Applications of Molecular Markers to Assess Genetic Diversity in Vegetable and Ornamental Crops – A Review

2018 ◽  
pp. 1-7
Author(s):  
Riaz Ahmad ◽  
Muhammad Akbar Anjum
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Climatic Factors ◽  
Correct Identification ◽  
Germplasm Management ◽  
Plant Resources ◽  
Breeding Programs ◽  
Ornamental Crops ◽  
Improvement Programs ◽  
Trained Manpower

Assessment of genetic diversity has attained much consideration during the last two decades for efficient germplasm management and its utilization in breeding programs. Molecular markers system is very helpful in correct identification of plants, successful management of plant resources, and to achieve various aspects of breeding programs in vegetables and ornamental crops. Applications of molecular markers for appraisal of DNA variations in plants provide significant approach in field of molecular genetics. Morphological markers are not appropriate for evaluation of genetic diversity due to less differentiating traits among species, genera or their individuals. These are also highly affected by climatic factors. So, molecular markers system is very effective method for detailed DNA finger printing of crop plants. However, successful use of molecular markers in crop breeding programs relies on strong coordination among plant breeders, biotechnologists and trained manpower as well as proper financial support. The current review explains the basic descriptions of different molecular markers and their applications for genetic improvement programs in some vegetables and ornamental plants.

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

2012 ◽  
Vol 92 (6) ◽  
pp. 1121-1133 ◽  
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.

Genetic diversity and population structure of Algerian chickpea (Cicer arietinum) genotypes: use of agro-morphological traits and molecular markers linked or not linked to the gene or QTL of interest

2020 ◽  
Vol 71 (2) ◽  
pp. 155
Author(s):  
Djihad Bellemou ◽  
Teresa Millàn ◽  
Juan Gil ◽  
Aissa Abdelguerfi ◽  
Meriem Laouar
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Cicer Arietinum ◽  
Morphological Traits ◽  
Ascochyta Blight ◽  
Principal Component ◽  
Breeding Programs ◽  
Average Value ◽  
Conservation Of Genetic Resources ◽  
Resistant Genotypes

Assessment of genetic diversity among chickpea (Cicer arietinum L.) germplasm at the morphological and molecular levels is fundamental for chickpea breeding and conservation of genetic resources. Genetic variability of 46 chickpea genotypes including 42 Algerian genotypes and four control varieties was evaluated by using 15 agro-morphological traits. Eleven molecular markers including nine simple sequence repeats, one sequence characterised amplified region (SCY17) and one gene-specific (CaETR4) were used to characterise the 46 genotypes and eight references varieties added for disease resistance or susceptibility. Genotypes resistant to ascochyta blight were identified by the markers SCY17 and CaETR4 present together. High diversity was observed for all measured morphological traits between genotypes. Yield components, plant height, phenological traits and growth habit were the traits most involved in variation among genotypes and were partitioned into four groups by using principal component analysis. All molecular markers were polymorphic. In total, 91 alleles were obtained ranging from 2 to 21 per locus with average of 8.27 alleles per marker. Polymorphism information content ranged from 0.58 to 0.99 with an average value of 0.87. UPGMA clustering and Bayesian-based model structure analysis grouped genotypes into two clusters, but the distribution of the genotypes by cluster was not the same for the two analyses. According to the presence of markers indicating resistance to ascochyta blight (SCY17 and CaETR4), three resistant genotypes (FLIP 82-C92, ILC 6909, ILC 7241) were selected and should be tested in controlled conditions for confirmation. Considering the narrow diversity of cultivated chickpea, the Algerian genotypes can be considered as interesting for future breeding programs.

scholarly journals Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

2016 ◽  
Author(s):  
Juan José Martínez ◽  
Pablo Melgarejo ◽  
Pilar Legua ◽  
Francisco García ◽  
Francisca Hernández
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Plant Material ◽  
Phenotypic Variability ◽  
Geographical Area ◽  
Geographic Origin ◽  
Germplasm Management ◽  
Morphometric Characteristics ◽  
Germplasm Bank ◽  
Improvement Programs

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

scholarly journals Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

2010 ◽  
Vol 10 (4) ◽  
pp. 298-304 ◽  
Author(s):  
Tesfahun Alemu Setotaw ◽  
Eveline Teixeira Caixeta ◽  
Guilherme Ferreira Pena ◽  
Eunize Maciel Zambolim ◽  
Antonio Alves Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

Identification of research to improve the efficiency of breeding strategies for white clover in Australia - a review

2002 ◽  
Vol 53 (3) ◽  
pp. 239 ◽  
Author(s):  
M. Z. Z. Jahufer ◽  
M. Cooper ◽  
J. F. Ayres ◽  
R. A. Bray
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
White Clover ◽  
Molecular Breeding ◽  
Computer Modelling ◽  
Future Research ◽  
Specific Reference ◽  
Breeding Strategies ◽  
Breeding Programs ◽  
Conventional Breeding

A major challenge faced by today’s white clover breeder is how to manage resources within a breeding program. It is essential to utilise these resources with sufficient flexibility to build on past progress from conventional breeding strategies, but also take advantage of emerging opportunities from molecular breeding tools such as molecular markers and transformation. It is timely to review white clover breeding strategies. This background can then be used as a foundation for considering how to continue conventional plant improvement activities and complement them with molecular breeding opportunities. In this review, conventional white clover breeding strategies relevant to the Australian dryland target population environments are considered. Attention is given to: (i) availability of genetic variation, (ii) characterisation of germplasm collections, (iii) quantitative models for estimation of heritability, (iv) the role of multi-environment trials to accommodate genotype-by-environment interactions, (v) interdisciplinary research to understand adaptation to dryland environments, (vi) breeding and selection strategies, and (vii) cultivar structure. Current achievements in biotechnology with specific reference to white clover breeding in Australia are considered, and computer modelling of breeding programs is discussed as a useful integrative tool for the joint evaluation of conventional and molecular breeding strategies and optimisation of resource use in breeding programs. Four areas are identified as future research priorities: (i) capturing the potential genetic diversity among introduced accessions and ecotypes that are adapted to key constraints such as summer moisture stress and the use of molecular markers to assess the genetic diversity, (ii) understanding the underlying physiological/morphological root and shoot mechanisms involved in water use efficiency of white clover, with the objective of identifying appropriate selection criteria, (iii) estimation of quantitative genetic parameters of important morphological/physiological attributes to enable prediction of response to selection in target environments, and (iv) modelling white clover breeding strategies to evaluate the opportunities for integration of molecular breeding strategies with conventional breeding programs.

Molecular Markers for Phylogenetic Studies and Germplasm Conservation

2021 ◽  
pp. 103-132
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Germplasm Conservation ◽  
Germplasm Management ◽  
28S Rrna ◽  
Phylogenetic Studies ◽  
Phylogeny And Evolution ◽  
Historical Developments ◽  
Tree Building ◽  
New Evidence

Application of molecular markers in phylogenetic studies has become increasingly important in recent times. Availability of fast DNA sequencing techniques and robust statistical analysis methods provided new momentum to this field. Different nuclear encoded genes (16S rRNA, 5S rRNA, 28S rRNA), mitochondrial encoded genes (cytochrome oxidase, mitochondrial 12S, cytochrome b, control region), and few chloroplast encoded genes (rbcL, matK, rpi16) have been used as molecular markers. This method allows researchers to obtain new evidence concerning their phylogeny and biodiversity. Measurement of genetic diversity is important for development of strategies for effective germplasm management. The DNA-based technologies can overcome all the limitations of traditional methods used for the estimation of genetic diversity. This chapter deals with historical developments of molecular phylogeny, use of molecular markers in phylogeny, and evolution of phylogenetic tree building methods.

scholarly journals Genetic diversity assessment of ancient mulberry (Morus spp.) in Lebanon using morphological, chemical and molecular markers (SSR and ISSR)

2021 ◽  
Vol 35 (3) ◽  
pp. 243-253
Author(s):  
Aline Kadri ◽  
Shoaib Saleh ◽  
Ahmad Elbitar ◽  
Ali Chehade
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Crop Improvement ◽  
Germplasm Management ◽  
Diversity Assessment ◽  
Geographical Regions ◽  
Relative Separation ◽  
Morus Spp ◽  
High Level ◽  
Issr Primers

Lebanon has ancient mulberry trees which are the remnants of the abundant orchards that dominated its lands during the nineteenth century. Lebanese mulberry germplasm has not been assessed yet. This study aims to collect local old rainfed mulberry accessions from different geographical regions and assess their diversity by using morphological and molecular markers (SSR and ISSR). Genetic diversity of 70 accessions of mulberry were evaluated by using 27 morphological traits. The dendrogram based on the morphological attributes showed a relative separation of the different accessions based on fruits color and taste. Molecular analysis was performed for the accessions by using selected SSR and ISSR primers. The primers marked a high discriminating power (0.7 to 0.89). The dendrogram constructed on the base of UPGMA method showed 13 different groups. The clustering patterns indicated no location nor local name specificity among mulberry accessions. The combination of SSR and ISSR primers was informative for estimating the extent of mulberry genetic diversity. It can be concluded that there is a high level of genetic diversity within mulberry trees in Lebanon. These results will be useful for mulberry germplasm management in terms of biodiversity protection and as a valuable source of gene pool for crop improvement.

scholarly journals Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

2016 ◽  
Author(s):  
Juan José Martínez ◽  
Pablo Melgarejo ◽  
Pilar Legua ◽  
Francisco García ◽  
Francisca Hernández
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Plant Material ◽  
Phenotypic Variability ◽  
Geographical Area ◽  
Geographic Origin ◽  
Germplasm Management ◽  
Morphometric Characteristics ◽  
Germplasm Bank ◽  
Improvement Programs

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

scholarly journals Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2214 ◽  
Author(s):  
Juan J. Martinez-Nicolas ◽  
Pablo Melgarejo ◽  
Pilar Legua ◽  
Francisco Garcia-Sanchez ◽  
Francisca Hernández
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Plant Material ◽  
Phenotypic Variability ◽  
Geographical Area ◽  
Geographic Origin ◽  
Germplasm Management ◽  
Morphometric Characteristics ◽  
Germplasm Bank ◽  
Improvement Programs

Background.Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties.Methods.Fifty-three pomegranate (Punica granatumL.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic).Results.The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering.Conclusions.As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

scholarly journals Genetic structure and molecular diversity of Brazilian grapevine germplasm: management and use in breeding programs

2020 ◽  
Author(s):  
Geovani Luciano de Oliveira ◽  
Anete Pereira de Souza ◽  
Fernanda Ancelmo de Oliveira ◽  
Maria Imaculada Zucchi ◽  
Lívia Moura de Souza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Core Collection ◽  
Association Studies ◽  
Allelic Diversity ◽  
Germplasm Management ◽  
Breeding Programs ◽  
Wild Grapevine ◽  
Molecular Profiles

AbstractThe management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.

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