Source: AUBURN UNIVERSITY submitted to
EXPLORING THE GENETIC ADAPTATIONS OF SOUTHEASTERN GRAPEVINES (VITIS SPP.) THROUGH COMPARATIVE EXPRESSION PROFILING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0205463
Grant No.
(N/A)
Project No.
ALA016-040
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2005
Project End Date
Sep 30, 2008
Grant Year
(N/A)
Project Director
Goertzen, L. R.
Recipient Organization
AUBURN UNIVERSITY
108 M. WHITE SMITH HALL
AUBURN,AL 36849
Performing Department
BIOLOGICAL SCIENCES
Non Technical Summary
The genetic basis for agronomically important traits in crop plants is rarely known. Additionally the evolutionary forces that have shaped crop-related biodiversity such as native germplasm are poorly understood. This project will examine wild grape species and identify genes that contribute to agronomically important traits.
Animal Health Component
25%
Research Effort Categories
Basic
75%
Applied
25%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011139106050%
2021139106050%
Goals / Objectives
This project will create genome-wide, tissue specific expression profiles for several Southeastern grape species. It will also quantify intraspecific variation in gene expression for individual species and selected tissue types. This will allow for an examination of the relationship between differentially transcribed genes and phenotype.
Project Methods
Commercially available microarray chips will be used to examine expression differences between native grape species. This will include estimates of the variation in gene expression between individuals (for specific tissues) within species and populations. Preliminary sampling will focus on Vitis palmata, V. rotundifolia, and V. mustangensis.

Progress 10/01/05 to 09/30/08

Outputs
OUTPUTS: Several successful microarray experiments have been performed to date. These include DNA-DNA hybridizations for the control species Vitis vinifera, as well as for V. shuttleworthii. Microarray data have been calibrated using BLAST analyses of V. shuttleworthii EST data to the recently published V. vinifera genome sequence. Several thousand probes with predicted 100% similarity to V. shuttleworthii genomic DNA have been compared to hybridization results for V. vinifera DNA to V. vinifera chipsets. PARTICIPANTS: Dr. Xiangqin Cui of the Statistical Genetics Section at UAB is participating in the project. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
This project has created genome-wide, tissue specific expression profiles for several Southeastern grape species. It has also quantified intraspecific variation in gene expression for individual species and selected tissue types. This will allow for an examination of the relationship between differentially transcribed genes and phenotype. APPROACH: Commercially available microarray chips were used to examine expression differences between native grape species. This included estimates of the variation in gene expression between individuals (for specific tissues) within species and populations. Preliminary sampling focused on Vitis palmata, V. rotundifolia, and V. mustangensis. The use of EST/genomic data to compare the in silico predictions of hybridization performance to the actual microarray experiments are quite novel. This approach may be followed in other systems with sufficient molecular tools or genomic data resources. Fresh tissue and RNA of target species have been acquired. Statistical design of the microarray experiments have been developed in collaboration with faculty from the Section of Statistical Genomics at UAB. DNA-DNA hybridization experiments have been developed as controls for the RNA-level expression analysis. An additional analysis, comparing sequence level divergence from 10,000 ESTs of wild species to the Vitis vinifera genome has been developed to compare the performance of microarray chips to this in silico experiment. Grapevine cultivars that have the highest quality of fresh and dried fruit lack disease and stress resistance. The identification of resistance genes in native species will ultimately limit the need for fungicides and pesticides that have environmental and health safety issues associated with their use. Methods that seek to discover genes of agronomic importance are a key element in the continued improvement of agriculture in Alabama. The research proposed here will contribute greatly to our understanding of key agronomic traits of muscadine and bunchgrapes - increasingly important specialty crops in Alabama.

Publications

  • No publications reported this period


Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: Several successful microarray experiments have been performed to date. These include DNA-DNA hybridizations for the control species Vitis vinifera, as well as for V. shuttleworthii. Microarray data have been calibrated using BLAST analyses of V. shuttleworthii EST data to the recently published V. vinifera genome sequence. Several thousand probes with predicted 100% similarity to V. shuttleworthii genomic DNA have been compared to hybridization results for V. vinifera DNA to V. vinifera chipsets. PARTICIPANTS: Dr. Xiangqin Cui of the Statistical Genetics Section at UAB as well as graduate student Ivan Shoemaker are participating in the project.

Impacts
The use of EST/genomic data to compare the in silico predictions of hybridization performance to the actual microarray experiments are quite novel. This approach may be followed in other systems with sufficient molecular tools or genomic data resources.

Publications

  • No publications reported this period


Progress 01/01/06 to 12/31/06

Outputs
Fresh tissue and RNA of target species have been acquired. Statistical design of the microarray experiments have been developed in collaboration with faculty from the Section of Statistical Genomics at UAB. DNA-DNA hybridization experiments have been developed as controls for the RNA-level expression analysis. An additional analysis, comparing sequence level divergence from 10,000 ESTs of wild species to the Vitis vinifera genome has been developed to compare the performance of microarray chips to this in silico experiment.

Impacts
Grapevine cultivars that have the highest quality of fresh and dried fruit lack disease and stress resistance. The identification of resistance genes in native species will ultimately limit the need for fungicides and pesticides that have environmental and health safety issues associated with their use. Methods that seek to discover genes of agronomic importance are a key element in the continued improvement of agriculture in Alabama. The research proposed here will contribute greatly to our understanding of key agronomic traits of muscadine and bunchgrapes - increasingly important specialty crops in Alabama.

Publications

  • No publications reported this period