Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

By Chih-Wei Tung, Keyan Zhao, Mark H. Wright, M. L. Ali, Janelle Jung, Jennifer A. Kimball, W. Tyagi, M. Thomson, Kenneth L. McNally, H. Leung and 8 more. Rice, 2010

89 citations recorded by the source corpus.

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 custom-designed 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 long-term 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.

View Paper: https://www.semanticscholar.org/paper/372fe69194d42b343f4e1e295e14fb9d451d7017

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. M. Thomson
2. G. Eizenga
3. Keyan Zhao
4. Chih-Wei Tung
5. A. McClung
6. J. Cobb
7. Susan McCouch
8. G. DeClerck

Citations in the corpus

• Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement (2013, background): “The tremendous innovation in genomics technology over the last two decades has been driven by multi-faceted collaborations between chemists, biologists and engineers, and today, costs continue to decline while accuracy and throughput continue to increase (Elshire et al. 2011; Tung et al. 2010).”
• High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform (2011, methodology): “Thus SNP markers are now rapidly overtaking SSRs due to new SNP genotyping platforms that offer multiplexed sets of markers for different applications, making it feasible to mainstream MAS into conventional breeding programs.”
• High-Throughput SNP Genotyping to Accelerate Crop Improvement (2014, background): “At each step, the SNP validation efforts of the previous generation helped to eliminate problematic SNP markers and narrow down sets of robust, evenly spaced, high quality SNPs for diversity analysis and genome-wide scans (Tung et al. 2010).”
• Development of genome-wide SNP assays for rice (2010, background): “…re-sequencing is necessary to enlarge the SNP-discovery pool and more adequately represent the range of natural variation found in rice and its closest ancestors, as well as to identify SNPs within individual gene pools of interest to plant breeders (Tung et al. 2010, Yamamoto et al. 2010).”