Abstract

Internationally, grape breeders have been using traditional breeding approaches to introgress Ren4 resistance against powdery mildew (Erysiphe necator) from a wild Asian grapevine (Vitis romanetii) into cultivated grapevines (V. vinifera). The goal of this work was to use genomic tools to identify candidate genes underlying the Ren4 resistance phenotype. Full- and half-sib families segregating for Ren4 resistance were analyzed using Genotyping-by-Sequencing (GBS), and 70 GBS tags were identified as specifically tagging the Ren4 locus. These tags were used to identify BAC clones at the locus, and a scaffolded BAC assembly was generated using Velvet and SSPACE. This assembly spanned 13.7Mb, and predominately aligned with the correct chromosomal region of the PN40024 reference genome. Two de novo transcriptomes were generated using Trinity for the wild source of Ren4 and a Ren4 introgression line. RNA-seq expression analysis of F1 full-sibling progeny identify candidate genes, 29 of which aligned to the BAC assembly. The integration of these diverse genomic technologies resulted in the identification of 7 Ren4 candidate genes, and the correctness of analyses was independently confirmed by cloning and Sanger sequencing of candidate genes. The integration of these novel approaches accelerated the characterization of the Ren4 locus, and will enhance the genetic improvement of grapevine via marker-assisted breeding or biotechnology.

Library of Congress Subject Headings

Grape powdery mildew disease--Genetics; Plant immunology; Grapes--Genetics

Publication Date

9-25-2014

Document Type

Thesis

Student Type

Graduate

Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Michael V. Osier

Advisor/Committee Member

Lance Cadle-Davidson

Advisor/Committee Member

Gary R. Skuse

Comments

Physical copy available from RIT's Wallace Library at SB608.G7 L45 2014

Campus

RIT – Main Campus

Plan Codes

BIOINFO-MS

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