Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

<p>Abstract</p> <p>Background</p> <p>Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa.</p> <p>Results</p> <p>A small-insert partial genomic library of <it>Coffea canephora</it>, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT >> AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10^-6and 10^-12for arabicas and robustas respectively) and unbiased corrected estimates (10^-20and 10^-43for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee.</p> <p>Conclusion</p> <p>The conventional approach of genomic library was successfully employed although with low efficiency to develop a set of 44 new genomic microsatellite markers of coffee. The characterization/validation of new markers demonstrated them to be highly informative, and useful for genetic studies namely, genetic diversity in coffee germplasm, individualization/bar-coding for germplasm protection, linkage mapping, taxonomic studies, and use as conserved orthologous sets across secondary genepool of coffee. Further, the relative frequency and distribution of different SSR motifs in coffee genome indicated coffee genome to be relatively poor in microsatellites compared to other plant species.</p

Intra and intergeneric transferable gene-derived orthologous microsatellite markers in <i>Eucalyptus</i> and <i>Corymbia</i> species

<p>This study describes the development and application of a novel strategy that targets repeat domains in the orthologous genic region of two <i>Eucalyptus</i> species to derive Expressed Sequence Tags (EST)-based functional orthologous microsatellite markers and their characterization in four <i>Eucalyptus</i> and two <i>Corymbia</i> species. About 13,468 ESTs of <i>Eucalyptus</i> <i>globulus</i> were assembled into unigenes, screened for repeat motifs and then mapped on the <i>Eucalyptus</i> <i>grandis</i> genome. The simple sequence repeat (SSR)-positive orthologous sequences of <i>E. grandis</i>, along with 13,380 genomic sequences of <i>Eucalyptus</i> <i>camaldulensis</i>, were then screened for di- and tri-nucleotide repeat motifs and 230 primer pairs were designed. Functional annotation was carried out through homology search and gene ontology using <i>E. grandis</i> transcript database. Of 230 SSRs, 179 were validated in <i>E. camaldulensis</i> and a subset of 20 SSRs was used for characterization and cross species/genera transferability using 130 individuals from both <i>Eucalyptus</i> and <i>Corymbia</i>. The average values of number of alleles, polymorphic information content, observed and expected heterozygosity were 10.57, 0.59, 0.43 and 0.62, respectively, in <i>E. camaldulensis</i>. High marker transferability within the genus <i>Eucalyptus</i> (up to 98%) and <i>Corymbia</i> (up to 80%) was observed.</p

NJ tree showing relationship within and between arabica and robusta germplasm based on the allelic diversity generated using the new SSR markers

<p><b>Copyright information:</b></p><p>Taken from "Development of new genomic microsatellite markers from robusta coffee (Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies"</p><p>http://www.biomedcentral.com/1471-2229/8/51</p><p>BMC Plant Biology 2008;8():51-51.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396172.</p><p></p

NJ tree showing relationship between 14 and two taxa based on the allelic diversity generated using the new SSR markers

<p><b>Copyright information:</b></p><p>Taken from "Development of new genomic microsatellite markers from robusta coffee (Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies"</p><p>http://www.biomedcentral.com/1471-2229/8/51</p><p>BMC Plant Biology 2008;8():51-51.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396172.</p><p></p