Special Topic : Rice Breeding Research , rethink and revolutionize rice breeding : an interview with Qifa Zhang

More than 100 Nobel laureates recently signed a letter urging Greenpeace to end its opposition to genetically modified organisms (GMOs). With an ever-increasing demand for food, China finds itself confronted with the same question: is it time to rethink and reassess its stance towards GMO? Rice is one of the most important food crops in China and around the world. In recent years, Chinese scientists have made important progress in rice functional genomics research including identifying genes and regulatory mechanisms and platforms and technologies for breeding new varieties. However, in contrast to the progress in scientific research, the commercial, social and policy framework remains largely unresolved. National Science Review (NSR) spoke with Qifa Zhang (Zhang), Professor at Huazhong Agricultural University, Academician of the Chinese Academy of Sciences and Foreign Associate of National Academy of Sciences, USA. In this interview, Prof. Zhang shares with us his views and insights on the frontier research in rice studies and commercialization of transgenic rice in China.


Special Topic: Rice Breeding
Research, rethink and revolutionize rice breeding: an interview with Qifa Zhang

By Zisong Ma
More than 100 Nobel laureates recently signed a letter urging Greenpeace to end its opposition to genetically modified organisms (GMOs).With an ever-increasing demand for food, China finds itself confronted with the same question: is it time to rethink and reassess its stance towards GMO? Rice is one of the most important food crops in China and around the world.In recent years, Chinese scientists have made important progress in rice functional genomics research including identifying genes and regulatory mechanisms and platforms and technologies for breeding new varieties.However, in contrast to the progress in scientific research, the commercial, social and policy framework remains largely unresolved.National Science Review (NSR) spoke with Qifa Zhang (Zhang), Professor at Huazhong Agricultural University, Academician of the Chinese Academy of Sciences and Foreign Associate of National Academy of Sciences, USA.In this interview, Prof. Zhang shares with us his views and insights on the frontier research in rice studies and commercialization of transgenic rice in China.

NSR:
First of all, could you describe the principal aspects of progress in rice research and breeding in recent years?Zhang: Rice was the first crop to be whole-genome sequenced, and is also the model plant for functional genomics research.With the development of high-throughput techniques in recent years, significant progress has been achieved in rice omics platforms, re-sequencing, functional gene cloning and analysis of regulatory networks.These can be briefly summarized as follows.
(i) Established a saturated mutant library/database of rice.Currently, there are over 670 000 lines of various types of insertion mutants, and ∼300 000 insertions can be uniquely mapped in the genome.Based on the current annotation of 56 797 genes in the rice genome, the mutants are estimated to have tagged ∼70% of the rice genes.(ii) Developed the NGS (next-generation sequencing)-based high-throughput genotyping platform.Zhang: High-yield records have been frequently refreshed under specific experimental conditions, for instance, Madagascar set a record of 21 tons per hectare, while the yield reached 18 tons per hectare in Yongsheng County (Yunnan Province) a few years ago.There have been many examples that manipulating a single gene can greatly increase the yield of a rice plant under certain genetic backgrounds, like in the cases of Ghd7 or Ghd8 that we showed.However, it is not easy to further improve the yield level for varieties that are already producing an excellent yield.
The maximum yield potential of rice per unit area has been explored for years.From my personal perspective, there should be an upper limit.Many factors should be considered when discussing this issue.Currently, light-use efficiency (LUE) is often discussed, and is believed to be an important factor in increasing the yield by improving the LUE value.This may be correct at certain stages.However, with advance in breeding, perhaps the biggest constraint is the field capacity, or specifically, population structure and suitable plant type.How to design the population structure and plant type to maximize LUE and yield in a specific area should be simulated and estimated in rice 'design breeding'.NSR: Improving yield is one of the main objects for rice breeding.However, the goals of breeding can vary in different countries, even different regions.What are the plans and goals for rice breeding in China?Zhang: For a long time, rice production in China has faced a number of problems, including: (i) stagnated yield level per unit area; (ii) damages by insects and diseases and overapplication of pesticides, and pressures for high yield and excessive use of chemical fertilizers, leading to sharp contradiction between resources, environment and agriculture production; (iii) frequent drought and shortage of water resources; and (iv) extreme weather conditions.These issues pose a severe challenge to rice production and the sustainable development of agriculture.China advocates green development as its long-term Downloaded from https://academic.oup.com/nsr/article-abstract/3/3/328/2236607 by guest on 14 February 2019 INTERVIEW goal.We proposed the concept of Green Super Rice (GSR), breeding new varieties with traits of resistance to diseases and insects, tolerance to drought and stress, nutrient efficiency, while achieving high yield and good quality by integrating genomics, molecular technologies with germplasm resources.Development and utilization of GSR varieties are expected to reduce the use of pesticides, fertilizers and water but still ensure high quality and yield, leading to resource-efficient and environmentfriendly crops.
Meanwhile, through rice breeding, we should aim to meet the demands for nutritional quality, addressing functional components that improve human health and nutritional status.Moreover, rice breeding should also consider the needs arising from transforming from traditional to modern, mechanized agriculture.The goals of breeding and related technologies should also always adjust according to the real needs in different situations.At the government level, the regulation system for varietal approval should also be timely adjusted to meet these needs.NSR: How will the new technology (such as CRISPR, etc.) influence the rice research and breeding?Zhang: With the rapid development of biotechnology, new gene manipulation techniques are constantly emerging.Gene (genome)-editing techniques, like CRISPR, displaying powerful features and a wide range of application potential, will have a profound influence on research and breeding of crops.Specifically, in basic research, new gene (genome)-editing techniques make it easy to inactivate or activate any endogenous genes.These techniques have now been widely used in functional genomics research.Regarding the application of new technology in breeding, genetic variation introduced by gene-editing techniques or by conventional breeding techniques do not differ at the molecular level.We are unable to distinguish them with current technology, which means that we can use GMO technology to produce non-GMO products, to expedite breeding.There is great consensus that the genome-editing technique in breeding The hurdle, however, is that although the MOA issued the biosafety certificate, they have yet to introduce administrative measures for approving GM rice varieties.
-Qifa Zhang has significant potential; however, large-scale application may still be years away.NSR: Could you briefly describe the process from laboratory bench to commercial application when breeding rice?Zhang: Let us take transgenic rice as an example.After obtaining the transgenic lines in the laboratory, we need to complete a pilot test, an environmental release experiment and pre-production test in the field with gradually increasing scale.During this time, a full environmental assessment, and food and feed safety assessment must also be completed, in order to apply for the biosafety certificate.After receiving the biosafety certificate, crop varietal approval still needs to be applied.Furthermore, production permit for genetically modified seeds and business licenses are a must for successful commercialization.Assuming all these processes are completed smoothly, the whole procedure takes at least 10 years.
In 2009, the Ministry of Agriculture (MOA) issued biosafety certificates for two transgenic rice lines (Huahui No.1 and Bt.Shanyou 63) expressing an insecticidal gene.In fact, we obtained the transgenic materials in 1998, and in 1999 these two lines were evaluated by an Expert Committee organized by MOA, demonstrating very good field resistance to the targeted insects.During the last decade, in cooperation with breeding institutions throughout China, Huahui No.1 was used as the gene donor to produce a large batch of insect-resistant, high-yield, good-quality hybrid rice series, which are ready for commercial production.The hurdle, however, is that although the MOA issued the biosafety certificate, they have yet to introduce administrative measures for approving GM rice varieties.
Data released in 2014 by the United States Department of Agriculture showed that the commercialization of transgenic insect-resistant corn reduces the use of pesticides by 90% in United States corn production.If the China insect-resistant rice is successfully commercialized, it should also have a similar effect.Recently, the FDA of USA approved transgenic apple and transgenic salmon.The introduction of these two foods did not cause any social uproar or protest.Thus, we should address the concerns within Chinese society and actively promote the development and industrialization of GMO in China.Developing GMO can overcome the technical bottleneck of crop improvement and meet the food security challenges we face.
This is the first phenotype measurement facility for rice.(v) Developed rice whole-genome SNP array chips.Based on genome sequencing and functional genomics research, the rice whole-genome SNP arrays (RICE 6K, and 60K and 90K) for genomic breeding have been developed with China's own intellectual property rights.(vi) Identified a large number of functional genes for agronomic traits and their regulatory networks.This is the area with very tense competition internationally.I would first mention a few examples of the results outside China.A series of genes regulating rice yield has been characterized in different contexts.For example, overexpression of OsglHAT1 resulted in an increase of grain weight and yield.The resistance-related gene DRO1 and HYR can increase rice yield under drought stress.The gene OsFIE2 In the last five years, papers published by Chinese scientists account for ∼40% of papers on rice genes in high-profile journals like Cell, Nature, Science, Nature Genetics, Nature Biotechnology, Plant Cell, PNAS etc., clearly marking the great stride by Chinese scientists in rice genomics.NSR: As you mentioned, gene modification can significantly increase rice yield.What is the current maximum rice yield under laboratory conditions?Is there a theoretical maximum value of unit yield?
regulates grain filling.Also, the root structure gene SPIKE and photosynthetic carbon metabolism gene TGW6 were cloned.Stress-related genes such as OsPIL1, PSTOL1, RSS1, HST1 were found to resist different stresses including droughts, low phosphorus and salt.A new salt-tolerant rice cultivar Kaijin was developed.Progress has also been made in identifying genes involved in regulating contents of metal elements and trace elements in rice.Scientists in China have made tremendous progress in cloning agronomically important genes, many of which hold great promise in breeding application.In particular, they uncovered a novel mechanism of strigolactone signal transduction that regulated rice tillering, establishing the molecular network that may facilitate breeding rice varieties with ideal plant architecture.A study on the S5 locus for indica-japonica hybrid sterility and wide compatibility illustrated a mechanism for regulating intersubspecific hybrid fertility, thus laying the foundation for utilizing heterosis between rice subspecies.A QTL for cold tolerance was identified, which revealed the mechanism why the allele from 'japonica' rice was more tolerant to cold than allele from 'indica' rice, which may also be