Laboratory Protocols CIMMYT Applied Molecular Genetics Laboratory

https://tspace.library.utoronto.ca/bitstream/1807/49180/1/ej11062.pdf

Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers

Eggplant is a major crop in Turkey, which produces more of this crop than all of Europe; consequently, germplasm resources are of concern for the country. Molecular characterization of eggplant genotypes collected from different geographical regions of Turkey was carried out using SSR and RAPD markers. With amplification of five SSR loci, the number of alleles per microsatellite locus ranged from 2 to 10, with a total of 24 alleles. The greatest number of alleles was found at the emf21H22 locus (10 alleles); followed by emh11O01 and emf21C11 as five and four alleles, respectively. The average number of alleles per locus was 4.8. Using 11 decamer RAPD primers, 100 bands were amplified, among which 29 were polymorphic. The number of bands per primer ranged from seven (OPH10, OPH19, OPH20, OPH03) to 14 (OPB07). Primer OPB07 was the most polymorphic, generating 64% polymorphic bands; the rest of the primers gave less than 50% polymorphism. UPGMA dendrograms were used to examine the genetic relatedness of the genotypes.

/pdf/genetic-diversity-of-eggplant-solanum-melongena-germplasm-t5fmoawmm2.pdf

Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers.

Popcorn breeding programs in Brazil have emerged but despite some advances there is still a lack of material performance studies specially regard to seed quality, in different agricultural seasons. This research was carried out to estimate the popcorn combining ability from biparental crosses between eight tropical and one temperate lines in two agricultural seasons (2008 and 2009) with regard to eight traits related to seed quality, in addition to three agronomic traits related to popping expansion. Method 4, proposed by Griffing (Model 1), was used to verifying the importance of the dominance effect in the genetic control of the seed quality traits, favouring the identification of superior hybrids through seed tests in the laboratory with low cost. The lines from Zelia and CMS42 were promising in obtaining hybrids with superior seed quality and greater popping expansion. The hybrids Zelia × IAC-112, CMS42 × UEM M2-1, CMS43-1 × IAC-112 and UEM M2-2 × Zaeli expressed superior SCA for grain yield, popping expansion and at least two seed quality traits. These hybrids are materials of interest for cultivation in different planting seasons.

Combining ability of popcorn lines for seed quality and agronomic traits

The assessment of genetic diversity is a primary concern of plant breeders and germplasm curators for which morphological traits are internationally accepted descriptors but are often associated with limitations due to G × E interactions. Phenotypic, ISSR, and SSR markers were employed to determine the genetic diversity and relationships among 20 commercially cultivated sesame genotypes representing different geographical regions of India. A narrow range of genetic dissimilarity (0.01–0.12) with mixed clustering was observed using morphological descriptors. A total 279 band positions with 57% polymorphism was amplified by ISSR primers, whereas 36 allelic positions with 73% polymorphism were produced by SSR primers with 100% reproducibility. The ISSR primers with high discrimination power were identified producing genotype-specific bands and distinguishing all the sesame genotypes used in this study. A poor correlation and lack of perfect congruence between phenotypes and marker-based analysis was indicated by the UPGMA dendrogram and PCA analysis. Our results suggest that SSR and ISSR markers provide a powerful tool for genotype identification and establishment of genetic relationships among sesame genotypes. We recommend the use of molecular markers for testing, required for obtaining intellectual property rights, and also for the analysis of genotypic diversity among sesame varieties.

Comparative potential of phenotypic, ISSR and SSR markers for characterization of sesame ( Sesamum indicum L.) varieties from India

Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S(7) inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes. These popcorn genotypes: "Yellow Pearl Popcorn" (P1-1 and P1-5), "Zelia" (P1-2 and P1-4), "Curagua" (P1-3), "IAC 112" (P9-1 and P9-2), "Avati Pichinga" (P9-3 and P9-5), and "Pisankalla" (P9-4) have different soil and climate adaptations. Using RAPD marker analysis, each primer yielded bands of variable intensities that were easily detected, as well as non-specific bands, which were discarded from the analysis. The nine primers used yielded 126 bands, of which 104 were classified as polymorphic, giving an average of 11.6 polymorphisms per primer. Using SSR procedures, the number of alleles per locus ranged from two to five, giving a total of 47 alleles for the 14 SSR loci. When comparing the groups formed using SSR and RAPD markers, there were similarities in the combinations of genotypes from the same genealogy. Correlation between genetic distances obtained through RAPD and SSR markers was relatively high (0.5453), indicating that both techniques are efficient for evaluating genetic diversity in the genotypes of popcorn that we evaluated, though RAPDs yielded more polymorphisms.

/pdf/efficiency-of-rapd-versus-ssr-markers-for-determining-f0tt0oexq9.pdf

A. S. Mott

Papers

Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines.