Development of gene-specific DNA markers for coconut and pineapple through in silico approach

Issue Date

6-2017

Abstract

In this research, the authors utilized in silico strategies later combined with genome sequence information to develop DNA markers targeting genes of interest in coconut (Cocos nucifera L.) and pineapple (Ananas comosus L.). The authors selected seven genes as candidates for glandular trichome-based resistance to coconut scale insect in coconut, and four major genes in the lycopene biosynthesis pathway for pineapple. The general procedure entailed searching for homologs of genes of interest in model organisms like Arabidopsis thaliana (L.) Heynh., and tomato Solanum lycopersicon L. and close taxonomic relatives (i.e. African oil palm, Elaeis guineensis Jacq. for coconut), followed by identification of regions for primer design like open reading frames (ORFs), conserved regions and exons. Upon availability of genome sequence first for pineapple through the Comparative Genomics website, and alter a draft sequence in coconut through the Coconut Genomics program of DOST-PCAARRD [Department of Science and Technology-Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development], in silico polymerase chain reaction has shown the presence and lengths of corresponding theoretical PCR amplification fragments. Additional primers were designed based on homolog contig sequences. Availability and access to the genome sequence has increased precision in primer design through comparative genomics. Using this approach, the authors were able to design 51 gene-specific primers for coconut and 57 for pineapple, and shown to have actual amplification in genomic DNA samples of different crop varieties. The DNA markers will be used in high-throughput mining for natural and/or induced point mutations in target gene regions towards genomics-assisted molecular breeding.

Source or Periodical Title

Philippine Journal of Crop Science

ISSN

0115-463X

Volume

42

Issue

Supplement no. 1

Page

97

Document Type

Article

Language

English

Subject

Coconut; Pineapple; Plant breeding

En – AGROVOC descriptors

COCOS NUCIFERA; ANANAS COMOSUS; DNA; GENETIC MARKERS; GENES; PCR; NUCLEOTIDE SEQUENCE

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