Multiplex SSR-PCR analysis of genetic diversity and redundancy in the Philippine rice (Oryza sativa L.) germplasm collection

Issue Date

8-2014

Abstract

Rice germplasm conservation is vital to ensuring the availability of a rich gene pool for future varietal improvement programs. However, with limited resources for gene banking, there is a need to identify and prioritize unique accession in the PhilRice gene bank for maximum resource utilization. A robust and unequivocal way to identify duplicates is through multiplex SSR-PCR DNA fingerprinting. The present study established the optimal concentrations and reaction conditions for the successful amplification of PCR products using a multiplex panel composed of rice simple sequence repeat (SSR) markers, namely RM312, RM316, RM515 and RM171. The panel was then used to analyze the genetic diversity and identify duplicates among the 427 rice germplasm accessions with similar or identical variety names from the PhilRice genebank. A total of alleles were detected at the 4 SSR loci. The polymorphism information content (PIC) values of the SSR markers were moderately high ranging from 0.459 to 0.643. A dendrogram was constructed using the Dice similarity coefficient land UPGMA algorithm. The multiplex SSR-PCR panel produced unique profiles of 31 accessions that, being genetically distinct, should be maintained as part of the main collection of the genebank. There were 17 accessions identified as possible redundants having a bootstrap value greater than 95%. Additional SSR and morphological markers will be required to further strengthen the evidence for redundancy, and hence justify removal of unnecessary duplicates from the collection.

Source or Periodical Title

Philippine Journal of Crop Science

ISSN

0115-463x

Volume

39

Issue

2

Page

22-43

Document Type

Article

Frequency

tri-quarterly

Physical Description

tables, dendrograms

Language

English

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