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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

Title: New high density genetic marker technology for use in breeding

Authors
item McClung, Anna
item McClung, Anna
item Zhao, K -
item Eizenga, Georgia
item Ali, M -
item Bustamante, C -
item Mccouch, S -

Submitted to: Texas Experiment Station Field Day Handout
Publication Type: Experiment Station
Publication Acceptance Date: May 30, 2010
Publication Date: July 8, 2010
Citation: Mcclung, A.M., Zhao, K., Eizenga, G.C., Ali, M.L., Bustamante, C.D., Mccouch, S.R. 2010. New high density genetic marker technology for use in breeding. Texas Experiment Station Field Day Handout.

Technical Abstract: Recent advances in genetic marker technology have enhanced our ability to evaluate rice breeding materials more quickly and with greater coverage. In 2005, as a result of an international collaboration, the japonica rice variety, Nipponbare, was the first crop plant to be completely sequenced. Subsequently, an indica cultivar was sequenced allowing comparison of the genetic differences between these two representatives of the major sub-populations which are the basis for most of the rice grown in the world. In 2008, the Oryza SNP Project, sequenced 20 world rice cultivars, two from the USA (Cypress and M202). We used these data to identify 1536 SNP markers (single nucleotide polymorphisms) and evaluated a panel of 400 diverse cultivars. The objective was to identify material that was vastly different at a genetic level to guide breeders in development of cultivars and hybrids and to find smaller chromosomal regions that were examples of specific genes that had been bred into cultivars. For example, in the tropical japonica material from the USA, a clear indica introgression on chromosome 12 was observed that was associated with the blast resistance gene Pi-ta. This type of information provides breeders with insights into marker assisted selection strategies that will conserve genomic regions or facilitate recombination. In addition, the 1536 “SNP chip” was used in collaboration with the RiceCAP project to evaluate about 400 elite cultivars from all of the US rice breeding programs. This analysis demonstrated how US breeding programs have relatively unique genepools, although there are cultivars which are clearly a synthesis of multiple breeding programs. Such detailed genomic information will be useful to breeders to help identify the best cultivars to cross to maximize genetic recombination. Although the 1536 SNP chip provided greater marker saturation than previously available, it also demonstrated that there are large linkage blocks within US cultivars that appear to have no genetic diversity. We are now developing genetic tools that will provide tens of thousands of SNP markers on any cultivar, in an effort to better map these regions. As the result of research collaborations that span the globe and bring researchers from breeding, genomics, and bioinformatics together, the US rice research community has been able to participate in the development of cutting-edge genomic technologies. The next steps will require the ability to effectively analyze massive datasets of genomic information so that these technologies can be translated into practical breeding tools. For more information contact Anna McClung 870-672-9300 ext 275, anna.mcclung@ars.usda.gov.

Last Modified: 4/19/2014
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