Genome sequence characterization of candidate host factor genes for virus resistance in tomato (Solanum lycopersicon Mill.) and rice (Oryza sativa Linn.)

Date

6-2016

Degree

Bachelor of Science in Agricultural Biotechnology

College

College of Agriculture and Food Science (CAFS)

Adviser/Committee Chair

Haydee F. Galvez

Restrictions

Restricted: Not available to the general public. Access is available only after consultation with author/thesis adviser and only to those bound by the confidentiality agreement.

Abstract

This study involves the nucleotide sequence-based characterization of the three candidate host factor genesfor virus infectionin tomato. The target host factor genes were deltaCOP, HSC70 and SK4-1/SKK, and were mined for potential sequence polymorphism in six tomato genotypes namely Hawaii 7996, Super Apollo, WVA (Solanum pimpinellifolium), and AVRDC Ty-lines ? VB4, VB9 and VB15. Previously designed PCR primers (CG4, CG7 and CG10) for these host factorgeneswere validated and used to characterize the inherent DNA variations at intron and/or exon genomic sequences among these sampled tomato genotypes. This wasbased on multiple local alignment in reference with the full gene sequences annotated in the tomato SGNgenome database. The orthologous protein sequences of the tomato candidate host factor genes were identified in Oryza sativa Japonica and other 16 plant speciesthrough appropriate bioinformatics analysis in the SGN and Gramene-Ensembl Plant database. The retrieved protein sequences were used to construct the phylogenetic tree to display the genetic relationship and probable ontology of the candidate host factor genes among the studied plant species. The retrieved genomic sequences of the candidate host factor genes in rice were also used to design five (5) primer pairs for the deltaCOP, three (3) primer pairs for the HSC70, and five (5) primer pairs for the SK4-1/SKK gene homologs of Oryza sativa Japonica.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

LG 993.5 2016 A127 /A88

Notes

major in Crop Biotechnology

Document Type

Thesis

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