Although rice productivity has more than doubled in recent decades, an additional 25% increase is needed by 2030 to meet the demands of a growing population.
The increase has to be achieved with less land, water and under more severe environmental stresses due to climate change, according to the International Rice Research Institute (IRRI). Accelerated genetic gains are needed to improve yield potential, stability and grain quality of rice. But rice has large within-species genetic diversity and varietal group differentiation, making it a tough grain to crack.
More complete knowledge of the genetic diversity in the gene pool and associations of diverse alleles with important rice traits are needed so that rice improvements can be made using breeding strategies, IRRI said.
Researchers are trying to make that a reality with the release this October of new data from the 3,000 Rice Genomes Project (3K RGP), an international research program that has sequenced 3,024 rice varieties from 89 countries. The genomes were re-analyzed against five popular varieties that represent the three main subgroups of cultivated rice — indica, japonica and aus.
The results, which come in at a massive 120 terabytes, are now publicly available online as an Amazon Web Services (AWS) Public Data Set. Access to the data is free, and is governed by the stipulations for data analysts and users from the Toronto Statement. Funding for the research was provided by the Global Rice Science Partnership.
“The dataset provides access to millions of genetic markers that can be used to design sustainable crops for the future, that is, ones that are high yielding and more nutritious while at the same time requiring less water, fertilizer and pesticides,” said Rod Wing, director of the Arizona Genomics Institute at the University of Arizona, Tucson, Arizona, U.S., and a pioneer in rice genome sequencing.
3,000 rice GENOMES project
Rice diversity is massive — there are more than 230,000 germplasm accessions of rice maintained in genebanks worldwide. The International Rice Genebank of the T.T. Chang Genetic Resources Center at the International Rice Research Institute (IRRI) in the Philippines alone contains more than 127,000 rice accessions from all over the world. An accession is a collection of plant material from a particular location, and it is assigned an identification number.
These accessions have genes/traits that can be used to make rice cultivation more sustainable, with a smaller environmental footprint. Traits targeted for improvement include higher nutritional quality; tolerance of pests, diseases, and environmental stresses, such as flood and drought; and reduced greenhouse gas emissions.
In an attempt to sequence some of this diversity across the rice species, the Chinese Academy of Agricultural Sciences (CAAS), the Beijing Genomics Institute (BGI) Shenzhen and the IRRI launched in 2012 the 3K RGP program.
The three research institutions have sequenced 3,024 rice varieties that are housed in IRRI and CAAS genebanks. Funding was provided by grants from the Bill & Melinda Gates Foundation and the Chinese Ministry of Science and Technology.
The varieties chosen for sequencing include most rice mega-varieties growing in large areas of different ecosystems throughout Asia, according to the IRRI. Parental lines of popular varieties and selected genetic mapping populations were also included. Researchers said this approach should capture most of the genetic variation in rice.
The resulting 3K RGP dataset has millions of genomic sequences from a diverse set of rice varieties. A large part of the project is to link the genetic information to the physical traits of the different accessions. Researchers will have to assess each of the accessions for the desired traits, which breeders can then link to genetic markers in the available genome sequences from 3K RGP.
IRRI hopes this will speed the traditional breeding process, which has remained virtually unchanged. In the past, breeders would make crosses based on physical traits they observed, hoping the offspring would have the desired traits. Often, time-consuming trial and error was necessary with multiple generations, before they saw success.
Now, with the genetic information of specific rice accessions in hand, breeders and researchers can make more informed choices when crossing varieties. This could result in faster development of rice varieties suited for poor and environmentally stressed areas around the world, IRRI said.
“Through the Global Rice Science Partnership (GRiSP), IRRI is leading the development of an informal global effort — the International Rice Phenotyping Network — to systematically evaluate the 3K RGP sequenced lines and to connect plant performance to specific genes,” Hei Leung, IRRI principal scientist told IRRI’s Rice Today in 2014. “By closely integrating these resources into breeding programs based on modern molecular breeding and selection strategies, varietal development in hundreds of rice breeding programs will be accelerated over the next five years, delivering improved varieties to farmers and consumers at a faster pace than before.”
Data access and analysis tools for the 3K RGP are being made available through the International Rice Informatics Consortium (IRIC). One of the tools, the SNP-Seek database, provides user-friendly access to a type of genetic marker called single nucleotide polymorphisms identified from the data.
Another tool in SNP-Sneek, the JBrowse genome browser, displays chromosome-specific SNP data derived from the set.
“The great thing about the release of this dataset is that it is immediately useable,” said Kenneth McNally, senior scientist in IRRI’s T.T. Chang Genetic Resources Center and a project team member. “It comes with tools to help researchers visualize and analyze genetic information.”
Wing said the dataset is a powerful tool that will unite researchers from around the world, and help drive the next green revolution.
Researchers are reviewing the results from the 3,024 genomes currently sequenced, and will determine if they can identify enough critical genes for rice improvement.
“At that point, we will decide how many more of the remaining 180,000 accessions in the IRGC and CAAS genebanks we may need to sequence and analyze,” Leung said.
The IRRI also gave the genomes to the International Treaty on Plant Genetic Resources for Food and Agriculture, which is working to create an international system for storing genetic data of food crop seeds.
In October, delegates from the Food and Agriculture Organization-based treaty agreed to proceed with creation of a Global Information System (GLIS). World governments and organizations are storing genetic material in seed banks, but without a single source to the data, it is difficult for researchers and plant breeders to know what is held where, FAO said.
“The genetic information that IRRI is making available to us, and the public at large, is a hugely generous and significant show of support to our endeavors to make all relevant information on genetic resources on plant crops available for future food security,” said Shakeel Bhatti, secretary of the international treaty.
Bhatti said the global system will contain a virtual gene library that will include data from seed banks, research centers and farmers’ organizations. The IRRI rice genomes were the first contribution to the system.
“It is going to take time to get it fully functional because of the vast array of interests involved, but it will greatly facilitate the work of all the actors along the seed value chain, in developing and developed countries,” Bhatti said.