IC4R002-Microarray-2011-21915109

Project Title

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

The Background of This Project

• Understanding the genetic basis of physiological, developmental and morphological variation in domesticated Asian rice ( Oryza sativa ) is critical for improving the quality, safety, reliability and sustainability of the world ’ s food supply. Human population growth, particularly in developing countries where rice is the main source of caloric intake 1 , coupled with climate change and the intensive water, land and labour requirements of rice cultivation 2 , creates a pressing and continuous global need for new, stress tolerant, resource-use effi cient, and highly productive rice varieties. To assist in this endeavour, the scientifi c community has created a wealth of genomic and plant breeding resources, including high-quality genome sequences 3,4 , dense SNP maps 5-7 ,extensive germplasm collections 6,8,9 and public databases of genomic information.
• Despite the availability of these scientifi c resources, most of what we know about the genetic architecture of complex traits in rice is based on traditional quantitative trait locus (QTL) linkage mapping using bi-parental populations. While providing valuable insights 12 , the QTL approach is clearly not ‘ scalable ’ to investigate the genomic potential and tremendous phenotypic variation of the more than 120,000 accessions available in public germplasm reposi- tories. Genome-wide association study (GWAS) mapping makes it possible to simultaneously screen a very large number of accessions for genetic variation underlying diverse complex traits. An extra advantage of the GWAS design for rice is the homozygous nature of most rice varieties, which makes it possible to employ a genotype or sequence once and phenotype many times over strategy, whereby once the lines are genomically characterized, the genetic data can be reused many times over across diff erent phenotypes and environments.
• In this project, the researchers present a genome-wide association study in a global collection of 413 diverse rice ( O. sativa ) varieties from 82 countries using a high-quality custom-designed 44,100 oligonucleotide genotyping array. For these varieties, we systematically phenotyped 34 morphological, developmental and agronomic traits over two consecutive fi eld seasons. Our mapping strategy evaluated variation both within and among four of the major subgroups of rice, revealing significant heterogeneity of genetic architecture among groups, as well as gene-by-environment eff ects. Unlike previous GWAS studies in rice 5 , purifi ed seed stocks of the rice strains and all the genotypic and phenotypic information generated over th course of this study are publicly available, creating a valuable, open source translational research platform that can be rapidly expanded through community participation to enhance the power and resolution of GWAS in rice.

Plant Materials & Treatment

• The Rice Diversity Panel consists of 413 Asian rice ( O. sativa ) cultivars, including many landraces, which originated from 82 countries, representing all the major rice-growing regions of the world 15 . Th e panel contains 87 indica , 57 aus , 96 temperate japonica , 97 tropical japonica , 14 groupV / aromatic , and 62 highly admixed accessions. All accessions were purifi ed for two generations (single seed descent) before DNA extraction. In all, 20 of these 413 accessions were purifi ed as part of the Oryza SNP project 6 . Six cultivars (Azucena, Moroberekan, Nipponbare, Dom-Sofi d, IR64, M-202) were purifi ed separately,and once as part of the Oryza SNP panel.

Research Findings

• A rice diversity panel consisting of 413 inbred accessions of O. sativa collected from 82 countries ( Fig. 1 ; Supplementary Data 1 ) was genotyped using an Aff ymetrix single nucleotide polymorphism (SNP) array containing 44,100 SNPs (hereaft er referred to as the 44 K chip). With a genome size of ~ 380 Mb (ref. 13), this custom-designed genotyping chip provides high quality data (less than 4.5 % missing data), with ~ 1 SNP per 10 kb across the 12 chromosomes of rice. Th e diversity panel was evaluated for 34 traits related to plant morphology, grain quality, plant develop- ment and agronomic performance using fi eld-grown plants with replications within and between years.

Labs working on this Project

• Department of Biological Statistics and Computational Biology, Cornell University , Ithaca , New York 14850 , USA .
• Department of Genetics, Stanford University , Stanford , California 94305 , USA . 3 Department of Plant Breeding and Genetics, Cornell University , Ithaca , New York 14850 , USA . 4 USDA ARS,
• Dale Bumpers National Rice Research Center , Stuttgart , Arkansas 72160 , USA . 5 Rice Research and Extension Center, University of Arkansas , Stuttgart , Arkansas 72160 , USA . 6 Institute of Biological and Environmental Sciences, University of Aberdeen , Aberdeen AB24 3UU , UK . 7
• Department of Soil Science, Bangladesh Agricultural University , Mymensingh 2202 , Bangladesh .

Corresponding Author

Susan R. McCouch (email: srm4@cornell.edu ) & Carlos D. Bustamante(email: cdbustam@stanford.edu ) .