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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.


Functional relevance of mulberry EST sequences annotated using NCBI database.
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pone.0162909.g002: Functional relevance of mulberry EST sequences annotated using NCBI database.

Mentions: A total of 264 EST sequences satisfied all the criteria for a SSR marker and were selected for marker development. Based on the function, the genes were grouped into different categories like characterized (all sequences with known function), uncharacterized, hypothetical, predicted and sequences with no similarity. About 53% (145) of the EST sequences analyzed had well-defined function that includes major classes such as transcription factors, transporters, ligases, splicing factors, chaperonins, kinases, and ribosomal proteins (Fig 2). The hypothetical and predicted proteins were the other major portions of the selected EST sequences that occupied 24% and 16%, respectively. Around 6% EST sequences did not show any similarity with the existing database sequences and only 1% was uncharacterized sequences (Fig 2).


Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
Functional relevance of mulberry EST sequences annotated using NCBI database.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0162909.g002: Functional relevance of mulberry EST sequences annotated using NCBI database.
Mentions: A total of 264 EST sequences satisfied all the criteria for a SSR marker and were selected for marker development. Based on the function, the genes were grouped into different categories like characterized (all sequences with known function), uncharacterized, hypothetical, predicted and sequences with no similarity. About 53% (145) of the EST sequences analyzed had well-defined function that includes major classes such as transcription factors, transporters, ligases, splicing factors, chaperonins, kinases, and ribosomal proteins (Fig 2). The hypothetical and predicted proteins were the other major portions of the selected EST sequences that occupied 24% and 16%, respectively. Around 6% EST sequences did not show any similarity with the existing database sequences and only 1% was uncharacterized sequences (Fig 2).

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.