Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)

Chih Wei Tung; Keyan Zhao; Mark H. Wright; M. Liakat Ali; Janelle Jung; Jennifer Kimball; Wricha Tyagi; Michael J. Thomson; Kenneth McNally; Hei Leung; Hyunjung Kim; Sang Nag Ahn; Andy Reynolds; Brian Scheffler; Georgia Eizenga; Anna McClung; Carlos Bustamante; Susan R. McCouch

doi:10.1007/s12284-010-9056-5

Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)

Chih Wei Tung, Keyan Zhao, Mark H. Wright, M. Liakat Ali, Janelle Jung, Jennifer Kimball, Wricha Tyagi, Michael J. Thomson, Kenneth McNally, Hei Leung, Hyunjung Kim, Sang Nag Ahn, Andy Reynolds, Brian Scheffler, Georgia Eizenga, Anna McClung, Carlos Bustamante, Susan R. McCouch

Agronomy and Plant Genetics

Research output: Contribution to journal › Article › peer-review

70 Scopus citations

Abstract

We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype-genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a customdesigned Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our longterm goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.

Original language	English (US)
Pages (from-to)	205-217
Number of pages	13
Journal	Rice
Volume	3
Issue number	4
DOIs	https://doi.org/10.1007/s12284-010-9056-5
State	Published - Dec 2010

Bibliographical note

Funding Information:
With financial support from the collaborators around the world (www.ricesnp.org), we are currently re-sequencing 100–150 accessions of wild and cultivated Asian and African rice using Illumina GAII technology. Accessions are selected to represent the diversity of O. sativa, O. rufipogon/O. nivara, O.glaberrima and O. barthii and we are generating 5–55× genome coverage for each. A parallel effort is being undertaken for other wild Oryza genomes as part of the OMAP project by the Wing lab (http://www.omap.org/). These re-sequencing efforts are providing the plant breeding community with vital information about the distribution and frequencies of SNP alleles within and between populations of both wild and cultivated materials. This information will allow us to undertake evolutionary and population genetics analyses enabling the selection of the most informative SNPs for targeted applications in genetics, breeding and germplasm management.

Keywords

Chromosome segment substitution lines
Genome-wide association mapping
Linkage disequilibrium
Oryza rufipogon
Oryza sativa
Rice phenotyping
SNP genotyping

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Tung, C. W., Zhao, K., Wright, M. H., Ali, M. L., Jung, J., Kimball, J., Tyagi, W., Thomson, M. J., McNally, K., Leung, H., Kim, H., Ahn, S. N., Reynolds, A., Scheffler, B., Eizenga, G., McClung, A., Bustamante, C., & McCouch, S. R. (2010). Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice, 3(4), 205-217. https://doi.org/10.1007/s12284-010-9056-5

Tung, CW, Zhao, K, Wright, MH, Ali, ML, Jung, J, Kimball, J, Tyagi, W, Thomson, MJ, McNally, K, Leung, H, Kim, H, Ahn, SN, Reynolds, A, Scheffler, B, Eizenga, G, McClung, A, Bustamante, C & McCouch, SR 2010, 'Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)', Rice, vol. 3, no. 4, pp. 205-217. https://doi.org/10.1007/s12284-010-9056-5

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abstract = "We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype-genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a customdesigned Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our longterm goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.",

keywords = "Chromosome segment substitution lines, Genome-wide association mapping, Linkage disequilibrium, Oryza rufipogon, Oryza sativa, Rice phenotyping, SNP genotyping",

author = "Tung, {Chih Wei} and Keyan Zhao and Wright, {Mark H.} and Ali, {M. Liakat} and Janelle Jung and Jennifer Kimball and Wricha Tyagi and Thomson, {Michael J.} and Kenneth McNally and Hei Leung and Hyunjung Kim and Ahn, {Sang Nag} and Andy Reynolds and Brian Scheffler and Georgia Eizenga and Anna McClung and Carlos Bustamante and McCouch, {Susan R.}",

note = "Funding Information: With financial support from the collaborators around the world (www.ricesnp.org), we are currently re-sequencing 100–150 accessions of wild and cultivated Asian and African rice using Illumina GAII technology. Accessions are selected to represent the diversity of O. sativa, O. rufipogon/O. nivara, O.glaberrima and O. barthii and we are generating 5–55× genome coverage for each. A parallel effort is being undertaken for other wild Oryza genomes as part of the OMAP project by the Wing lab (http://www.omap.org/). These re-sequencing efforts are providing the plant breeding community with vital information about the distribution and frequencies of SNP alleles within and between populations of both wild and cultivated materials. This information will allow us to undertake evolutionary and population genetics analyses enabling the selection of the most informative SNPs for targeted applications in genetics, breeding and germplasm management.",

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AU - Kimball, Jennifer

AU - Tyagi, Wricha

AU - Thomson, Michael J.

AU - McNally, Kenneth

AU - Leung, Hei

AU - Kim, Hyunjung

AU - Ahn, Sang Nag

AU - Reynolds, Andy

AU - Scheffler, Brian

AU - Eizenga, Georgia

AU - McClung, Anna

AU - Bustamante, Carlos

AU - McCouch, Susan R.

N1 - Funding Information: With financial support from the collaborators around the world (www.ricesnp.org), we are currently re-sequencing 100–150 accessions of wild and cultivated Asian and African rice using Illumina GAII technology. Accessions are selected to represent the diversity of O. sativa, O. rufipogon/O. nivara, O.glaberrima and O. barthii and we are generating 5–55× genome coverage for each. A parallel effort is being undertaken for other wild Oryza genomes as part of the OMAP project by the Wing lab (http://www.omap.org/). These re-sequencing efforts are providing the plant breeding community with vital information about the distribution and frequencies of SNP alleles within and between populations of both wild and cultivated materials. This information will allow us to undertake evolutionary and population genetics analyses enabling the selection of the most informative SNPs for targeted applications in genetics, breeding and germplasm management.

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N2 - We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype-genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a customdesigned Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our longterm goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.

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ER -

Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.)

Abstract

Bibliographical note

Keywords

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