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Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae

View Article: PubMed Central - PubMed

ABSTRACT

Improving mulberry leaf production with enhanced leaf quality holds the key to sustain the ever increasing demand for silk. Adoption of modern genomic approaches for crop improvement is severely constrained by the lack of sufficient molecular markers in mulberry. Here, we report development and validation of 206 EST derived SSR markers using transcriptome data generated from leaf tissue of a drought tolerant mulberry genotype, Dudia white. Analysis of transcriptome data containing 10169 EST sequences, revealed 1469 sequences with microsatellite repeat motifs. We designed a total of 264 primers to the most appropriate repeat regions, of which 206 were locus specific. These markers were validated with 25 diverse mulberry accessions and their transferability to closely related species belonging to family Moraceae was examined. Of these markers, 189 revealed polymorphism with up to 8 allelic forms across mulberry species, genotypes and varieties with a mean of 3.5 alleles per locus. The markers also revealed higher polymorphic information content of 0.824 among the accessions. These markers effectively segregated the species and genotypes and hence, can be used for both diversity analysis and in breeding applications. Around 40% of these markers were transferable to other closely related species. Along with the other genic and genomic markers, we report a set of over 750 co-dominant markers. Using these markers we constructed the first genetic linkage map of mulberry exclusively with co-dominant markers.

No MeSH data available.


Diversity analysis of mulberry and closely related species belongs to Moraceae using 206 EST-SSR markers.
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pone.0162909.g006: Diversity analysis of mulberry and closely related species belongs to Moraceae using 206 EST-SSR markers.

Mentions: The ability of a marker to distinguish between related and unrelated individuals determines its usefulness of the marker. A neighbor joining algorithm based on UPGMA was adopted to assess the diversity among species and genotypes. The dendrogram illustrated in Fig 6 indicated a clear segregation of mulberry and other species into two distinct clades. Further, the three mulberry species used in this study were grouped into single cluster which was distinctly different from the mulberry genotypes. Since, the genomic DNA of Dudia white was used for marker development, the entire set of markers amplified in Dudia white and hence, this genotype grouped itself into a separate cluster away from the rest of the accessions. Among the accessions screened, the maximum genetic similarity was observed between S-36 and V-1 and least was between Dudia white and Macrora (S2 Table).


Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
Diversity analysis of mulberry and closely related species belongs to Moraceae using 206 EST-SSR markers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036888&req=5

pone.0162909.g006: Diversity analysis of mulberry and closely related species belongs to Moraceae using 206 EST-SSR markers.
Mentions: The ability of a marker to distinguish between related and unrelated individuals determines its usefulness of the marker. A neighbor joining algorithm based on UPGMA was adopted to assess the diversity among species and genotypes. The dendrogram illustrated in Fig 6 indicated a clear segregation of mulberry and other species into two distinct clades. Further, the three mulberry species used in this study were grouped into single cluster which was distinctly different from the mulberry genotypes. Since, the genomic DNA of Dudia white was used for marker development, the entire set of markers amplified in Dudia white and hence, this genotype grouped itself into a separate cluster away from the rest of the accessions. Among the accessions screened, the maximum genetic similarity was observed between S-36 and V-1 and least was between Dudia white and Macrora (S2 Table).

View Article: PubMed Central - PubMed

ABSTRACT

Improving mulberry leaf production with enhanced leaf quality holds the key to sustain the ever increasing demand for silk. Adoption of modern genomic approaches for crop improvement is severely constrained by the lack of sufficient molecular markers in mulberry. Here, we report development and validation of 206 EST derived SSR markers using transcriptome data generated from leaf tissue of a drought tolerant mulberry genotype, Dudia white. Analysis of transcriptome data containing 10169 EST sequences, revealed 1469 sequences with microsatellite repeat motifs. We designed a total of 264 primers to the most appropriate repeat regions, of which 206 were locus specific. These markers were validated with 25 diverse mulberry accessions and their transferability to closely related species belonging to family Moraceae was examined. Of these markers, 189 revealed polymorphism with up to 8 allelic forms across mulberry species, genotypes and varieties with a mean of 3.5 alleles per locus. The markers also revealed higher polymorphic information content of 0.824 among the accessions. These markers effectively segregated the species and genotypes and hence, can be used for both diversity analysis and in breeding applications. Around 40% of these markers were transferable to other closely related species. Along with the other genic and genomic markers, we report a set of over 750 co-dominant markers. Using these markers we constructed the first genetic linkage map of mulberry exclusively with co-dominant markers.

No MeSH data available.