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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.


Construction of genetic linkage map in mulberry exclusively using co-dominant markers.
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pone.0162909.g007: Construction of genetic linkage map in mulberry exclusively using co-dominant markers.

Mentions: Overall, linkages were robust and a minimum LOD value of 3 was fixed. A total of 134 (111 genomic and 23 genic) markers segregating in 1:1 test ratio could be aligned on the map (Table 8; Fig 7). The markers covered a total map distance of 4263.5 cM on 14 linkage groups. The linkage map with a total of 14 linkage groups matches the karyotype of mulberry (2n = 28). The distribution of the markers was random and unequal between linkage groups and clustered in some regions (LG2 and LG4). The distance between two linked markers varied from 5.0 cM between MUL3SSR140 and MUL3SSR158 to 49.8 cM between MESTSSRCP243 and MESTSSRCP267 on LG4. The average map distance observed between two linked markers was 31.8 cM. The largest linkage group LG4 had map coverage of 1923.6 cM with 51 markers followed by LG2 with 33 markers spanning 1325.5 cM (Table 8; Fig 7).


Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae
Construction of genetic linkage map in mulberry exclusively using co-dominant markers.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0162909.g007: Construction of genetic linkage map in mulberry exclusively using co-dominant markers.
Mentions: Overall, linkages were robust and a minimum LOD value of 3 was fixed. A total of 134 (111 genomic and 23 genic) markers segregating in 1:1 test ratio could be aligned on the map (Table 8; Fig 7). The markers covered a total map distance of 4263.5 cM on 14 linkage groups. The linkage map with a total of 14 linkage groups matches the karyotype of mulberry (2n = 28). The distribution of the markers was random and unequal between linkage groups and clustered in some regions (LG2 and LG4). The distance between two linked markers varied from 5.0 cM between MUL3SSR140 and MUL3SSR158 to 49.8 cM between MESTSSRCP243 and MESTSSRCP267 on LG4. The average map distance observed between two linked markers was 31.8 cM. The largest linkage group LG4 had map coverage of 1923.6 cM with 51 markers followed by LG2 with 33 markers spanning 1325.5 cM (Table 8; Fig 7).

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.