtained by crossing the lines D3, D5 and G1/1, as demonstrated using comparative analysis. A total of 338 polymorphic products were generated using 20 arbitrary primers. Cluster analysis using the Unweighted-Pair Group Method with Arithmetic Mean (UPGMA) in the Molecular image Gel Doc™ XR (Bio-Rad) software based on the Dice’s coefficient of genetic similarity showed a division of the studied forms into two groups based on genetic similarity. The ecotype E16 formed one of the groups whereas all of the other ecotypes observed in this study clustered into the second group. A high level of polymorphism among the studied lucerne forms was detected indicating an interesting gene pool awaiting future exploration. Analysis of variance also supported a high diversity among the studied forms. This study provides insightful information into the heterosis effect of synthetic populations or hybrids of F1 lucerine by providing correlations between the genetic background of the inbred lines and their ability to produce a specific yield.

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555 Estimation of Genetic Diversity among Citrullus Accessions using RAPD Markers

HortScience ◽

10.21273/hortsci.35.3.491d ◽

2000 ◽

Vol 35 (3) ◽

pp. 491D-491

Author(s):

Amnon Levi ◽

Claude E. Thomas ◽

Anthony P. Keinath ◽

Todd C. Wehner

Keyword(s):

Genetic Similarity ◽

Rapd Markers ◽

Genetic Relatedness ◽

Plant Introduction ◽

Group Method ◽

Similarity Coefficients ◽

High Confidence ◽

Core Collections ◽

The Third ◽

Pair Group

Genetic relatedness was estimated among 42 U.S. plant introduction (PI) accessions of the genus Citrullus (37 PIs of which were reported to have disease resistance and five watermelon cultivars) using 30 RAPD primers. These primers produced 662 RAPD markers that could be scored with high confidence. Based on these markers, genetic similarity coefficients were calculated, and a dendrogram was constructed using the unweighted pair-group method with arithmatic average (UPGMA). The analysis delineated three major clusters. The first cluster consisted of a group of five watermelon cultivars, a group of C. lanatus var. lanatus accessions and a group of C. lanatus var. lanatus accessions that contained some C. lanatus var. citroides genes. The second cluster consisted of the C. lanatus var. citroides accessions, while the third cluster consisted of the C. colocynthis accessions. The two C. lanatus clusters differentiated from each other and from the C. colocynthis cluster at the level of 58.8% and 38.9% genetic similarity. Our results indicate that closely related Citrullus PIs may have resistances to the same diseases. Thus, molecular markers may be a useful tool in the development of core collections of Citrullus PIs with resistance to diseases.

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Inter- and Intraspecific RAPD Variation in Four Ipomoea Species

HortScience ◽

10.21273/hortsci.30.4.773a ◽

1995 ◽

Vol 30 (4) ◽

pp. 773A-773

Author(s):

Dapeng Zhang ◽

Wanda W. Collins

Keyword(s):

Genetic Similarity ◽

Rapd Analysis ◽

Group Method ◽

Randomly Amplified Polymorphic Dna ◽

Similarity Coefficients ◽

Ipomoea Trifida ◽

Pair Group ◽

Ipomoea Triloba ◽

Ipomoea Species ◽

Unweighted Pair Group Method

Randomly amplified polymorphic DNA (RAPD) analysis was performed on 18 accessions belonging to four different species of the genus Ipomoea, including sweetpotato and three related species. Twenty-two out of 30 primers tested revealed polymorphisms among these four species. Eight primers were selected on the basis of the number and repeatability of polymorphism produced. With these, a total of 98 different DNA bands were obtained and 85% of them were polymorphic. Based on the presence/absence of the bands, a genetic similarity among accessions and among species was calculated. Unweighted pair-group method with arithmetical averages (UPGMA) based on the similarity coefficients clearly discriminated these four species. Ipomoea trifida and sweetpotato share more genetic similarity. Ipomoea triloba and I. leucantha fall into another cluster. This study demonstrated that RAPD techniques can be a very useful tool for genotype/accession identification and studying the genetic relationship among genotypes/accessions of sweetpotato and among species of Ipomoea.

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

10.1101/866111 ◽

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.

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Molecular characterization of watermelon cultivars using microsatellite markers

Horticultura Brasileira ◽

10.1590/s0102-05362013000400003 ◽

2013 ◽

Vol 31 (4) ◽

pp. 522-527 ◽

Cited By ~ 1

Author(s):

Renata Natália CS Gama ◽

Carlos Antônio F Santos ◽

Rita de Cássia S Dias ◽

Flávio F Souza

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Genetic Similarity ◽

Group Method ◽

Reaction Products ◽

Base Pairs ◽

Arithmetic Means ◽

Pair Group ◽

Total Dna

Allelic patterns and genetic similarity among 17 watermelon cultivars were established using microsatellite markers. For visualization of the genetic similarity, the dendrogram UPGMA (Unweighted Pair Group Method with Arithmetic Means) was generated by the similarity matrix of the Jacquard coefficient, based on 34 alleles of ten microsatellite loci. Total DNA was extracted by the CTAB 2x method and PCR (Polymerase Chain Reaction) products were analyzed in denaturing polyacrylamide 6% gels, stained with silver nitrate. The number of base pairs was estimated by the method of inverse mobility, based on known size product regression. Similarity ranged from 34 to 100%, reflecting high genetic variability. Analyzed loci were not enough to distinguish all 17 watermelon cultivars. The pairs 'Sugar Baby' and 'Omaru Yamato', 'Charleston Gray' and 'Sunshade', 'Crimson Sweet' and 'Nova Crimson' presented 100% of similarity. In dendrogram two groups were observed at 0.42 similarity cut point, with Citrullus colocynthis, positioned as an out group. One watermelon group was formed predominantly by cultivars derived from 'Crimson' and another group was formed by cultivars of different types such as 'Sugar Baby', 'Charleston Gray' and 'Pérola'. Allele pattern and base pair (bp) estimates for the 34 alleles in the 10 microsatellite loci revealed in the present study are a first endeavor to use microsatellite markers in situations of cultivar protection for the watermelon agribusiness in Brazil. They can also be used in situations of commercial disputes regarding certification of the main watermelon cultivars used in the country.

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AFLP fingerprinting analysis of genetic polymorphism of 12 indigenous chicken breeds

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001234 ◽

2007 ◽

Vol 4 (1) ◽

pp. 33-38 ◽

Cited By ~ 6

Author(s):

Gao Yu-Shi ◽

Tu Yun-Jie ◽

Tong Hai-Bing ◽

Wang Ke-Hua ◽

Chen Kuan-Wei

Keyword(s):

Dna Fingerprinting ◽

Genetic Similarity ◽

Group Method ◽

Similarity Coefficients ◽

Indigenous Chicken ◽

Aflp Data ◽

Pair Group ◽

Pooled Dna ◽

Chicken Breeds ◽

Polymorphic Bands

AbstractA total of six amplified fragment length polymorphism (AFLP) primer combinations were used to detect genetic variation of pooled DNA in a sample of 12 chicken breeds indigenous to China, and AFLP DNA fingerprinting of each chicken breed was constructed. Polymorphic bands, specific bands and genetic similarity coefficients of 12 chicken breeds were calculated from AFLP data. A total of 279 polymorphic bands were generated by the six primer combinations, giving, on average, 46.5 polymorphic markers detected per primer combination. Nine specific bands were produced in the pooled DNA of Jiuyuan black and Dongxiang black chickens. However, one specific band was produced in the pooled DNA of Wenchang and Xingyi bantam chickens. An unweighted-pair-group method using average linkages (UPGMA) cluster analysis revealed that the 12 chicken breeds could be divided into three groups. Genetic similarity coefficients and the UPGMA tree of the 12 chicken breeds were consistent with their breeding history as well as their geographical distribution. Based on AFLP DNA fingerprinting, genetic diversity, genetic relationship and identification of chicken breeds can be analysed.

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Low Genetic Diversity Indicates the Need to Broaden the Genetic Base of Cultivated Watermelon

HortScience ◽

10.21273/hortsci.36.6.1096 ◽

2001 ◽

Vol 36 (6) ◽

pp. 1096-1101 ◽

Cited By ~ 50

Author(s):

Amnon Levi ◽

Claude E. Thomas ◽

Todd C. Wehner ◽

Xingping Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Citrullus Lanatus ◽

Plant Introduction ◽

Group Method ◽

Similarity Coefficients ◽

Arithmetic Average ◽

Pair Group ◽

Low Genetic Diversity ◽

Genetic Base

Genetic diversity and relatedness were assessed among 46 American cultivars of watermelon (Citrullus lanatus var. lanatus), and 12 U.S. Plant Introduction accessions (PIs) of Citrullus sp. using 25 randomly amplified polymorphic DNA (RAPD) primers. These primers produced 288 distinct reproducible bands that could be scored with high confidence among cultivars and PIs. Based on the RAPD data, genetic similarity coefficients were calculated and a dendrogram was constructed using the unweighted pair-group method with arithmetic average (UPGMA). The cultivars and C. lanatus var. lanatus PIs differentiated at the level of 92% to 99.6% and 88% to 95% genetic similarity, respectively. In contrast, the C. lanatus var. citroides, and C. colocynthis PIs were more divergent and differentiated at the level of 65% to 82.5% and 70.5% genetic similarity, respectively. The low genetic diversity among watermelon cultivars in this study emphasizes the need to expand the genetic base of cultivated watermelon.

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Analysis of Genetic Relatedness of Dieffenbachia Cultivars Using AFLP Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.1.0081 ◽

2004 ◽

Vol 129 (1) ◽

pp. 81-87 ◽

Cited By ~ 8

Author(s):

Jianjun Chen ◽

Richard J. Henny ◽

David J. Norman ◽

Pachanoor S. Devanand ◽

Chih-Cheng T. Chao

Keyword(s):

Genetic Similarity ◽

Genetic Relatedness ◽

Single Species ◽

Aflp Markers ◽

Group Method ◽

Similarity Coefficients ◽

Somaclonal Variants ◽

Pair Group ◽

Multiple Dimensions ◽

Primer Sets

Dieffenbachia Schott is an important ornamental foliage plant genus. A total of 30 species has been recognized, but most cultivars come from or are related to a single species, D. maculata (Lodd.) G. Don. At least 11 of the cultivars are sports or somaclonal variants. As a result, the potential lack of genetic diversity in cultivated Dieffenbachia has become a concern. However, no research has been conducted to determine the genetic relatedness of the cultivars. This study analyzed the genetic similarity of 42 Dieffenbachia cultivars using amplified fragment length polymorphism (AFLP) markers. Six primer sets, selected from an initial screening of 48, generated a total of 453 scorable AFLP fragments of which 323 (71%) are polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints. A dendrogram was constructed using the unweighted pair-group method of arithmetic averages, and principal coordinated analysis was carried out to show multiple dimensions of the distribution of the cultivars. The 42 cultivars were divided into three clusters; clusters I and II comprise 18 and 23 cultivars, respectively. Jaccard's similarity coefficients for cultivars in the clusters I and II varied from 0.44 to 0.95 and 0.41 to 0.87, respectively. These results indicate that broadening the genetic variability in the Dieffenbachia gene pool is needed, but the genetic similarity of many cultivars is not as close as previously thought. Additionally, Jaccard's similarity coefficients between most sports or somaclonal variants and their parents were 0.73 or lower, suggesting that accumulation of somatic mutations through tissue culture may play a role in the increased variation between some sports or variants and their parents.

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

Genome ◽

10.1139/g02-100 ◽

2003 ◽

Vol 46 (1) ◽

pp. 51-58 ◽

Cited By ~ 46

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.

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