Applications of bulking in molecular characterization of plant germplasm: a critical review

2003 ◽  
Vol 1 (2-3) ◽  
pp. 161-167 ◽  
Author(s):  
Yong-Bi Fu
Keyword(s):  
Genetic Variation ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Low Frequency ◽  
Molecular Techniques ◽  
Technical Problems ◽  
Germplasm Identification ◽  
Plant Germplasm ◽  
Germplasm Collections

AbstractCharacterization of plant germplasm using molecular techniques is playing an increasingly important role in the management and utilization of plant genetic resources, but has its limitations in the screening of large numbers of accessions held in seed genebanks worldwide. Bulking individual plants from one accession or group to form a representative sample is a promising approach to widening the scope of a characterization, but it is not without technical problems in detecting genetic variation. This review was conducted to assess the technical pitfalls of bulking, and to evaluate the effectiveness of various bulking methods in the assessment of genetic variation and genetic relationships, and in the identification of plant germplasm. Clearly, some alleles, particularly those occurring at low frequency, may go undetected in a bulked sample, depending on the bulking methods and the molecular techniques used. As a result, genetic diversity estimates and genetic relationship inferences can be significantly biased. Germplasm identification may not be always reliable. Thus, it is imperative that the detection limit imposed by bulking be assessed for a newly initiated molecular germplasm characterization and bias be considered in interpretation of the resulting characterization data. Equally imperative is the need for continuous efforts of exploring efficient bulking procedures for the screening of large germplasm collections, particularly by the newly developed marker systems.

Identification and Genetic Variation among Hibiscus Species (Malvaceae) Using RAPD Markers

2006 ◽  
Vol 61 (1-2) ◽  
pp. 123-128 ◽  
Author(s):  
Suvakanta Barik ◽  
Sunil Kumar Senapati ◽  
Subhashree Aparajita ◽  
Anuradha Mohapatra ◽  
Gyana Ranjan Rout
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Plant Genetic Resources ◽  
Flower Colour ◽  
Morphological Characters ◽  
Germplasm Identification ◽  
Major Cluster ◽  
Identification Of Species

Abstract Germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or cultivars identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and determination of genetic variation within the two species of Hibiscus and 16 varieties of Hibiscus rosa-sinensis L. through random amplified polymorphic (RAPD) markers. Primer screening was made by using the DNA of variety “Prolific”. Genetic analysis was made by using ten selected decamer primers. A total of 79 distinct DNA fragments ranging from 0.3 to 2.5 kb were amplified by using ten selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 16 varieties and two species formed one cluster. The first major cluster consisted of three varieties and a second major cluster consisted of two species and 13 varieties. The genetic distance was very close within the varieties and also among the species. Thus, these RAPD markers have the potential for identification of species/varieties and characterization of genetic variation within the varieties. This is also helpful in Hibiscus breeding programs and provides a major input into conservation biology

Identification and Analysis of Genetic Variation among Rose Cultivars Using Random Amplified Polymorphic DNA

2005 ◽  
Vol 60 (7-8) ◽  
pp. 611-617 ◽  
Author(s):  
Anuradha Mohapatra ◽  
Gyana Ranjan Rout
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Plant Genetic Resources ◽  
Flower Colour ◽  
Morphological Characters ◽  
Breeding Programs ◽  
Rose Breeding

Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, cultivars or species identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and analysis of genetic variation within 34 rose cultivars through random amplified polymorphic DNA (RAPD) markers. Analysis was made by using twenty five decamer primers. Out of twenty five, ten primers were selected and used for identification and analysis of genetic relationships among 34 rose cultivars. A total of 162 distinct DNA fragments ranging from 0.1 to 3.4 kb was amplified by using 10 selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 34 rose cultivars form 9 clusters. The first cluster consists of eight hybrid cultivars, three clusters having five cultivars each, one cluster having four cultivars, two clusters having three cultivars each and two clusters having one cultivar each. The genetic distance was very close within the cultivars. Thus, these RAPD markers have the potential for identification of clusters and characterization of genetic variation within the cultivars. This is also helpful in rose breeding programs and provides a major input into conservation biology.

Identification of Tinospora cordifolia (Willd.) Miers ex Hook F. & Thomas Using RAPD Markers

2006 ◽  
Vol 61 (1-2) ◽  
pp. 118-122 ◽  
Author(s):  
Gyana Ranjan Rout
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Plant Genetic Resources ◽  
Flower Colour ◽  
Morphological Characters ◽  
Tinospora Cordifolia ◽  
Identification Of Species

Abstract Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, plant identification has relied on morphological characters like growth habit, floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and genetic variation within 15 clones of Tinospora cordifolia through random amplified polymorphic DNA (RAPD) markers. Analysis was made using forty decamer primers. Out of them, 15 primers were selected and used for identification and genetic relationships within 15 clones. A total of 138 distinct DNA fragments ranging from 0.2 to 3.2 kb were amplified using 15 selected random primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The genetic distance was very close within the clones. Thus, these RAPD markers have the potential for identification of species and characterization of genetic variation within the population. This study will be helpful to know the genetic background of the medicinal plants with high commercial value, and also provides a major input into conservation biology

Utilization of plant genetic resources in breeding for sustainability

2003 ◽  
Vol 1 (1) ◽  
pp. 11-18 ◽  
Author(s):  
M. O. Humphreys
Keyword(s):  
Genetic Variation ◽  
Genetic Resources ◽  
Related Species ◽  
Plant Genetic Resources ◽  
Gene Pools ◽  
International Treaty ◽  
Food And Agriculture ◽  
United Nations Food ◽  
Potential Use

AbstractUK agriculture is undergoing significant change with reduced subsidies for food production, increasing consumer demands for food safety and traceability, and environmental concerns including climate and demographic change. The International Treaty on Plant Genetic Resources for Food and Agriculture adopted by the United Nations Food and Agriculture Organisation supports the use of genetic resources for research and breeding. Mining genetic resources for useful genetic variation is perceived as a major benefit of genebanks. However, utilization by breeders may be constrained by poor characterization of genetic resources, a widening gap between improved and unimproved material, and the disruption of well- adapted genotypes during introgression. Breeders working with grasses and forage legumes for sustainable agriculture are fortunate in the wealth of genetic variation available both within the primary species of interest and among related species. New DNA technologies allow more targeted approaches to the use of these genetic resources. Possibilities for gene transfer between related species using conventional techniques expand the available gene pools while potential use of genetic transformation extend these even further.

Identification and assessment of genetic relationships in three Chlorophytum species and two high yielding genotypes of C. borivilianum through RAPD markers

Biologia ◽  
2011 ◽  
Vol 66 (2) ◽  
Author(s):  
Sanghamitra Samantaray ◽  
Tarun Patel ◽  
K. Geetha ◽  
Satyabrata Maiti
Keyword(s):  
Rapd Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Banding Patterns ◽  
Major Cluster ◽  
Breeding Programmes ◽  
Important Input ◽  
Identification And Characterization

AbstractConservation of identified germplasm is an important component for efficient and effective management of plant genetic resources. Since Chlorophytum species are important medicinal plants, studies were carried out for identification and establish genetic relationships in three species of Chlorophytum and two high yielding genotypes of Chlorophtum borivilianum using RAPD markers. Out of one hundred primers tested, 47 decamers amplified a total of 454 distinct bands ranging from 0.25–3.0 kbp to identify and to evaluate genetic relationships between and among three species of Chlorophytum and two genotypes of Chlorophtum borivilianum. The cluster analysis indicated that three species of Chlorophytum and two genotypes (NRCCB-1 and NRCCB-2) of C. borivilianum formed two major clusters. The first major cluster constituted C. arundinaceum and C. tuberosum, and the second major cluster composed of two subclusters; the first subcluster represented NRCB-1 and NRCB-2 where as the second subcluster represented C. borivilianum. Thus, the RAPD markers have the potential for identification and characterization of genetic relatedness among the species and genotypes. C. borivilianum along with two genotypes also showed similar banding patterns which could be chosen as candidate markers for differentiating the other two species such as C. arundinaceum and C. tuberosum. This would helpful for breeding programmes and provides an important input in conservation biology.

scholarly journals Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

2017 ◽  
Vol 47 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Magdalena Szeliga ◽  
Joanna Ciura ◽  
Mirosław Tyrka
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Veratrum Album ◽  
Metabolic Properties

Abstract Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

scholarly journals Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Charles E. Wani ◽  
Ibrahim A. Yousif ◽  
Muntasir E. Ibrahim ◽  
Hassan H. Musa
Keyword(s):  
Genetic Variation ◽  
Genetic Difference ◽  
Genetic Relationships ◽  
Indigenous Chicken ◽  
Commercial Strain ◽  
Pcr Product ◽  
D Loop ◽  
Chicken Breeds ◽  
Networks Analysis

The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm=4.622).

scholarly journals Simple Sequence Repeat (SSR) Variation in a Collection of Malus Species and Hybrids

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 440C-440 ◽  
Author(s):  
Stan C. Hokanson ◽  
Amy K. Szewc-McFadden ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Plant Genetic Resources ◽  
Sequence Repeat ◽  
Discrimination Power ◽  
Banding Patterns ◽  
Germplasm Collections ◽  
Duplication Events ◽  
Primer Sets ◽  
Simple Sequence

A diverse collection of 133 Malus species and hybrids from the USDA Plant Genetic Resources Unit's core subset collection was screened with five simple sequence repeat (SSR) primer pairs in order to determine genetic identities and overall levels of genetic variation. The number of amplification products (alleles) per locus (primer pair) in this collection ranged from 6 to 39, with some genotypes showing complex banding patterns of up to four products per locus, suggesting that duplication events may have occurred within the genome. Five primer sets unequivocally differentiated all but 10 pairs of genotypes in the collection, with seven of these 10 being pairs of the same species. Within three of the species holdings surveyed, M. honanensis, M. sargentii, and M. sikkimensis, no genetic variation was revealed with the SSR markers. The discrimination power for the combined loci in this collection was nearly one, which indicates that the likelihood of two genetically different accessions sharing the same alleles at all the loci included in this study would be nearly impossible. Coupled with results from a previous survey of M. × domestica accessions, this finding suggests that with five SSR primer pairs, the majority of the Malus holdings could be assigned a unique fingerprint identity. The average direct count heterozygosity over all loci was 0.620, ranging in value from 0.293 to 0.871 over individual loci. These heterozygosity counts will be compared with a survey of naturally occurring M. sieversii to determine whether current repository holdings are representative of the overall levels of diversity occurring in Malus. Information generated with this study, coupled with passport and horticultural data will inform curatorial decisions regarding deaccessioning of duplicate holdings and plans for future germplasm collections.

Sequence-related amplified polymorphism (SRAP) markers for assessing genetic relationships and diversity in sugarcane germplasm collections

2008 ◽  
Vol 6 (3) ◽  
pp. 222-231 ◽  
Author(s):  
Andru Suman ◽  
Collins A. Kimbeng ◽  
Serge J. Edmé ◽  
John Veremis
Keyword(s):  
Genetic Relationships ◽  
Crop Improvement ◽  
Saccharum Officinarum ◽  
Essential Information ◽  
Germplasm Collections ◽  
High Discriminatory Power ◽  
Sugarcane Germplasm ◽  
Sugarcane Hybrids ◽  
Species Specific

Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic relationships among members of the Saccharum species. A panel of 31 SRAP primer combinations were used to score 30 genotypes of Saccharum officinarum, Saccharum spontaneum, Saccharum robustum, Saccharum sinense, Saccharum barberi and sugarcane hybrids, with Miscanthus and Erianthus included as outgroups. The amplifications produced 1364 DNA fragments for an average of 44 per primer combination, with 83% (1135) being polymorphic and 8.7% (119) being species specific. Based on the Dice index, all 30 genotypes were differentiated from each other with genetic similarity (GS) estimates ranging from 0.60 to 0.96 (mean = 0.79). Both the dendrogram [obtained by the unweighted pairgroup method with arithmetic mean or (UPGMA)] and the non-metric multidimensional scaling method grouped the genotypes according to their phylogenetic relationships. Erianthus and Miscanthus were separated as two outgroups (at GS levels of 0.56 and 0.72, respectively) into two major clusters: cluster I separated the S. robustum, S. sinense, S. barberi and hybrids as different subgroups with each one including some S. officinarum clones, while cluster II included the S. spontaneum clones, exclusively. A S. officinarum–S. spontaneum sequence comparison of some of the monomorphic and polymorphic bands revealed 65–90% homology with rice, corn or sugarcane sequences deposited in databases. The high discriminatory power coupled with the possibility that most of the amplicons may be amplifying gene-rich regions of the genome makes SRAP a potentially robust tool for genetic mapping aimed at marker-assisted introgression in sugarcane.

Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

2020 ◽  
Vol 8 (3) ◽  
pp. 247-288
Author(s):  
Melaku Alemu
Keyword(s):  
Genome Mapping ◽  
Plant Protection ◽  
Abiotic Factors ◽  
Plant Genetic Resources ◽  
Management Strategies ◽  
Molecular Techniques ◽  
Successful Implementation ◽  
Global Food Security ◽  
Production Strategies

The second Sustainable Developmental Goals (SDG), among the seventeen SDG, is concerned with the pursuit of global food security and agricultural sustainability, which become the key to the success of the entire SDG. Whereas agricultural production and productivity are heavily threatened by the incidence of pests that inflict huge losses in various forms. This calls for prompt applications of biotechnology for the fast, accurate and reliable means for characterization of plant generic resources and pests as it is the pre-requisite and gateway for designing appropriate plant protection and production strategies. It is imperative that pests be identified properly so that judicious use of the literature can be made and sustainable management strategies can be implemented at the right stage. To this end, the application of biotechnology has made significant advances for reliable characterization of plant genetic resources as well as accurate diagnosis of pests, study of their genetic diversity and variability, detailed mechanisms of their transmission and evolutionary relationships. Accordingly, this review article covers the comprehensive account of the various molecular techniques, genome mapping and OMICS sciences utilized for characterization plants and pests that ultimately allow the detailed study of the biology and epidemiology of pests at any stage of their life cycle. The resulting data are eventually employed for enhancing successful implementation of sustainable plant protection and production strategies. In conclusion, the increasing projections of transboundary pests, environmental and abiotic factors together with the continuous scientific advancements and breakthroughs have made biotechnology to be an important engine of bioeconomy for generating invaluable products, processes and services. Int. J. Appl. Sci. Biotechnol. Vol 8(3): 247-288

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