Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery

Ramil Mauleon,Kenneth Mcnally,Ruaraidh Sackville-Hamilton,Hei Leung,Richard Bruskiewich

doi:10.1038/npre.2010.5114.1

Ramil Mauleon, Kenneth Mcnally + Show 3 more

Open Access

https://doi.org/10.1038/npre.2010.5114.1

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Abstract

AbstractRice diversity is the foundation for rice improvement programs. At IRRI, over 100,000 rice accessions are deposited, and intelligent use of this diversity can not only help solve current production problems but also create future production opportunities and tackle climate change challenges. To fully explore and utilize rice diversity, two ingredients are needed: 1 - the genetic blueprints of diverse rice accessions in use, 2 - plant populations with recombined genotypes allowing expression of phenotypic variation and discovery of new genes/QTLs for use in breeding programs. Sequencing of the genomes & obtaining SNP genotypes of many rice accessions is feasible due to decreasing cost of advanced DNA sequencing technologies. Coupled with the creation of populations suitable for trait dissection / phenotyping, discovery of gene functions and allelic variations causal to important agronomic traits becomes possible. This in turn will provide rich biological evidences to the rice/cereal crop genome annotation community.

Highlights

Precise phenotyping of traits in target environments for an integrated Rice Diversity Platform
IRRI contributing to Rice SNP consortium webpage:
Sample from the Rice SNP set of 2500 lines for subsets targeted to specific traits and environments

Summary

C4 Rice

1.2: Characterizing genetic diversity and creating novel gene pools & associated informatics. Genotype 2500 rice lines spanning range of diversity o 2000 – IRRI; 500 – NSF-AFRI (groups 1,2,3). Precise phenotyping of traits in target environments for an integrated Rice Diversity Platform (group 4). With QC by 384 plex SNPs Resolve choices (remove duplicates) by using SNP fingerprints. IRRI contributing to Rice SNP consortium webpage:. List of germplasm accessions being purified 384-plex SNP chips specific for different varietal groups Training workshops for SNP analysis. Working with Susan McCouch (Cornell University) to develop custom 384-plex SNP sets (Illumina BeadXpress) for different subgroups:. In-house functional SNP assays (fewer SNPs by many lines) Improve data quality by implementing barcoding and LIMS. Sample from the Rice SNP set of 2500 lines for subsets targeted to specific traits and environments.

89 Genomes sequenced by Illumina for chip design

Jahn et al Colorado State Univ IRRI