Development and characterization of STMS molecular markers and genetic diversity analysis of mungbean [Vigna radiata (L.) Wilczek]

Mung bean is an important crop in Asia because of its high protein content and other economic uses. However, because of the unavailability of polymorphic DNA markers, genomic research of mung bean is lacking. In this study, we developed and characterised simple sequence repeat (SSR) molecular markers by screening SSR-enriched partial genomic libraries with SSR probes and used them to analyse the genetic diversity of mung bean. Thus, we isolated, cloned, sequenced a genomic library that contained microsatellite loci from the mung bean variety ‘MCV-1’. The polymorphisms of microsatellite loci were evaluated using the unweighted pair group method of arithmetic means, and MDS cluster analysis showed genetic relationships in a panel of 96 mung bean core collection genotypes. Genetic diversity analysis results showed contrasted levels of variability within cultivated and wild accessions. A total of 98 alleles were detected using 19 polymorphic markers, with an average of 4.9 alleles per locus, whereas observed heterozygosity ranged from 0.1 to 0.5, with a mean of 0.42 per locus. The number of alleles and the high level of polymorphism make these new markers useful for gene tagging, diversity analyses and marker assisted selection in mung bean.

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Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis

Canadian Journal of Plant Science ◽

10.4141/cjps2011-240 ◽

2012 ◽

Vol 92 (6) ◽

pp. 1121-1133 ◽

Cited By ~ 9

Author(s):

S. C. Debnath ◽

Y. L. Siow ◽

J. Petkau ◽

D. An ◽

N. V. Bykova

Keyword(s):

Genetic Diversity ◽

Antioxidant Activity ◽

Molecular Markers ◽

Molecular Techniques ◽

Diversity Analysis ◽

Full Potential ◽

Genetic Diversity Analysis ◽

Wide Range ◽

Berry Crops ◽

Improvement Programs

Debnath, S. C., Siow, Y. L., Petkau, J., An, D. and Bykova, N. V. 2012. Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis. Can. J. Plant Sci. 92: 1121–1133. An improved understanding of important roles of dietary fruits in maintaining human health has led to a dramatic increase of global berry crop production. Berry fruits contain relatively high levels of vitamin C, cellulose and pectin, and produce anthocyanins, which have important therapeutic values, including antitumor, antiulcer, antioxidant and anti-inflammatory activities. There is a need to develop reliable methods to identify berry germplasm and assess genetic diversity/relatedness for dietary properties in berry genotypes for practical breeding purposes through genotype selection in a breeding program for cultivar development, and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic materials independent of environmental influences. Significant progress has been made in diversity analysis of wild cranberry, lowbush blueberry, lingonberry and cloudberry germplasm, and in strawberry and raspberry cultivars and advanced breeding lines developed in Canada. Inter simple sequence repeat (ISSR) markers detected an adequate degree of polymorphism to differentiate among berry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in the current berry improvement programs. Although multiple factors affect antioxidant activity, a wide range of genetic diversity has been reported in wild and cultivated berry crops. Diversity analysis based on molecular markers did not agree with those from antioxidant activity. The paper also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques including expressed sequence tag-polymerase chain reaction (EST-PCR) analysis to develop improved environment-friendly berry cultivars suited to the changing needs of growers and consumers.

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Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

Asian Journal of Biology ◽

10.9734/ajob/2021/v12i130156 ◽

2021 ◽

pp. 36-48

Author(s):

Farhana Afrin Vabna ◽

Mohammad Zahidul Islam ◽

Md. Ferdous Rezwan Khan Prince ◽

Md. Ekramul Hoque

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Molecular Diversity ◽

Genetic Relationships ◽

Group Method ◽

Diversity Analysis ◽

Average Value ◽

Rice Landraces ◽

Boro Rice ◽

Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

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Congruence between morphological and molecular markers for genetic diversity analysis applied to forage palm genotypes propagated via bioreactors

Industrial Crops and Products ◽

10.1016/j.indcrop.2020.112230 ◽

2020 ◽

Vol 147 ◽

pp. 112230

Author(s):

Selma Silva Rocha ◽

Luciana Cardoso Nogueira Londe ◽

Samy Pimenta ◽

Maurício Mendes Cardoso ◽

Nívio Poubel Gonçalves ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Diversity Analysis ◽

Genetic Diversity Analysis

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Genetic diversity analysis of pearl millet (Pennisetum glauccum [L.] R. Br.) accessions using molecular markers

AFRICAN JOURNAL OF BIOTECHNOLOGY ◽

10.5897/ajb2009.000-9493 ◽

2009 ◽

Vol 8 (22) ◽

pp. 6046-6052 ◽

Cited By ~ 6

Author(s):

Govindaraj M ◽

Selvi B ◽

Arun Prabhu D ◽

Rajarathinam S

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Pearl Millet ◽

Diversity Analysis ◽

Genetic Diversity Analysis

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Applications of molecular markers in Genetic Diversity Studies of maize

Nigerian Journal of Biotechnology ◽

10.4314/njb.v37i1.11 ◽

2020 ◽

Vol 37 (1) ◽

pp. 101-108

Author(s):

Degife Asefa Zebire

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Inbred Lines ◽

Hybrid Breeding ◽

Diversity Analysis ◽

Crop Species ◽

Heterotic Groups ◽

Genetic Diversity Analysis ◽

Diversity Studies ◽

Genetic Diversity Study

Molecular markers are efficient for exploiting variations in genotypes as they are not influenced by environmental factors and also speed up breeding programs. They are used to detect large numbers of distinct divergence between genotypes at the DNA level. Genetic diversity study helps to estimate the relationship between inbred lines to make the best hybrid combinations. Lines which are clustered in different heterotic groups are considered as the best hybrid combinations to carry out further breeding activities. Molecular markers are used to meet a number of objectives, including genetic diversity analysis and prediction of hybrid performances in divergent crop species. Agro-morphological and molecular markers have been utilized to study genetic diversity so far. In maize, the uses of molecular markers are important for the evaluation of genetic diversity of inbred lines and in clustering them into heterotic groups. These markers determine genetic similarity of the lines and are used to assess the genetic diversity of maize. Molecular markers have proven valuable for genetic diversity analysis of many crop species and genetically diverse lines are important to improve hybrid breeding. Keyword: Molecular marker; Genetic diversity; Genetic variation, Diversity Array technology; cluster analysis

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Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

BioMed Research International ◽

10.1155/2013/317912 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 8

Author(s):

Suping Feng ◽

Helin Tong ◽

You Chen ◽

Jingyi Wang ◽

Yeyuan Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genomic Library ◽

Trinucleotide Repeats ◽

The Other ◽

Diversity Analysis ◽

Dominant Type ◽

Genetic Diversity Analysis ◽

Ssr Loci ◽

Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat

Molecular Genetics and Genomics ◽

10.1007/s00438-003-0960-x ◽

2003 ◽

Vol 271 (1) ◽

pp. 91-97 ◽

Cited By ~ 81

Author(s):

R. A. Queen ◽

B. M. Gribbon ◽

C. James ◽

P. Jack ◽

A. J. Flavell

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Diversity Analysis ◽

Genetic Diversity Analysis

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Genetic diversity analysis of Rose varieties from Grandiflora group based on ISSR molecular markers

BIO Web of Conferences ◽

10.1051/bioconf/20213800140 ◽

2021 ◽

Vol 38 ◽

pp. 00140

Author(s):

Sophia S. Yudanova ◽

Svetlana A. Plugatar ◽

Zinaida K. Klimenko ◽

Vera K. Zykova ◽

Olena L. Rubtsova ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Diversity Analysis ◽

Morphometric Characters ◽

Climate Conditions ◽

Genetic Diversity Analysis ◽

Statistical Comparison ◽

Separate Branch ◽

Issr Molecular Markers ◽

Continental Climate

Kinship and genetic diversity determination among six rose varieties from the Grandiflora group were carried out using ISSR thechnics. The studied varities were divided into 3 clades: I) ‘Lezginka’, ‘Queen Elizabeth’ and ‘Koralovy surpriz’ varieties; II) ‘Gurzuf’ and ‘Love’ varieties; III) ‘Komsomolsky ogonek’ variety formed a separate branch. This division into clades was confirmed by a statistical comparison of morphometric characters. On the basis of the obtained data, it can be concluded that the analysis using the selected primer group is well-suited for differentiation rose varieties into groups, which makes it possible, for one thing, to determine the genetic distance between varieties, and for another, to use these data in the future by certification of the varieties promising by resistance characters to the continental climate conditions.

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Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses

Archives of Biological Sciences ◽

10.2298/abs1103667m ◽

2011 ◽

Vol 63 (3) ◽

pp. 667-679 ◽

Cited By ~ 13

Author(s):

Kumar Mishra ◽

Sandhyarani Nishani ◽

J Jayarama

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Genetic Relationships ◽

Resolving Power ◽

Diversity Analysis ◽

Srap Marker ◽

Genetic Diversity Analysis ◽

Species Specific ◽

Coffee Species ◽

Issr Primers

The identification and genetic relationships of 23 coffee species and one coffee-related species Canthium diccocum were studied using ISSR and SRAP markers. The average polymorphism information content of SRAP primers (0.81) was lower than ISSR primers (0.86), whereas the average resolving power of the SRAP primers (9.74) is higher than the ISSR primers (8.64). The genetic similarity among the species ranged from 0.30 to 0.89 using ISSR and 0.11 to 0.90 using SRAP marker systems. Based on marker analysis, all twenty three coffee species were clustered into two major groups. Both the markers amplified species-specific fragments and are useful in genetic diversity analysis of coffee.

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