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United States Department of Agriculture

Agricultural Research Service

Research Project: Mississippi Rice Variety Acceleration Breeding Project Proposal - Phase 2

Location: Genomics and Bioinformatics Research Unit

2012 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 resequencing data was generated using a number of lines during the year. The lines processed for DNA extraction and put onto a next generation DNA sequencer were: Saber, Dixiebelle, Carolina Gold Select, Hidalgo, Sabine, Deltabelle, Carolina Gold, Bengal and IAC 600. To date the data is in the bioinformatics pipeline so no conclusion can be made about the amount or quality of sequence data generated at this time. However, data generated from previous years work, which was in part supported by the Mississippi Rice Promotion Board, has been released and published in two separate publications. The first represents an international effort to develop and validate a cheap and efficient DNA marker technology to enhance rice breeding efforts. This technology could be used for rapid incorporation of traits into existing cultivars or assist with the integration traits from exotic germplasm. The second deals with the candidate gene identification of genes associated with sheath blight resistance. While this type of analysis is still in it's infancy the paper does demonstrate the power of the technology and gives hope to the idea that genes associated with important traits can be found more quickly and thus utilized to improve rice cultivars.

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 2011 appears to have been more targeted compared to the past and seems to be having a larger impact on the breeding program. However the full impact of the marker data can only be evaluated by the collaborators. To date, 2,784 plant samples have been processed to generate 3,648 genotype data points. All samples were genotyped with the marker for amylose content and a subset of these were genotyped with all known blast resistance markers. Single panicle samples from the 2011 growing season were submitted in January/February to ascertain purity before planting. This type of analysis will assist in making the MSU breeding program more efficient as impure lines can be targeted for purity improvement in the field while more pure lines can be fast tracked for more in depth evaluation. Participants are in the same location and often converse through face to face meetings or phone conversations.


Last Modified: 11/27/2014
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