Enriched mini-genomic library for the development and characterization of simple sequence repeat (SSR) markers in sugarcane (saccharum sp. hybrids)

Abstract

© 2019, College of Agriculture and Food Science, University of the Philippines Los Banos. All rights reserved. Enriched mini-genomic libraries of sugarcane variety VMC 87-599 were constructed using AatII and PstI restriction enzymes. A total of 517 sequences were obtained from the combined libraries. BLASTn homology revealed that majority (49%) of the sequences had no significant similarity whereas 22% had similarity with Saccharum officinarum, 12% with both Sorghum bicolor and Zea mays, 2% with Setaria italica, 1% with Oryza sativa, and 2% with other grass species. Also, 3.6% of the sequences had similar gene identity that is organellar and 12.7% nuclear. Of the total sequences, 54 (4.64%) had SSRs and 63 primers were developed with 11 primers mined from genic sequences. SSR repeat motifs were predominantly tetranucleotide (51%) and trinucleotide (30%). The primer sets were used to screen 20 sugarcane accessions of which 46 primers were amplified fragments. A total of 326 alleles were detected with the mean value of 7 alleles per locus. The average PIC value of the 46 optimized primers ranged from 0 to 0.94 with a mean value of 0.73. Cluster analysis of genotypic data of 20 accessions from 46 primers revealed 5 clusters at a dissimilarity coefficient of 0.5. SSR markers designed from the enriched library. These are highly informative and can be utilized for sugarcane genetics and breeding.

Source or Periodical Title

Philippine Agricultural Scientist

ISSN

317454

Page

95-106

Document Type

Article

Subject

Genomic mini-library, Methylation-sensitive restriction enzymes, Primer design, SSR, Sugarcane

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