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.

Assessment of Morphological and Molecular Genetic Diversity in Pigeonpea [Cajanus cajan (L.) Millspaugh]

2021 ◽  
Author(s):  
Tuntun Naing ◽  
S.K. Verma ◽  
Harikant Yadav ◽  
Charupriya Chauhan ◽  
Ashish Gautam ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Block Design ◽  
Molecular Genetic ◽  
Germplasm Conservation ◽  
Morphological Diversity ◽  
Sufficient Information ◽  
Additional Information ◽  
Molecular Genetic Diversity ◽  
Morphological Studies

Background: The estimation of genetic diversity in pigeonpea is crucial for desiging breeding programmes and germplasm conservation. Morphological studies alone do not provide sufficient information to understand genetic diversity. Molecular analysis using SSRs can provide additional information on genetic diversity that can be used for selection of diverse parents. Methods: The experimental material for present study consisted of 50 diverse genotypes of pigeonpea. The fifty genotypes were planted in Randomized Complete Block Design consisted of three replications during the kharif 2020-21. The estimation of morphological genetic diversity was done by Mahalanobis D2 statistics. The molecular genetic diversity analysis was done by using 30 molecular markers in same genotypes. Result: The assessment of morphological diversity revealed that the fifty pigeonpea genotypes were grouped into four different clusters with cluster I as the largest cluster (33 genotypes). The molecular markers differentiated the 50 genotypes in five major clusters with cluster II as the largest cluster (24 genotypes). The results of present study suggested that morphological and molecular diversity in pigeonpea is different. On the basis of genetic distance, the genotypes RVSA 2014-1 and PA 406 were found most genetically distant and may be used in hybridization programme to create diverse progenies.

scholarly journals Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

2020 ◽  
Author(s):  
Alemneh Mideksa Egu ◽  
Kassahun Tesfaye ◽  
Kifle Dagne New ◽  
Xuebo Hu New
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
In Situ Conservation ◽  
Germplasm Conservation ◽  
Pharmaceutical Products ◽  
Gene Pools ◽  
Vernonia Galamensis ◽  
Diversity Assessment

Abstract Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study was initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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.

Genetic diversity and evolution of Brassica genetic resources: from morphology to novel genomic technologies – a review

2016 ◽  
Vol 15 (5) ◽  
pp. 388-399 ◽  
Author(s):  
Mohamed A. El-Esawi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Genetic Resources ◽  
Gene Pool ◽  
Species Identity ◽  
Genomic Technologies ◽  
Efficient Management ◽  
Phylogenetic Studies ◽  
Breeding Programmes

AbstractBrassica species have an economic and medicinal importance. Estimation of the amount and distribution of genetic diversity within Brassica species is essential for establishing efficient management, conservation and breeding practices. This review discusses the taxonomy, gene pool, and Brassica-derived phytochemicals and their nutraceutical importance. It also surveys the recently advanced studies of the genetic diversity and phylogenetic studies of Brassica species at the level of morphological, cytological, biochemical and molecular markers that have proven to be useful for evaluating the genetic variation, taxonomic relationships and species identity, and could be useful for improving Brassica crops through future promising breeding programmes.

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.

scholarly journals Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Fatimah FATIMAH ◽  
Rahayu Rahayu ◽  
Jamal Wiwoho ◽  
Sunny Ummul Firdaus ◽  
Pujiyono Pujiyono ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Germplasm Conservation ◽  
Morphological Characterization ◽  
Forest Area ◽  
Eucalyptus Species ◽  
Germplasm Management ◽  
Potential Marker ◽  
Management And Conservation

Abstract. Rahayu, Fatimah, Wiwoho J, Firdaus SU, Pujiyono, Marimin, Arianto DP, Pramono A. 2021. Genetic diversity of eucalypts for germplasm conservation in Forest Area with the Special Purpose of Mount Bromo, Karanganyar, Indonesia. Biodiversitas 22: 4223-4235. As a repository of a gene pool, eucalypts germplasm enriches biodiversity, maintains ecosystem sustainability, and aids in conservation. Therefore, this study aims to analyze the genetic diversity of eucalypts (Corymbia and Eucalyptus) for the development of germplasm conservation in Forest Area with the Special Purpose (KHDTK) Bromo Forest, Karanganyar, Indonesia. In this study, 14 simple sequence repeat (SSR) markers were used to assess the genetic diversity among 20 accessions (Corymbia and 5 Eucalyptus species) from Central and West Java. Subsequently, the genetic parameters were measured and a phylogenetic tree was constructed. The result showed that the SSR markers have high variability, although they belong to different genera. Furthermore, the genetic diversity showed 49 alleles with an average of 3 alleles per locus, while the polymorphism information content (PIC) values were 0.55. There were 4 SSR markers (EMBRA13, EMBRA8, EMCRC11, and EMBRA2) with high PIC value, while the gene diversity (He) of Corymbia and 5 Eucalyptus showed a low level of genetic diversity. The genetic relationship and population structure were divided into genera Corymbia and Eucalyptus. For further application, the eucalypt cultivated in the KHDTK Bromo Forest can contribute as a reference set and 14 SSR markers as a potential marker in combination with morphological characterization to generate a database for germplasm management and conservation.

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers

2021 ◽  
Vol 48 (3) ◽  
pp. 2253-2260
Author(s):  
Lameck A. Nyabera ◽  
Inosters W. Nzuki ◽  
Steven M. Runo ◽  
Peris W. Amwayi
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Western Kenya
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