Partnerships essential to produce new genomics rice hybrids for Africa

Partnerships, communication and sharing ‘big data’ technology essential in developing new Chinese Green Super Rice hybrids for Asia and Africa

Wild African rice growing in Niger. Online source, May 2020.

There are complex technological, collaborative and funding partnerships involved in producing the set off 78 new Green Super Rice (GSR) hybrid rice varieties now being tested in African and Asian rice growing countries.

Since the 2008 world food crisis, the issue of how to feed the growing human population has become more urgent. This is noting that rice is a diet staple for half the world’s population, and that increasing rice production would help to feed an even greater percentage of the human population.  However, to do this, rice production would have to increase by at least 25% by 2030 to keep pace with population growth and demand.  To do this, we will need ‘super rice’ varieties and this is where the Chinese Green Super Rice project fits in – growing high-yielding rice varieties that are resistant to pests, diseases and droughts and that will increase farmer yields. The new rice hybrids must be able to cope with often challenging current conditions. The technology must also allow for the on-going development of rice hybrids that can cope with future climate change growing conditions. Developing those high-producing rice varieties involved rice germplasm collections, complex genomic methodologies and many different partners.

The Green Super Rice (GSR) project is a partnership between the Chinese Academy of Agricultural Sciences (CAAS), the International Rice Research Institute (IRRI) and the BGI Genomics in China. The Chinese Academy of Agricultural Sciences (CAAS) is a scientific research organization with a mission of implementing basic and applied research, as well as research into new technologies that have an impact on agriculture, while IRRI is an independent, non-profit, research and educational institute, founded in 1960 by the Ford and Rockefeller foundations with support from the Philippine government. BGI Genomics is the Beijing Genomics Institute, a Chinese genome sequencing company, formed in 1999 to participate in the Human Genome Project as a genetics research centre.  The Chinese Green Super Rice project is funded by the Chinese government and the Bill & Melinda Gates Foundation (BMGF), with the BMGF investing $18 million in the project.

What is hybrid rice?

`Hybrid crop plants are produced by crossing two inbred varieties of a particular crop, with the resulting offspring having heterosis (hybrid vigour)  and superior  traits in terms of agronomic properties. As a result of heterosis, hybrid rice has a yield of 15‒20% over the best inbred variety grown under the same conditions. However, rice is difficult to hybridise by conventional cross-pollination and new selections are made by simply searching for better-producing plants. Rice has a huge range of within-species genetic diversity so thousands of variants do exist.

In the 1970s, Chinese researchers discovered a mechanism which allowed the cross-breeding of rice to create new varieties, and more recently, genotype analysis and molecular plant breeding allows for almost unlimited mixing and matching of rice genes.  Even with this mechanism (cytoplasmic male sterility), rice breeding and selection was difficult because of the vast array of traits and it was difficult to select superior varieties against a back ground of unknown genetic diversity.  This why it became essential to find out more about the genetic diversity in the Oryza sativa (Asian rice) gene pool and investigate how the many diverse alleles connect with important rice traits. This was the ultimate purpose of the ambitious 3000 Rice Genomes Project,  with the idea that the more systematic use of genomic data could be used along with conventional rice breeding strategies to search for better adapted rice varieties.  Molecular plant breeding methods also allow new rice varieties to be developed within four to six years, rather than ten to twelve years using conventional plant breeding.

The 3000 Rice Genomes Project  (3K RGP)

The 3000 Rice Genomes Project is a collaborative project that carried out the sequencing of 3 024 Oryza sativa  (Asian) rice genomes selected from 89 countries in order to create as massive sequence dataset. From gene sequencing efforts, approximately 18.9 million single nucleotide polymorphisms (SNPs) in rice were discovered along with knowledge that the Oryza sativa gene pool into five varietal groups.  This meant that researchers at last understood the perplexing genomic diversity within O sativa.  

The 3K RGP project identified 29 million single nucleotide polymorphisms (SNPs), 2.4 million small indels (small insertions and deletions in the genome) and over 90 000 structural variations that contribute to the rice variation. Many of the SNPS are linked to novel alleles (forms of genes) important for rice phenotypes (i.e. the way genes manifest themselves in the whole plant). Using pan-genome analyses, researchers identified more than 10 000 novel full-length protein-coding genes that allowed researchers to explain many previous events in rice breeding during domestication – and will help them advance the adaptive characteristics of new rice varieties.

The huge rice genomic data set is intended to be a resource for understanding the genetic variation in rice and for the discovery of genes associated with economically important traits. This data will serve as a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or classical breeding approaches. The genomic sequences were lodged in the GigaDB.org (http://dx.doi.org/10.5524/200001) database.

The 3024 rice varieties and  lines chosen for sequencing in the 3K RGP included 2466 accessions from the rice gene bank collection at the International Rice Research Institute (IRRI) and 534 accessions from the China National Crop Gene Bank (CNCGB) at the Institute of Crop Sciences, at the Chinese Academy of Agricultural Sciences (CAAS). The work was carried out as a global public good and funded by the Bill & Melinda Gates Foundation and the Chinese Ministry of Science and Technology.

The 3K RGP was mooted as a major new approach in big-data-based crop research and digitalized plant breeding.  Because of the massive amount of data (100 TB) generated from the 3000 Rice Genomes Project, the DNAnexus platform was used to allow the integration of genetic data with other data types and has been effectively used in medical genomic research applications.  The DNAnexus platform combines cloud computing and bioinformatics, especially in a project “whose sheer volume and scope was unprecedented in the agricultural community, says DNAnexus. The genomic ‘big data’ approach creates many new rice selections for further testing in a fraction of the time that field testing and selection would take.

In 2014, the publication and release of this enormous data set was set to coincide with World Hunger Day to highlight one of the primary goals of 3K RGP  which was to develop resources that will aid in improving global food security, especially in the poorest areas of the world.

A typical genome mapping output graphic.  Source: Plant Science 242 (2015). Kurokawa et al. DOI:  10.1016/j.plantsci.2015.09.008

As part of the collaboration, seeds from each rice strain analysed by 3K RBP were stored the International Rice Genebank Collection housed at IRRI.  This ensured that the actual seeds and their genetic information remained coupled to provide genetically defined strains are available for developing the most appropriate hybrid strains for different rice growing environments, as well keeping track of field testing data. The Rice Galaxy online open resource for plant science is designed so that rice breeders with little computational knowledge can undertake sequence bioinformatics analyses by researches without computational expertise.

Rice growing in Africa. Internet source, May 2020.

What is Green Super Rice?

Green Super Rice (GSR) is set of 78 newly developed ‘super’ hybrid rice varieties bred for Asian and African small-holder farmers and developed from the 3000 Rice Genomes project.

Since 2008, AfricaRice has been involved in evaluating Chinese hybrid rice lines in sub-Saharan Africa (SSA) through the GSR project to make Chinese rice cultivars (inbred and hybrid varieties) accessible to rice farmers in Africa and Asia with the hope that GSR varieties will benefit at least 20 million smallholder rice farmers and boost rice productivity and farmer incomes in the target regions. The target regions for the GSR project include nine Asian countries (Philippines, Vietnam, Laos, Cambodia, Indonesia, Sri Lanka, Bangladesh, India, and Pakistan) and nine African countries (Mozambique, Tanzania, Rwanda, Liberia, Ethiopia, Uganda, Nigeria, Mali and Senegal).  GSR will also be tested in China, in Sichuan, Yunnan and Guizhou provinces, and Guangxi Zhuang and Ningxia Hui autonomous regions of China.  In the Philippines, GSR farmers already have an estimated income advantage of more than USD 231 per hectare, says IRRI,  and that  growing these ‘super’ rice varieties now covers more than two million hectares in 11 countries. 

The GSR project has also been involved in training of almost 60 PHD and Masters students from 15 target countries through different Chinese institutions, IRRI and AfricaRice. More than 900 scientists from the country partners received advanced training on GSR breeding and crop management. Lastly, more than 3 000 farmers received short-term training on GSR seed production and crop management.

Testing of Africa-specific GSR varieties in Africa

Testing of Africa-specific GSR varieties in Africa was channelled through AfricaRice and the agricultural research entities of the target countries in Africa (Ethiopia, Liberia, Mali, Nigeria, Rwanda, Senegal, Tanzania and Uganda) and their rice growing associations of small-holder rice growers.  Africa’s average rice yields using conventional rice are around 2 tonnes per hectare, the lowest in the world. Developing the hybrid rice technology capacity of national partners, farmers, non-government organizations, and the private sector is a major component of the AfricaRice strategy.

A road map for Green Super Rice hybrid testing, release, and dissemination in Nigeria and Mali has been developed. By the end of 2014, Mozambique, Rwanda, Tanzania and Uganda had formally released new African GSR cultivars for testing, with Mali and Senegal having new GSR cultivars in the pipeline for testing release.   By 2018, another fifteen new African Super Green Rice varieties became available for testing by smallholder farmers in seven more Africa countries.  The aim was that, once fully tested GSR cultivars are available, the GSR seed will be given to the commercial sector in each country to scale-up production of Certified Seed for farmers.  Hopefully, as the Green Super Rice project involved philanthropic funding and publicly accessible gene banks, these hybrid varieties will indeed be a ‘gift’  to poor farmers and quality seed will be affordable.

Effective communication at all levels vital in a large multi-partner agricultural R&D project

Communication for this complex and long term project was very vital, and occurred firstly at an international level, involving international researchers and regional rice-breeding entities.  Main collaborators included the Chinese Academy of Agricultural Sciences (CAAS), the International Rice Research Institute (IRRI) and its partners like AfricaRice, plus US commercial biotech suppliers who supplied the molecular breeding technology and the funder, the Bill & Melinda Gates Foundation.  The initial 3000 Rice Genomics Project data was stored on the cloud to be accessible by any international researcher or plant breeder. Also, various online DNA platforms like Galaxy Rice enabled the communication of genomic data with rice breeders with little knowledge of software development and coding, so that they could work effectively with large genomic datasets.

Within Africa, the Green Super Rice project involved a link between IRRI and AfricaRice and down the line to the national agricultural research entities of the target countries (Ethiopia, Liberia, Mali, Nigeria, Rwanda, Senegal, Tanzania and Uganda).  Communication at farm level in Africa occurred through farmer participation in field trials, farmer’s days and information sharing. In other words, there would be no direct contact between Chinese researchers and the grass-roots African stakeholders, with the attendant language and cultural challenges so often experienced at the many Chinese Agricultural Technology Demonstration Centres in Africa. 

AfricaRice is also strengthening is collaboration with strengthening its collaboration with many additional partners, particularly through its participation in the Hybrid Rice Development Consortium (HRDC) coordinated by IRRI, with aims to strengthen collaboration between the private and public sector and improve hybrid rice technology dissemination. Africa’s Rice’s African national partners also acknowledge that capacity building is urgently needed to help farmers and seed producers adopt new ‘super rice’ technology.

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