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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.


Validation of EST-SSR markers in diverse accession belongs to Moraceae.Note: The representative electropherogram showing the amplification profile and scoring of Moraceae accessions screened in a capillary electrophoresis system.
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pone.0162909.g004: Validation of EST-SSR markers in diverse accession belongs to Moraceae.Note: The representative electropherogram showing the amplification profile and scoring of Moraceae accessions screened in a capillary electrophoresis system.

Mentions: To validate the markers, the 206 unambiguous markers were used to screen for the amplification of the genomic DNA of a set of 25 diverse mulberry accessions and species which were selected based on the available passport information to represent a large diversity [1] (Table 1; Fig 4). More than 90% of the 206 locus specific markers displayed polymorphism among the mulberry accessions and species and amplified a total of 620 loci. These markers revealed an average allelic diversity of 3.5 per marker locus which ranged between 1 and 8 alleles per marker locus among all the accessions/species screened. The markers were effective in detecting heterozygosity among the mulberry species which ranged between 0 and 1 with a mean of 0.56. The computed mean PIC value among the species was 0.743. These markers revealed a mean heterozygosity of 0.154 among mulberry genotypes and varieties ranging between 0 and 1. The markers also revealed a higher PIC value of 0.824 and genetic diversity of 84% among the mulberry accessions which were more than that of the mulberry species (Table 5). The results indicated that the genic markers developed can be effectively used for both genetic diversity studies as well as for genetic mapping and QTL discovery applications in mulberry.


Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
Validation of EST-SSR markers in diverse accession belongs to Moraceae.Note: The representative electropherogram showing the amplification profile and scoring of Moraceae accessions screened in a capillary electrophoresis system.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0162909.g004: Validation of EST-SSR markers in diverse accession belongs to Moraceae.Note: The representative electropherogram showing the amplification profile and scoring of Moraceae accessions screened in a capillary electrophoresis system.
Mentions: To validate the markers, the 206 unambiguous markers were used to screen for the amplification of the genomic DNA of a set of 25 diverse mulberry accessions and species which were selected based on the available passport information to represent a large diversity [1] (Table 1; Fig 4). More than 90% of the 206 locus specific markers displayed polymorphism among the mulberry accessions and species and amplified a total of 620 loci. These markers revealed an average allelic diversity of 3.5 per marker locus which ranged between 1 and 8 alleles per marker locus among all the accessions/species screened. The markers were effective in detecting heterozygosity among the mulberry species which ranged between 0 and 1 with a mean of 0.56. The computed mean PIC value among the species was 0.743. These markers revealed a mean heterozygosity of 0.154 among mulberry genotypes and varieties ranging between 0 and 1. The markers also revealed a higher PIC value of 0.824 and genetic diversity of 84% among the mulberry accessions which were more than that of the mulberry species (Table 5). The results indicated that the genic markers developed can be effectively used for both genetic diversity studies as well as for genetic mapping and QTL discovery applications in mulberry.

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.