Location: Genomics and Bioinformatics Research2013 Annual Report
1a. Objectives (from AD-416):
Assist Mississippi State Rice breeding efforts through the application of DNA markers and the development of new relevant DNA markers.
1b. Approach (from AD-416):
Simple Sequence Repeat (SSR) DNA markers will be used to assist in marker assisted selection of advanced breeding lines. Second generation DNA sequencing will be used to discover relevant Single Nucleotide Polymorphism (SNP) markers in Mississippi State University (MSU) produced cultivars.
3. Progress Report:
The goals of this project were to develop techniques to rapidly and accurately test rice samples with DNA markers and then apply them to the Mississippi Breeding program. In general, advanced generations are screened for purity (homozygosity) and to determine if they carried alleles for Blast resistance. Seed quality traits like starch content and aroma also screened. Objective 1: Resequencing of the rice varieties This research is still in progress but re-sequencing data was generated using a number of lines during the year with the trait of interest for downstream analysis being chalk. Ideal rice is basically translucent but due to genetic and environmental factors the grains or portions thereof can be cloudy (known in the trade as chalky) which is undesirable. The lines processed for DNA extraction and put onto a next generation DNA sequencer were: Mermentau, CL111, Jazzman 2, Jupiter, LA2177, CL261, Della 2, LM-1, Catahoula, CL152, CL131, Jazzman, LA2013A, and LA2014B. To date the data is in the bioinformatics pipeline and analysis is proceeding with collaborators at Louisiana State University. So no conclusion can be made about the amount or quality of sequence data generated at this time, or any associations of specific genes and chalk quality. Objective 2: Genotyping of MSU rice breeding material As in the past, a major component of the research has been in the support of the Mississippi State University (MSU) rice breeding program. Working in conjunction with MSU, the application of DNA markers in 2012 resulted in 2,300 data points with each data point being a plan sample and DNA marker. Some testing was for variety confirmation, testing for varietal contamination or homogeneity of varieties under development. Varietal contamination studies were 24 hour rush jobs as the material was in Foundation Seed plots and the type of contamination could have had serious economic impact. Participants are in the same location and often converse through face to face meetings or phone conversations.