Assessment of genetic diversity in cashew germplasm using RAPD and ISSR markers

Thimmappaiah,; Santhosh, W.G.; Shobha, D.; Melwyn, G S

doi:10.1016/j.scienta.2008.11.022

Cited by 69 publications

(29 citation statements)

References 14 publications

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“…Therefore, the ISSR markers represent the more efficient marker system because of their capacity to generate several informative bands within a single amplification reaction. Similar results have been reported in cashew by Thimmappaiah et al (2009). In fact, ISSR exhibits a higher capacity to reveal polymorphisms and greater potential to determine intraand inter-genomic diversity than other arbitrary primer methods such as RAPD (Zietkiewicz et al 1994).…”

Section: Rapd and Issr Comparisonsupporting

confidence: 73%

“…Previously, the RAPD technique has been applied to assess genetic diversity in pea (Simioniuc et al 2002), green gram (Karuppanapandian et al 2006a), cow pea (Karuppanapandian et al 2006b), and black gram (Karuppanapandian et al 2007). The ISSR technique has been used to examine genetic relationships in genus Vigna (Souframanien and Gopalakrishna 2004) and several other crops (Awasthi et al 2004;Kuras et al 2004;Kuznetsova et al 2005;Thimmappaiah et al 2009). In black gram varieties, ISSR markers amplified polymorphic bands more efficiently than RAPD markers (77.8 compared with 66.5%, respectively; Table 3) and similar results have been obtained for several other crops, including wheat (Nagoaka and Ogihara 1997) and groundnut (Raina (Table 3).…”

Section: Rapd and Issr Comparisonmentioning

confidence: 99%

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Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

Karuppanapandian

Wang²,

Karuppudurai

et al. 2010

Can. J. Plant Sci.

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, W. 2010. Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) varieties. Can. J. Plant Sci. 90: 443Á452. The DNA fingerprinting methodologies, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were used to estimate genetic diversity and relationships among 20 black gram (Vigna mungo L. Hepper) varieties. Thirty selected RAPD primers amplified 255 bands, 168 of which were polymorphic (66.5%). On average, these primers produced 8.5 bands, 5.6 of which were polymorphic. Polymorphic band number varied from 2 (A-05) to 10 (OPA-02), with sizes ranging from 100 to 2550 bp. Twenty-four selected ISSR primers produced 238 amplified products, 184 of which were polymorphic (77.8%). On average, these primers generated 9.8 bands, with 7.7 polymorphic bands ranging in number from 4 (ISSR-13) to 11 (ISSR-03), and size from 100Á2650 bp. Genetic relationships were estimated using similarity coefficient (Jaccard's) values between different accession pairs; these varied from 30.7 to 85.0 for RAPD, and from 37.2 to 88.4 with ISSR. UPGMA analysis indicated that the varieties ranged in similarity from 0.50 to 1.00 (mean of 0.75) for RAPD, and from 0.47 to 1.00 (mean of 0.76) with ISSR. Cluster analysis of RAPD and ISSR results identified three clusters with significant bootstrap values, which revealed greater homology between the varieties. Principal coordinates analysis also supported this conclusion. Among the black gram varieties, WBU-108 and RBU-38 were highly divergent, whereas LBG-648 and LBG-623 were genetically similar. The markers generated by RAPD and ISSR assays can provide practical information for the management of genetic resources and these results will also provide useful information for the molecular classification and breeding of new black gram varieties.

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Section: Rapd and Issr Comparisonsupporting

confidence: 73%

Section: Rapd and Issr Comparisonmentioning

confidence: 99%

Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

Karuppanapandian

Wang²,

Karuppudurai

et al. 2010

Can. J. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…DNA profiling using RAPD markers have been standardized and employed successfully by different workers (Samal, 2002;Croxford et al, 2005 andThimmappaiah et al, 2009) to analyze samples of Anacardium species. The success in generating polymorphic loci depends on proper choice of primers for DNA amplification and extent of genetic variation among the test genotypes.…”

Section: Resultsmentioning

confidence: 99%

“…In the present investigation, RAPD produced as a whole 94 polymorphic amplicons out of total 107 scorable amplified products resulting 87.85% polymorphism. Thimmappaiah et al (2009) generated 60 bands in 100 cashew germplasm accessions, of which 51 bands were polymorphic (85%) and produced on an average of 5.45 polymorphic bands per primer. Similarly, Thimmappaiah (2011) assessed 60 accessions of cashew in another study using 20 RAPD markers that generated 138 bands, of which 8.1 bands were polymorphic per primer.…”

Section: Resultsmentioning

confidence: 99%

Molecular Assessment of Genetic Diversity and Identification of Elite Cashew Hybrids

Sethi

Tripathy

Lenka

et al. 2016

ijh

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Genetic diversity among 20 cashew hybrids and their eight parents were assessed using 15 RAPD primers which resulted 1742 alleles with an average of 62.21alleles per genotype. RAPD profiles revealed 94 polymorphic bands out of total 107 scorable bands resulting 87.85% polymorphism. On an average 7.66 bands were produced with a range of 4-15 amplicons per primer. The maximum number (14) of polymorphic bands (210 to 3250bp) was produced by primer OU-34 with high polymorphic information content (PIC) and resolving power (Rp) values. Cashew hybrids H 6 and D 19 maintained very high level of average genetic dissimilarity with rest of the test genotypes. The above hybrids comprising the most divergent genetic group (Cluster-I) had shown significantly above average productivity and these could enrich the cashew gene pool for further genetic improvement for nut quality and yield per se. Besides, the genotype-specific bands identified in the present study are useful for identification of cashew genotypes.

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“…For example, Thimmappaiah et al (2009) analyzed cashew germplasm with ISSR-and RAPD-markers separately and simultaneously, and found that combining the data from two marker systems ensure more efficient genotypes differentiation. However, a successful program for studying and conserving a biodiversity shouldn't be based exclusively on findings of RAPD and ISSRanalyses, since these markers are mainly targeting noncoding regions and may not correlate with adaptive characters.…”

Section: Discussionmentioning

confidence: 99%

Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

et al. 2013

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Abstract:We investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity "the percentage of polymorphic bands", and "the average Jaccard's genetic distance between plants", marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3-1.7 times higher than for the others, and the average genetic distance was 1.2-1.3 times higher. Different marker systems were ranked by the value of Nei's gene diversity and the Shannon's index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP-and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

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Assessment of genetic diversity in cashew germplasm using RAPD and ISSR markers

Cited by 69 publications

References 14 publications

Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

Molecular Assessment of Genetic Diversity and Identification of Elite Cashew Hybrids

Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

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