Identification of PCR-based Molecular Markers Linked to B, A Carotenoid-related Gene in Tomato

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 515c-515
Author(s):  
Yiping Zhang ◽  
John R. Stommel
Keyword(s):  
Molecular Markers ◽  
Rapd Markers ◽  
Significant Contribution ◽  
Random Amplified Polymorphic Dna ◽  
Isogenic Line ◽  
Breeding Programs ◽  
Tomato Fruits ◽  
Starting Point ◽  
Lycopersicon Cheesmanii ◽  
Β Carotene

β-carotene is the principal provitamin A caroteniod found in tomato fruits and makes a significant contribution to the fruits nutritional value. The dominant B gene conditions high levels of β-carotene in ripe tomato fruits. PCR-based molecular markers, including random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP), were used to identify marker linkage to the B locus. The study was conducted using a near-isogenic line (NIL) of the cultivar Rutgers isogenic for the B locus and bulk segregant analysis of an interspecific F2 population segregating for the B locus, which was derived from the cross of Lycopersicon cheesmanii accession LA 317 × L. esculentum cv. Floradade. Sixty-four AFLP primer pairs and 1018 arbitrary RAPD primers were screened for polymorphism between the pair of NILs and between the two bulks. A number of amplified RAPD and AFLP products were identified that were present in one line or bulk but not the other. Marker linkage with the B locus was confirmed by checking individual samples from the F2 and BC populations. Two RAPD markers were confirmed tightly linked with the B phenotype using the interspecific F2 population. Similarly, a single AFLP marker was identified with close linkage to the B phenotype using the NIL F2 population. The markers identified in this study can be useful in breeding programs with marker assisted selection and, if very tightly linked, as a starting point to isolate the gene.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals Genetic characterization of the Moxotó goat breed using RAPD markers

2005 ◽  
Vol 40 (3) ◽  
pp. 233-239 ◽  
Author(s):  
Rejane Rodrigues de Oliveira ◽  
Andréa Alves do Egito ◽  
Maria Norma Ribeiro ◽  
Samuel Rezende Paiva ◽  
Maria do Socorro Maués Albuquerque ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Rapd Markers ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Goat Breed ◽  
Breeding Programs ◽  
Analysis Of Molecular Variance ◽  
Polymorphic Bands

The objective of this study was to verify the genetic diversity between and within seven populations of Moxotó goat (n = 264) from the States of Pernambuco, Paraíba and Rio Grande do Norte, using RAPD (Random Amplified Polymorphic DNA). Moxotó, as well as other naturalized breeds, suffers genetic losses due to the indiscriminate miscegenation with breeds raised in the Northeast Region of Brazil. The genetic characterization of these genetic resources is essential to conservation and breeding programs. DNA was extracted from lymphocytes using a non-organic protocol. The 16 primers used were selected from 120 decamer oligonucleotide primers and generated 56 polymorphic bands. The analysis of molecular variance (AMOVA) showed that the greater part of total genetic variability (71.55%) was due to differences between individuals within populations, while 21.21% was among populations. The analysis of variance among the pairs of populations demonstrated that the populations located in Floresta, PE x Angicos, RN presented a smaller value of intrapopulational differentiation (8.9%), indicating low genetic variability among them. Nei's genetic distances varied between 0.0546 and 0.1868 in the populations. The dendrogram generated showed that the Canindé breed, used as outgroup, clustered with the populations of Moxotó, indicating a possible common origin of the naturalized goat breeds.

scholarly journals Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
RATIBA BΟUSBA ◽  
SARA GUERAICHE ◽  
MALIKA RACHED KANOUNI ◽  
RABAH BΟUNAR ◽  
ABDELHAMID DJEKΟUNE ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Triticum Durum ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Genotypic Diversity ◽  
Allelic Frequency ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Local Genotypes

Abstract. Bousba R, Gueraiche S, Kanouni MR, Bounar R, Djekoune A, Khammar H, Nadia Y. 2020. Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis. Biodiversitas 21: 2696-2701. Knowledge of genetic variability in durum wheat (Triticum durum Desf.) is of major importance in the development of breeding programs and the preservation of local landrace resources. The objective of this study is to highlight the molecular polymorphism among six durum wheat genotypes from different origins and characterized by different sensitivity to drought tolerance (tolerant, semi-tolerant, and non-tolerant). 15 Random Amplified Polymorphic DNA (RAPD) markers were used to assess the molecular diversity of these genotypes. Our results show a total of one hundred and sixty-nine amplicons, where one hundred and twenty-four are polymorphic bands. The number of bands per primer ranged from two (OPJ-06) to fifteen bands (primers OPE-13 and OPB-01). The values of the Allelic frequency varied from 1 (OPJ-06) to 0.20 (OPA-17) and 0.19 (OPE-13, OPO-06, B-19 and OPA-20). Also, the values of the coefficient of genetic similarity range from 0.69 to 0.80, these results indicate a large variation between tested genotypes. According to the dendrogram generated by the RAPD approach, we obtained four distinct groups: the first one (G1) contains GTADUR and KORIFFLA x SHAM, the second group (G2) contains the local genotype BIDI-17. However, the genotype WAHA was in the third group (G3), the fourth and fifth groups contained the genotypes CIRTA and TELL, respectively. A complementary analysis was done to estimate genetic differentiation, using CPA Analysis that indicated four groups among the six genotypes, where, the local genotypes BIDI-17 and CIRTA were classified together. For allele’s richness, the local genotypes show in this investigation, the highest values in comparison to the introduced genotypes, which suggested the performance of the RAPD markers (high polymorphism and fast genetic analysis). The molecular markers RAPD-PCR type, despite their non-specific characteristics, has shown a strong aptitude for genetic characterization in durum wheat and a high level of polymorphism, which makes it possible in a preliminary study to make exploitable discrimination. These results may be helpful in the improvement and varietal selection, and useful in accelerating breeding programs of durum wheat.

scholarly journals Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE) using RAPD Markers

2010 ◽  
Vol 53 (2) ◽  
pp. 375-387 ◽  
Author(s):  
Luciana do Valle Rego Oliveira ◽  
Ricardo Tadeu de Faria ◽  
Claudete de Fátima Ruas ◽  
Paulo Maurício Ruas ◽  
Melissa de Oliveira Santos ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Core Collection ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Breeding Programs

In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.

scholarly journals Study genetic diversity in maize inbreds and improved hybrid vigor in hybrids produce to determine commercial hybrids in Iraq

2015 ◽  
Vol 5 (3) ◽  
pp. 728-731
Author(s):  
Ziyad A. Abed
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Field Experiments ◽  
Random Amplified Polymorphic Dna ◽  
Hybrid Vigor ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Maize Inbreds ◽  
High Level

 A field experiments was conducted in greenhouse to determinate the genetic diversity among 7 genotypes from maize(4 inbreds and 3hybrids) by using molecular markers with Random Amplified polymorphic DNA(RAPD),that shown high level of polymorphism among genotypes of maize ,where the percentage of polymorphism ranged from(66%) and (83.33%) the highest number of polymorphism band (16) and size fragment ranged between (3800 bp) with the primer ( Bnlg 1185 ) and the lowest 180 with the primer( Bnlg 1464).The genetic distance value ranged between (0.3451) and (0.6534) ,where the lowest genic distance between (k1 and k2),while the highest genetic distance between(k4) and (k3xk4).In this study RAPD markers were shown to be powerful to detect genetic diversity and provided us high polymorphism values within genotypes of maize ,also we can conclude for useful those primers for genetic studies in plant breeding programs for developing synthetic cultivars or improved inbreds of maize. 

scholarly journals Random Amplified Polymorphic DNA (RAPD) Marker Variability between and within Gene Pools of Common Bean

1994 ◽  
Vol 119 (1) ◽  
pp. 122-125 ◽  
Author(s):  
Scott D. Haley ◽  
Phillip N. Miklas ◽  
Lucia Afanador ◽  
James D. Kelly
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Major Gene ◽  
Rapd Marker ◽  
Gene Pools ◽  
Navy Bean ◽  
Breeding Programs ◽  
Polymerase Chain

The objective of this study was to evaluate the degree of RAPD marker variability between and within commercially productive market classes representative of the Andean and Middle American gene pools of common bean (Phaseolus vulgaris L.). Six sets of near-isogenic lines were screened with oligonucleotide primers in the polymerase chain reaction-based RAPD assay. Simultaneous analyses with at least three sets of lines enabled us to score RAPD markers between the two major gene pools, races within the same gene pool, and different genotypes of the same race (within race). A “three-tiered” pattern of polymorphism was observed: between gene pools> between races> within races. The overall level of polymorphism between the Andean and Middle American gene pools was 83.4%. The overall level of polymorphism between races within the same gene pool was similar for Andean races (60.4%) and Middle American races (61.7%). The level of polymorphism between related commercial navy bean lines was 39.2% and between related commercial snap bean lines was 53.6 %. The inherent simplicity and efficiency of RAPD analyses, coupled with the number of polymorphisms detectable between related commercial genotypes, should facilitate the construction of RAPD-based genetic linkage maps in the context of populations representative of most bean breeding programs.

scholarly journals Associating Molecular Markers with Virus Resistance to Classify Sweetpotato Genotypes

2005 ◽  
Vol 130 (3) ◽  
pp. 355-359 ◽  
Author(s):  
M. Mcharo ◽  
D. LaBonte ◽  
R.O.M. Mwanga ◽  
A. Kriegner
Keyword(s):  
Molecular Markers ◽  
Qtl Analysis ◽  
Ipomoea Batatas ◽  
Rapd Markers ◽  
Dna Marker ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Multivariate Techniques ◽  
Accuracy Rates

Molecular markers linked to resistance to sweetpotato chlorotic stunt closterovirus [SPCSV (genus Crinivirus, family Closteroviridae)] and sweetpotato feathery mottle virus [SPFMV (genus Potyvirus, family Potyviridae)] were selected using quantitative trait loci (QTL) analysis, discriminant analysis and logistic regression. Eighty-seven F1 sweetpotato [Ipomoea batatas (L.) Lam.] genotypes from a cross of `Tanzania' and `Wagabolige' landraces were used to generate DNA marker profiles for this study. Forty-five of the clones were resistant to SPCSV while 37 were resistant to SPFMV. A combination of 232 amplified fragment length polymorphism (AFLP) markers and 37 random amplified polymorphic DNA (RAPD) markers obtained were analyzed to determine the most informative markers. All three statistical procedures revealed that AFLP marker e41m33.a contributed the greatest variation in SPCSV resistance and RAPD marker S13.1130 accounted for most of the variation in SPFMV resistance. The power of discriminant and logistic analyses is that you do not need a parent-progeny population. An evaluation of these two models indicated a classification and prediction accuracy rates of 96% with as few as four markers in a model. Both multivariate techniques identified one important discriminatory marker (e44m41.j) for SPCSV and two markers (e41m37.a and e44m36.d) for SPFMV that were not identified by QTL analysis.

scholarly journals Genetic Diversities within Camellia Species Confirmed by Random Amplified Polymorphic DNA (RAPD) Markers

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1105A-1105
Author(s):  
Lianghong Chen ◽  
Shizhou Wang ◽  
Mack Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Camellia Japonica ◽  
Average Percentage ◽  
Study Research ◽  
Camellia Reticulata ◽  
Camellia Species

In this study research was conducted to evaluate the feasibility of characterizing genetic variation within camellia species using random amplified polymorphic DNAs (RAPD) markers. Eight varieties of species Camellia japonica and four varieties of species Camellia reticulata, provided by the America Camellia Society, Fort Valley, Ga., were investigated. RAPD profiles generated by five selected 10-based random primers (out of 20 primers) exhibited distinct patterns of amplified bands for all 12 tested varieties. A total of 344 bands were produced among the eight varieties of species C. japonica, with an average of 8.6 bands, ranging from 220 to 2072 bp in size, scored per primer. Among the 344 amplified bands, 74.4% of the bands presented polymorphic. The four varieties of species C. reticulata produced a total of 180 markers, with an average percentage of 57.8% polymorphisms. The amplified bands were in the range of 236–1760 bp. An average of nine amplified bands was generated per primer. The large percentages of polymorphisms displayed among 12 varieties within the two different species indicate that the expected genetic diversity among varieties within camellia species existed. It was concluded that the RAPD molecular markers are capable of revealing appreciable levels of genetic variation within camellia species.

scholarly journals Identification of RAPD Markers Linked to Five Marker Genes (blu, dgs, y, arg, and a Flat Pod Mutant) in Common Bean

2002 ◽  
Vol 127 (4) ◽  
pp. 685-688 ◽  
Author(s):  
Gino E. Beltrán ◽  
Geunwha Jung ◽  
James Nienhuis ◽  
Mark J. Bassett
Keyword(s):  
Molecular Markers ◽  
Common Bean ◽  
Linkage Map ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Spontaneous Mutation ◽  
Marker Genes ◽  
Dark Green ◽  
Mapping Populations

The development of a complete linkage map, including both classical (visible) and molecular markers, is important to understand the genetic relationships among different traits in common bean (Phaseolus vulgaris L.). The objective of this study was to integrate classical marker genes into previously constructed molecular linkage maps in common bean. Bulked segregant analysis was used to identify 10 random amplified polymorphic DNA (RAPD) markers linked to genes for five classical marker traits: dark green savoy leaf (dgs), blue flower (blu), silvery [Latin: argentum] green pod (arg), yellow wax pod (y) and flat pod (a spontaneous mutation from round to flat pod in `Hialeah' snap bean). The genes for dark green savoy leaf (dgs) and blue flower (blu) were located in a previously constructed molecular linkage map. These results indicate that classical marker genes and molecular markers can be integrated to form a more complete and informative genetic linkage map. Most of the RAPD markers were not polymorphic in the two mapping populations used, and molecular markers from those mapping populations were not polymorphic in the F2 populations used to develop the RAPD markers. Alternative genetic hypotheses for the pod shape mutation in `Hialeah' are discussed, and the experimental difficulties of pod shape classification are described.

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.

Sign in / Sign up

Export Citation Format

Share Document