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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.


Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to Moraceae.
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pone.0162909.g005: Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to Moraceae.

Mentions: The usefulness of a locus specific SSR marker would be higher if it is transferable to other closely related species. We assessed the transferability of the mulberry genic SSR markers using three species belonging to the family Moraceae, namely fig, ficus and jackfruit. Of the 206 markers developed, 40% (83) were transferable to these closely related species (Table 6). The number of markers that were specific to a particular species and those shared between pairs of species and all the three species is illustrated in Fig 5. The PIC value revealed by these markers ranged between 0 and 0.743 with a mean of 0.666 and they detected a higher heterozygosity of 0.77 among the species (Table 7). The genetic diversity revealed by these markers among the other species of Moraceae was also high ranging from 27 to 77% with a mean of 68%.


Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to Moraceae.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0162909.g005: Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to Moraceae.
Mentions: The usefulness of a locus specific SSR marker would be higher if it is transferable to other closely related species. We assessed the transferability of the mulberry genic SSR markers using three species belonging to the family Moraceae, namely fig, ficus and jackfruit. Of the 206 markers developed, 40% (83) were transferable to these closely related species (Table 6). The number of markers that were specific to a particular species and those shared between pairs of species and all the three species is illustrated in Fig 5. The PIC value revealed by these markers ranged between 0 and 0.743 with a mean of 0.666 and they detected a higher heterozygosity of 0.77 among the species (Table 7). The genetic diversity revealed by these markers among the other species of Moraceae was also high ranging from 27 to 77% with a mean of 68%.

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.