Review Article | Published:

The rice genome revolution: from an ancient grain to Green Super Rice

Nature Reviews Geneticsvolume 19pages505517 (2018) | Download Citation

Abstract

Rice is a staple crop for half the world’s population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.

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Nature Reviews Genetics thanks Guo-Liang Wang, Jean Christophe Glaszmann, and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

Africa Rice: http://www.africarice.org/warda/genebank.asp

Consultative Group and International Agricultural Research (CGIAR): https://www.cgiar.org/

Ensemble Plants: http://plants.ensembl.org/index.html

funRiceGenes: http://funricegenes.ncpgr.cn/

GenBank: https://www.ncbi.nlm.nih.gov/assembly/?term=Oryza

Global Rice Phenotyping Network: http://ricephenonetwork.irri.org/

Gramene: http://oge.gramene.org/genome_browser/index.html

International Center for Tropical Agriculture (CIAT): http://ciat.cgiar.org/

International Rice Genebank: http://irri.org/our-work/research/genetic-diversity/international-rice-genebank

International Rice Informatics Consortia (IRIC): http://iric.irri.org/

International Rice Research Institute (IRRI): www.irri.org

Rice Annotation Project (RAP): http://rapdb.dna.affrc.go.jp/

Michigan State University DB (MSU-DB): http://rice.plantbiology.msu.edu/

Oryzabase: https://shigen.nig.ac.jp/rice/oryzabase/

Rice Information GateWay (RIGW): http://rice.hzau.edu.cn/cgi-bin/rice/download_ext

R498 at MBKBASE: www.mbkbase.org/R498

Rice Diversity database: http://www.ricediversity.org/data/index.cfm

SNP-Seek: http://snp-seek.irri.org/

TERRA-REF Field Scanalyzer in Arizona: www.terraref.org

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Acknowledgements

R.A.W. was supported by the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, the AXA Research Fund and NIFA-HATCH ARZT-1360510-H25-230. M.D.P. was supported by grants from the US National Science Foundation Plant Genome Research Program, the Zegar Family Foundation and the New York University Abu Dhabi Research Institute. Q.Z. was supported by grants from the National 863 Program 2104AA10A604, the National Key Research and Development Program 2016YFD0100903, the Earmarked Fund for the China Agriculture Research System of China (CARS-01-05) and the Bill and Melinda Gates Foundation. The authors also thank K. McNally and S. Klassen for critically reading the manuscript prior to publication.

Author information

Affiliations

  1. University of Arizona, Tucson, AZ, USA

    • Rod A. Wing
  2. International Rice Research Institute, Los Baños, Philippines

    • Rod A. Wing
  3. New York University, New York, NY, USA

    • Michael D. Purugganan
  4. New York University Abu Dhabi, Abu Dhabi, United Arab Emirates

    • Michael D. Purugganan
  5. Huazhong Agricultural University, Wuhan, China

    • Qifa Zhang

Authors

  1. Search for Rod A. Wing in:

  2. Search for Michael D. Purugganan in:

  3. Search for Qifa Zhang in:

Contributions

All authors contributed to all aspects of writing this Review.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Rod A. Wing or Qifa Zhang.

Supplementary information

Glossary

Lodging resistance

The ability of plants to withstand high-velocity winds, such as those from annual typhoons in the tropics. Typically, lodging resistance occurs by breeding for stiffer stalks, short stature or both.

Heterosis

Also known as hybrid vigour. A phenomenon whereby the hybrid produced by crossing two genetically distinct breeding lines (normally inbred) agronomically outperforms each of its parents (for example, in terms of higher yield and faster growth).

Genomic breeding

Approaches that use the data, knowledge, resources, genes and technologies generated by genomic research to enhance breeding programmes.

Genome types

The Oryza genus is composed of ~27 extant species that harbour 11 distinct genome types (GTs), 6 of which are diploid (n = 12; GTs: AA, BB, CC, EE, FF and GG) and 5 of which are polyploid (n = 24; GTs: BBCC, CCDD, HHJJ, HHKK and KKLL). These GTs were defined based on cytogenetics (that is, chromosome number, size and shape), fluorescence in situ hybridization (FISH) and genetic hybridization.

Introgression

The transfer of genes and genomic segments from one species or population to another through hybridization.

Field phenotyping

The use of state-of-the-art sensor and camera systems, mounted on tractors, gantries and drones, to measure plant phenotypic traits (such as height, leaf angle, 1,000-grain weight, disease pressure and canopy temperature, among others) over the course of a growing season.

Reference genomes

Also referred to as a reference sequence (RefSeq). A genome assembly that is used to represent the full genome sequence of a given organism. Ideally, a RefSeq will be gap-free and have zero sequence errors. However, genome assemblies can potentially be missing up to 50% of the full genome sequence, primarily owing to the sequencing technology used (for example, short read sequencing) and the assembly tools available.

Green Revolution

The substantial increase in grain production that began in the late 1960s and early 1970s. It was a result of widespread adoption of high-yielding wheat and rice varieties bred to incorporate semi-dwarf genes and a more systematic use of nitrogen fertilizers and pesticides.

Hybridization

The process or outcome of performing genetic crosses between individuals from distinct species or highly divergent populations.

Selective sweep

A genomic region that appears to be under natural or artificial selection. In the context of this Review, we consider it to be a region of the genome including and surrounding a domestication trait (for example, yield or grain shattering).

Abiotic stress

A stress considered to be of non-biological origin, such as heat, salt, drought, nutrient, light and dark, among others.

Genome-wide association studies

(GWAS). A mapping approach that relies on an observed statistical correlation between individual genomic variants (such as single nucleotide polymorphisms (SNPs)) and specific phenotypes in a natural population.

Artificial selection

Selection for desirable traits that is consciously and deliberately carried out by humans.

Resequencing

A technique used to sample an individual genome without the need to generate a full genome sequence. Resequencing data typically consists of short (250 bp) sequence reads at low (0.1–10-fold) genome coverage that are mapped by sequence complementarity to a reference sequence (RefSeq) to detect genetic variation (such as single nucleotide polymorphisms (SNPs) and indels) between the resequenced individual and the RefSeq.

Quantitative trait loci

(QTL). Genetic loci that contribute (positively or negatively) to non-discrete traits, such as yield, grain quality, water and heat stress.

Xian

Also known as indica, a major group of Asian cultivated rice that is widely grown in tropical and subtropical regions of Asia and is partially reproductively isolated from the geng rice.

Geng

Also known as japonica, a major group of Asian cultivated rice that is widely grown in temperate regions of Asia and other areas and is partially reproductively isolated from xian rice.

Living voucher specimens

Single-plant accessions selected to be representative of a particular species. In the case of most wild Oryza species, vouchers can be clonally propagated indefinitely.

Biotic stress

A stress considered to be of biological origin, such as plant pathogens (bacteria, fungi and viruses) and animal pests (insects and nematodes), among others.

Nucleotide binding site and leucine-rich repeat (NBS-LRR) proteins

Members of a large class of proteins encoded by many disease-resistance or insect-resistance genes (R genes) of plants. An NBS-LRR protein contains a nucleotide binding site (NBS) domain and a leucine-rich repeat (LRR) domain, which are believed to confer the specificity of resistance.

Effector-triggered immunity

A defence response that is initiated when a pathogen effector molecule is recognized by a cytoplasmically localized host nucleotide binding site and leucine-rich repeat (NBS-LRR) protein.

Pattern-triggered immunity

A defence response that is initiated when a pathogen-associated molecular pattern is recognized by the corresponding host pattern recognition receptor.

Breeding chip

A microarray that enables high-throughput genotyping and selection of offspring in breeding programmes.

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DOI

https://doi.org/10.1038/s41576-018-0024-z