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Keynote Speakers

Confirmed speakers

  • Gurdev Khush, University of California, Davis, USA
  • Jiayang Li, Institute of Genetics and Developmental Biology, CAS, China
  • Makoto Matsuoka, Nagoya University, Japan
  • Naoko Nishizawa, University of Tokyo, Japan
  • Rod Wing, University of Arizona, USA
  • Guo-Liang Wang, Ohio State University, USA
  • Yunde Zhao, University of California San Diego, USA
  • Guiderdoni Emmanuel, CIRAD, France
  • Dao-Xiu Zhou, Institute of Plant Sciences, Paris-Saclay, France
  • Qifa Zhang, Huazhong Agricultural University, China
  • Dabing Zhang, Shanghai Jiao Tong University, China
  • Bin Han, National Center for Gene Research, Shanghai, China
  • Yue-ie Hsing, Academia Sinica, Taiwan
  • Su-May Yu, Academia Sinica, Taiwan
  • Letian Chen, South China Agricultural University, China
  • Xiangdong Fu, Institute of Genetics and Developmental Biology, CAS, China
  • Ju-Kon Kim, Seoul National University, Korea
  • Nam-Soo Jwa, Sejong University, Korea
  • Wanqi Liang, Shanghai Jiao Tong University, China
  • Anna Joe, University of California Davis, USA
  • Jun Liu, Institute of Microbiology, CAS, China
  • Narottam Dey, Visva-Bharati University, India
  • Dong-Yup Lee, National University of Singapore, Singapore
  • Sichul Lee,Institute for Basic Science
  • Yuese Ning, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, China

Abstract

Gurdev Khush

From Mendelian Genetics to Rice Functional Genomics Advances during hundred and ten years

1908 First Mendelian Segregation
1910 Discovery of Chromosome No
1917 First Linkage in Rice
1943 First Publication of Rice Gene Symbols
1960 Rice Pachytene Karotype
1960 Linkage Groups
1980 Rice Trisomics
1984 Association of linkage groups with Chromosomes
1985 First International Rice Genetics Symposium
1985 Establishment of Rice Genetics Cooperative
1985 International Program on Rice Biotechnology
1988 First Molecular Genetic Map
1990 Uniform System of Numbering Rice Chromosomes
1991 Rice Genome Research Program (RGRP)
1998 International Network on Rice Genome Sequencing
2000 Functional Genomics of Rice
2005 First Domplete Genome Sequence of Rice

Jiayang Li

Ideal Plant Architecture 1: its regulatory network and application in breeding

Rice is one of the most important staple crops and also functions as an ideal model system for cereals. How to increase yield and improve quality has been one of the most challenging tasks for rice researchers and breeders. Plant architecture is a primary determinant of crop yield. Ideal Plant Architecture 1 (IPA1) encodes a key transcription factor having pleiotropic effects on regulating plant architecture in rice and substantially enhances grain yield. IPA1 expression is controlled at the post-transcriptional level by microRNA156 and microRNA529, but the regulation network of IPA1 is still elusive. Recently, we have revealed a complex regulatory network of IPA1, showing that its protein level is precisely and differentially regulated by E3 ligase at different tissues, its transcriptional activity by plant hormone strigolactones (SLs), and its transcript level by epigenetic regulation. Our findings further revealed that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield. Furthermore, we and our collaborators have been developing a molecular breeding system through integrating IPA1 and other elite alleles of different key regulators by design. Using this system, several demonstrating rice varieties have been developed with both increased rice yield and improved quality, showing that this system could efficiently develop new super rice with an accelerating breeding process. However, to fully meet the challenge of food supply, more efforts need to be made by providing more genetic resources and breeding super crops from optimal combinations of beneficial alleles.

Makoto Matsuoka

GWAS using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

Genome-wide association study (GWAS) could be a powerful tool for the identification of genes associated with agronomic traits in crop species. However, it is often difficult to identify unknown genes associated with the QTLs owing to the following reasons. The first is that diversity panels of crop species often represent strong population structure that generates spurious associations between phenotype and unlinked markers. Although several statistically robust models have been provided, it must be noted that false positives arising from population structure in crops may not be completely controlled. The second reason for the difficulty in identifying unknown genes is the large extent of linkage disequilibrium (LD). The extent of LD in the human genome was generally smaller than gene size, whereas LD in plants often ranges over several hundred kb, especially in self-pollinating crops such as rice and soybean. This results in the inclusion of many candidate genes within a single LD block exhibiting a significant signal, thus entailing the need for additional experiments to conclusively identify the causal gene(s).
In the present study, we attempted to identify genes associated with agronomic traits using GWAS with minimum additional experiments (i.e., only transgenic complementation tests). We focused on rice (Oryza sativa L.), which feeds more than three billion people in the world. Furthermore, rice is a good candidate because of its extremely strong population structure and the large extent of LD due to self-pollination. To perform GWAS efficiently, we carefully selected a population that had a low population structure but had a large phenotypic diversity. By performing whole-genome sequencing, we refined the number of candidate genes based on the estimated functional importance of each nucleotide polymorphism. We demonstrated that with careful experimental design, GWAS could be a powerful tool for the rapid identification of genes associated with agronomic traits.

Naoko K. Nishizawa

Transporters crucial for metal transport and distribution in rice

Natural metal chelators such as nicotianamine (NA) and mugineic acids family phytosiderophores (PS) are important in metal homeostasis in plants. They form stable complexes with metals, which are essential nutrients for plant growth. PS in graminaceous plants is known to play a major role in iron uptake from the soil. Furthermore, NA and PS are involved in intracellular and long-distance transport of metals. Transporter Of MAs 1 (TOM1) and its barley homologue (HvTOM1) those were the efflux transporter of deoxymugineic acid (DMA) involved in PS secretion from roots. Two TOM1 homologs (TOM2 and TOM3) were located on rice chromosome 11. We confirmed that TOM2 is involved in the internal transport of metals by DMA, which is required for normal plant growth. Yellow Stripe1-Like (YSL) family transporters are responsible for the transport of metal-chelate complexes both in graminaceous and non-graminaceous plants. We characterized OsYSL9 in rice (Oryza sativa L.), which is the only remaining uncharacterized rice member of the clade that includes ZmYS1. We showed that OsYSL9 is a plasma membrane localized transporter, which is involved in Fe distribution in developing rice seeds. In iron deficient roots, OsYSL9 expression was observed in vascular cylinder but not in cortex or epidermal cells, suggesting that OsYSL9 is not involved in iron uptake from the soil. At grain filling stage, OsYSL9 expression was transiently induced in the scutellum of embryo and endosperm near the embryo. Remarkable effects of OsYSL9-knockdown were observed in iron distribution in mature seeds. Iron concentration in the embryo isolated from mature brown seeds was decreased, while that in residual parts after removing the embryo was increased comparing with non-transgenic plants. Our results suggest that OsYSL9 is responsible for iron translocation from endosperm into embryo in developing seeds.

Rod A. Wing

Harnessing 15MY of Natural Variation across the Genus Oryza to Help Solve the 10-Billion People Question

The genus Oryza is composed of ~27 species that includes the world’s most important food crop – rice. Oryza is a virtually untapped reservoir of genes and traits that can be used for crop improvement. The International Oryza Map Alignment Project (IOMAP) is focused on capturing the natural variation that exists across that genus and to exploit that information to help solve the 10-billion people question – i.e. “How can we feed our world without destroying our world?”. My talk will focus on our current understating of the genome-biology of the genus Oryza. I will present recent work on the establishment and analysis of high-quality genome assemblies for representatives of each species of the Oryza, including the salt loving KKLL polyploid species Oryza coarctata.

Guo-Liang Wang

Regulation of the NLR immune receptor Piz-t in rice

Rice and wheat blast diseases, caused by hemibiotrophic fungal pathogen Magnaporthe oryzae, are major threats to food security in the developing countries. Use of resistance is key to the control of the diseases but the host resistance mechanism to the pathogen has not been fully understood. We used the AvrPiz-t-Piz-t pair as a model to elucidate the molecular basis of rice immunity against M. oryzae. Using AvrPiz-t as the bait in yeast two-hybrid screens, we identified 12 AvrPiz-t-interacting proteins (APIPs) and characterized the function of APIP5, APIP6, APIP10 and APIP12 in rice immunity. We found that AvrPiz-t suppresses the ligase activity of both E3 ligases APIP6 and APIP10 and targets both proteins for degradation. At the same time, both E3 ligases ubiquitinate AvrPiz-t that leads to degradation. Genetic analysis showed that APIP6, APIP10 and APIP12 are positive regulators of PAMP-triggered immunity (PTI). Molecular analysis showed that the transcription factor APIP5 is essential for the accumulation of the nucleotide-binding domain and leucine-rich repeat (NLR) Piz-t protein in rice. In return, Piz-t interacts with and stabilizes APIP5 to prevent necrotrophy at the late infection stage. Interestingly, APIP10 is a negative regulator of Piz-t. Silencing of APIP10 leads to induction of the Piz-t protein and cell death in transgenic rice. These results demonstrate that the Piz-t protein level is positively and negatively regulated by a transcription factor and an E3 ligase respectively, in rice.

Yunde Zhao

Development of CRISPR gene editing technology and its application in rice auxin biology

Auxin is an essential hormone and rice is an excellent model system for studying auxin biology. Several key auxin genes were first discovered in rice and subsequently characterized in other plant species. However, the auxin genes in rice were mainly discovered serendipitously and there is a need for a systematic research on how auxin regulates various agriculturally important traits. In this presentation, I will first describe our effort to develop gene editing technologies in rice that have enabled us to do 1) generation of targeted knockout mutants; 2) replacement of DNA fragments through homologous recombination; 3) introduction of targeted point mutations. The gene editing technologies we developed have allowed us to systematically analyze genes related to auxin biosynthesis, degradation, transport, and signaling in rice. We show that auxin plays key roles in all major development processes including root development, vascular pattern formation, and flower development. We also show that rice employs a sophisticated network to maintain auxin homeostasis.

Emmanuel Guiderdoni

Manipulating meiotic recombination in rice

Recombination, the major source of genetic diversity through allele shuffling, is hampered by the restricted number of crossovers (CO) between homolog chromosomes (typically 1-3 per homolog pair in a plant meiocyte) and an overall limitation of CO number, the CO homeostasis. Also, recombination frequency may vary by 100 fold across regions in large genomes, limiting access to genes of interest in « cold » regions.
Here, we present two approaches aiming at enhancing the overall CO frequency and modifying the distribution of COs.
It has been recently shown that FIGL1, FANCM and RECQ4 limit CO formation in Arabidopsis thaliana : Disrupting one or a combination of two of these anti-CO factors conducts to a 3 to 10-fold increase in CO frequency without affecting meiotic progression. RecQ4 is a highly conserved helicase that resolves DSB into non CO through Synthesis Dependent Strand Annealing (SDSA) in a minor CO pathway that normally accounts for 10% COs in Arabidopsis. Here, we demonstrate that Osrecq4l -/- plants exhibit an average 3.1-fold increase in CO compared to OsRECQ4l +/+ plants and displays normal meiosis and seed fertility.
SPO11 is an essential protein for triggering CO formation at the initiation of meiosis through its capacity of interacting with several partners to induce chromosomal double strand breaks (DSB). Based on a report in yeast, we wished to determine whether the expression of the SPO11-1 coding sequence fused to the GAL4 binding domain (BD) -hereafter referred as SpiX1- can locally enhance CO frequency at GAL4BD target sites (CGG11NCCG) in the rice genome. We generated a Spix1 transgenic line in cv. Kitaake and, using CRISPR/Cas9 mutagenesis, we demonstrated that Spix1 rescues fertility in a spo11-1 background, indicating that the fusion is functional at meiosis. Genome wide recombination was then examined in F2 populations of Kalinga 3/KitaakeSpix1 3 and Kalinga3/Kitaake null segregant (ns) using a genotyping by sequencing approach. The overall size of the genetic maps and the average number of CO per F2 plant were comparable in the two populations indicating an unchanged, overall recombination frequency. However, Spix1 stimulated recombination in the 5% intervals exhibiting the highest CO frequencies. Furthermore, the 4% intervals exhibiting the highest UAS density harbored a significant excess of recombinants in the Kalinga3/KitaakeSpix1 population. Genotyping of 5 intervals exhibiting an excess of recombinants in the Kalinga3/KitaakeSpix1 population localized recombination break points in the vicinity of UAS sites. Altogether, these results indicate that modulating recombination in rice is possible.

Dao-Xiu Zhou

Mechanisms underlying epigenomic reprogramming of rice developmental and stress responsive processes

Chromatin-based epigenomes are the basis of cell type-specific gene expression patterns and chromatin modification is essential for reprogramming of gene expression during development and adaptation to the changing environments in plants. Histone modifications such as lysine acetylation and methylations play an important role in chromatin-based regulation of plant developmental and responsive genes. However, it remains largely unclear how histone modification epigenomes are established and are reprogrammed during plant developmental transitions and rapid responses to environmental changes. We have been studying rice epigenomes and epigenomic mechanisms involved in development pf rice shoot apical meristems and crown roots. We have identified histone modification enzymes involved in epigenomic and gene expression reprogramming during vegetative shoot to panicle meristem transition, and during response to pathogen (Xoo) infection. Recently we have shown that recruitment of histone modification enzymes by a key regulator of crown root meristem is a mechanism of epigenomic reprogramming during crown root development. We will discuss our recent data on regulation of histone methylation in gene expression reprogramming during rice shoot apical meristem development and histone deacetylase functions in regulation of energy metabolism in rice.

Qifa Zhang

Evolutionary and biological processes underlying the S5 reproductive barrier in indica-japonica rice hybrids

In rice, hybrids between indica and japonica subspecies are usually highly sterile, which provides a model system for studying postzygotic reproductive isolation. We previously identified the S5 locus encoding a killer-protector system composed of three adjacent genes, ORF3, ORF4 and ORF5, which plays a major role in regulating female gamete fertility of hybrids. In follow-up studies, we investigated the evolutionary processes underlying the origin and establishment of the S5 system in the rice population as a functional barrier, and the biological processes casuing gamete abortion. We showed that the S5 system originated by gene duplication after the split of the Oryzeae tribe from other grasses, most likely through Helitron transposition. A combination of mutational steps generated incompatible indica and japonica alleles in pre-differentiated rice groups, giving rise to the trigenic S5 system. Natural selection in indica and founder effect associated with domestication of japonica rice increased the frequencies of incompatible alleles to form a functional reproductive barrier between the indica and japonica subspecies, and eventually resulted in genetic differentiation and restructuring of rice genetic composition. To characterize the biological processes causing female gamete abortion, we performed transcriptomic analyses of pistils from rice variety Balilla (BL), Balilla with transformed ORF5+ (BL5+) producing sterile female gametes, and Balilla with transformed ORF3+ and ORF5+ (BL3+5+) producing fertile gametes. RNA sequencing of tissues collected before (MMC), during (MEI), and after (AME) meiosis of the megaspore mother cell detected 19,269 to 20,928 genes as expressed. Introduciton of ORF5+ in BL induced differential expression of 8,339, 6,278 and 530 genes at MMC, MEI, and AME. At MMC, large-scale differential expression of cell wall modifying genes and biotic and abiotic response genes indicated that cell wall integrity damage induced severe biotic and abiotic stresses. The processes continued to MEI and induced ER stress as indicated by differential expression of ER stress responsive genes, leading to PCD at MEI and AME, resulting in abortive female gametes. In the BL3+5+/BL comparison, 3986, 749 and 370 genes were differentially expressed at MMC, MEI and AME. Large numbers of cell wall modification and biotic and abiotic response genes were also induced at MMC but largely suppressed at MEI without inducing ER stress and PCD, producing fertile gametes. These results may have general implications for the understanding of evolutionary and biological processes underlying reproductive barriers.

Dabing Zhang

Two rice receptor-like kinases maintain male fertility under changing temperatures

Plants employ dynamic molecular networks to control development in response to environmental changes, yet the underlying mechanisms are largely unknown. Here we report two rice leucine rich repeat receptor-like kinases (LRR-RLKs), Thermo-sensitive genic Male Sterile 10 (TMS10) and its close homolog TMS10-Like gene (TMS10L), which collaboratively regulate male fertility under fluctuating temperatures. TMS10 and TMS10L are conserved in both dicot and monocot proteins with unknown function. tms10 displays abnormal tapetal degeneration and aborted pollen development, causing male sterility under high temperatures, but normal male fertility under low temperatures. By contrast, tms10 tms10l double mutant shows complete male sterility under high and low temperatures. Biochemical and genetic assays indicate that the kinase activity conferred by the intracellular domain of TMS10 is essential for tapetal degeneration and male fertility under high temperature. Furthermore, indica or japonica rice varieties that contain mutations in TMS10, created by genetic crosses or genome editing, also exhibit the thermo-sensitive genic male sterile trait. This finding reveals that two LRR-RLKs, TMS10 and TMS10L, act as a key switch of post-meiotic tapetal development and pollen development in buffering the environmental temperature changes, providing insights into the molecular mechanisms by which plants develop phenotypic plasticity via genotype-environmental temperature interaction. In addition, the discovery of TMS10 provides a new genetic resource for potential establishment of a new hybrid seedproduction system in crops.

Bin Han

Understanding genetic basis of complex traits and heterosis in rice

Most of agronomically important traits, which are called complex traits, are usually controlled by multiple genes and affected by various environmental conditions. Although a lot of QTLs and genes related to rice complex traits have been cloned and functionally characterized, genetic basis and regulatory mechanisms underlying these complex traits are still unclear. We have implemented an integrated approach of genome-wide association study (GWAS) with functional analysis to catch up agronomic traits genes or QTLs in a diverse cultivated rice population. This approach informs that the associated loci with the agronomic traits such as panicle length, grain sizes, grain weight and grain filling rate can be further characterized through expressional profiling, in-depth genome analysis, transgenic study, genome editing, and population genetic analysis. We believe that allelic genetic variations responsible for the panicle and grain size complex traits can be effectively explored. The genetic basis of these complex traits will be characterized. Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. We have developed an integrated genomic approach to construct a genome map for elite hybrid rice varieties and their inbred parental lines. We therefore identified that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. We have further done large-scale genomic mapping for yield related traits and heterotic effects by analyzing over 10,000 rice lines produced from 17 elite rice lines. The large data of genomics and phenomics from the well-designed populations enabled us, for the first time, to identify the genetic contributors comprehensively and find out the exact causes of heterosis. We found that modern rice varieties can be classified into three major types, reflecting the major breeding systems. Within each group a few genomic regions from female parents linked to heterosis effects for improved yields were identified, but these loci varied across the three groups. The key heterosis-related genes often controlled several yield-related components simultaneously, severing as the major contributors of heterosis. For the individual yield components, the heterozygous state of the heterosis-related genes generally acted through the way of dominance complementation. Taking all the components into account, the hybrids with yield heterosis resulted from an optimal combination of multiple yield-related components, meaning better performance of overall yield in crop productions. These results inform on the genomic architecture of heterosis for yield traits in rice, which will be useful information for crop improvement program.

Yue-Ie Caroline Hsing

From rice to an oil-rich orphan cereal

Eccoilopus formosanus (Taiwan Oil Millet, TOM) is an orphan cereal endemic to Taiwan that was domesticated by the aboriginal population. TOM is a perennial C4 species, with the genome size of 2.6 Gb and chromosome number 2n=40. This orphan crop is still cultivated in mountain communities at altitudes up to 2000m. The seed of Taiwan oil millet is characterised by an exceptionally large embryo and consequently possesses substantial quantities of triacylglycerol and storage protein in addition to the starchy endosperm. This species secretes oil in the form of monoacylglycerols from the panicle and reproductive structures and exudes copious amounts of a pure fatty acid wax from pore-like structures on the leaf sheath. Transcriptomic analyses in vegetative tissues have identified genes associated with the regulation and biosynthesis of cuticular lipids and waxes. Taiwan Oil Millet is unique in protein-calorie rich seed and as an energy-rich biomass for forage or a source of unusual cuticular waxes of uniform composition for use as industrial feedstocks.
For the section “Translational genomics: from rice to other cereals”

Su-May Yu

Mechanisms of Nutrient Starvation, Hormone and Abiotic Stress Cross-signaling in Rice

Rice is the major dietary staple for nearly half of the human population, as well as being the most important model crop for functional genomics research to identify valuable genes that could be used for improvement of productivity in cereal crops (rice, wheat, maize, sorghum, etc.). Our recent studies have revealed signaling crosstalk between nutrient (C, N and P) deficiencies, hormones (GA and ABA), and abiotic stresses (drought, flooding, salt and cold), which plays an important role in rice growth and productivity under adverse environmental conditions. Unraveling the global regulatory mechanisms that coordinate expression of genes involved in nutrient deficiency and abiotic stress signal crosstalk is not only significant for understanding how plants balance nutrients to orchestrate efficient growth and stress response, but also facilitates the development of strategies aiming at promoting plant growth in both normal and adverse environments. We will demonstrate the regulatory mechanisms of signal crosstalk among nutrient deficiency, hormone, and abiotic stress that act at molecular, cellular and biochemical levels during rice growth and development. [1] Lee, K-W, Chen, P-W and Yu, S-M* (2014) Metabolic adaptation to sugar/O2 deficiency for anaerobic germination and seedling growth in rice. Plant, Cell & Environ 37: 2234-2244. (Review) [2] Yu, S-M*, Lo, S-F and Ho, THD (2015) Source-Sink Communication: Regulated by hormone, nutrient, and stress cross-signaling. Trends Plant Sci 20: 844-857 (Review).

Letian Chen

S1-mediated Interspecific Hybrid Sterillity Requires Peptidase-like Protein OgTPR1 in Rice

Hybrid sterility can maintain species barriers during speciation, but also hinders utilization of hybrid vigor in crop breeding. The S1 locus is the major genetic factor for the incompatibility between Asian rice (Oryza sativa L. ssp japonica and ssp indica) and African rice (Oryza glaberrima). Here, we fine-mapped S1 to a 29-kb region (in japonica rice), and found great structural variation in this region between the O. sativa and O. glaberrima genomes. Candidate genes for S1 were selected based on analyses of the sequence and gene expression. One candidate, the OgTPR1 gene encodes a peptidase-like protein OgTPR1 with two trypsin-like peptidase domains and one ribosome biogenesis regulatory domain in African rice; the truncated Asian rice OsTP1 protein has only one trypsin-like peptidase domain. The knockout phenotype of the S1-g allele (from O. glaberrima) by CRISPR/Cas9-editing indicated that the OgTPR1 determines the S1-mediated interspecific hybrid sterility. Thus, we revealed the molecular basis for S1-mediated hybrid sterility in rice and its genetic effect on speciation in Oryza. Moreover, our study provides a novel strategy to break the interspecific reproductive barrier by knocking out OgTPR1 in African rice cultivars by CRISPR/Cas9-editing, enabling the use of interspecific hybrid vigor in rice breeding programs.

Xiangdong Fu

Improving nitrogen use efficiency and grain yield in rice

In the past 50 years, the Green Revolution based on the adoption of semi-dwarf cereals was responsible for worldwide crop yield potential increases. However, introduction of semidwarf gene sd1 into rice caused the reduction of panicle branching and nitrogen-use efficiency, and increase in grain yields required significant increases in nitrogen fertilization levels, which in turn resulted in what are now well documented deleterious impacts on the environment. To uncover the role of the GA-DELLA regulatory system in control of nitrogen uptake and assimilation, we performed genetic screening to identify new components of GA signalling responsible for nitrogen assimilation. In the further experiments we reveal an interactive network for GA-mediated coordinated regulation of nitrogen acquisition and nitrogen-mediated growth responses. In addition, we also show that the different DEP1 alleles confer different nitrogen-mediated growth responses. The DEP1 protein physically interacts with RGA1 and RGB1, and reduced RGA1 or enhanced RGB1 activity represses nitrogen-mediated growth. We next performed a yeast two-hybrid screening to identify DEP1-interacting proteins. Further experiments showed that transcription factor DIP1 is a target of the detached Gβγ dimer, the DEP1-DIP1 interactions could enhance its transcriptional activity, and consequently promote co-operative transactivation of common target gene. Therefore, manipulation of G-protein signalling represents new strategies to increase panicle branching and grain yield in crops.

Ju-Kon Kim

Identification of a key player on nitrogen-use-efficiency of rice using nitrogen molecular sensors

Nitrogen (N) is an essential nutrient for plant growth and development. Crops obtain insufficient N sources from natural supply of soil and rest of N sources are inevitably supplied by N fertilizers. N fertilizers increase crop yields, however, overdose of the N fertilizers results in serious damages to environment. Especially, Japonica rice, which is widely planted in East Asia, shows low nitrogen-use-efficiency (NUE), being one of major causes of the environmental issues. Little is known about the molecular NUE mechanisms to solve the long-standing problem because of no typical N phenotype. To overcome the limitation, we tried to utilize in vivo N molecular sensors to monitor N status of rice. ALLANTOINASE (ALN) and UREIDE PERMEASE 1 (UPS1), genes that modulate ureide metabolism to control N balance of rice, were isolated as the N molecular sensors by high-throughput RNAseq analysis. ALN was strongly up-regulated under low N conditions, whereas UPS1 was sensitively up-regulated under high N conditions. Taking advantage of their nature in response to N, we generated N molecular sensors as proALN::ALN-LUC2 and proUPS1::UPS1-LUC2 in transgenic rice (Japonica cv. Dongjin) and isolated single copy number and homozygote of each molecular sensor in transgenic rice plants. Transgenic rice plants with proUPS1::UPS1-LUC2 sensor showed strong luciferase activity under high N conditions (> 1 mM ammonium nitrate), whereas transgenic rice plants with proALN::ALN-LUC2 sensor showed strong luciferase activity under low N conditions (< 1 mM ammonium nitrate). These results indicate that proALN::ALN-LUC2 and proUPS1::UPS1-LUC2 are the optimal N molecular sensors to detect N status in rice. We finally treated the transgenic rice plants with 1% EMS mutagen to generate an EMS mutant population. With the EMS mutant population (20,000 M1 lines), we are trying to identify a key player on NUE of rice using the N molecular sensors.

Nam-Soo Jwa

Pathgen effectors target the plant reactive oxygen species (ROS) system to cause desease

Recent researches on pathogen effectors and plant nucleotide binding domain and leucine rich repeat-containing (NLR) family proteins have shown that plants have very similar immune systems to animals, and attention is focused on evolutionary aspects. The perception of PAMPs by pattern recognition receptors (PRRs) leads to the rapid and strong production of ROS through activation of NADPH oxidase Respiratory Burst Oxidase Homologs (RBOHs). Reactive oxygen species (ROS) act as cellular signaling molecules to trigger plant immune responses, such as pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). By contrast, virulent pathogens possess effectors capable of suppressing plant ROS bursts in different ways during infection. PAMP-triggered ROS bursts are suppressed by pathogen effectors that target mitogen-activated protein kinase (MAPK) cascades. Moreover, pathogen effectors target vesicle trafficking or metabolic priming, leading to the suppression of ROS production. Collectively, pathogen effectors may have evolved to converge on a common host protein network to suppress the common plant immune system, including the ROS burst and cell death response in plants.

Wanqi Liang

OsINP1 and OsDAF1 control pollen aperture formation in rice

Pollen apertures are well-defined areas of the pollen wall where pollen tube germination is initiated. Though apertures play an essential role in plant reproduction, the molecular mechanism controlling their formation remains largely unknown. Here, we describe the isolation and characterization of two key regulators INAPERTURATE POLLEN1 (OsINP1) and DEFECTIVE IN APERTURE FORMATION1 (OsDAF1) which are involved in rice pollen aperture formation. Pollen grains of rice and other grass are characterized as by monosulcate, which is located at the distal pole. The germination pore is encircled by an annulus and covered by an operculum. Both mutants of osinp1 and osdaf1 display defective pollen aperture formation, pollen tube germination and male sterile.OsINP1 encodes a plant specific protein with unknown function, depletion of which leads to the loss of the aperture structure in rice pollens. Overexpression of OsINP1 does not affect the formation of normal aperture, but causes ectopic invagination of the pollen wall at random positions. The OsINP1 protein accumulates at a position on the microspore surface where the germination pore appears at later stage, suggesting that OsINP1 is required for the initiation of the aperture in rice pollens. OsDAF1 belongs to rice receptor like kinase (RLK) gene family and is specifically expressed in the pollen mother cell and the young microspore. OsDAP1 is initially ubiquitously distributed in the cytoplasm of the pollen mother cell at dyad stage. At tetrad stage, OsDAP1 is accumulated in a ring like structure at the distal pole. The loss of function mutant of OsDAF1 exhibits a flattened or disappearance of the annulus structure surrounding the germination pore. We also revealed that the size of the aperture is controlled by the dosage of OsDAF1. Overexpression of OsDAF1 results in a larger annulus structure and a larger aperture accordingly, suggesting that OsDAF1 serves essential roles in controlling the size and pattern formation of the aperture in rice pollen grains. Our studies provide insights into the mechanisms how species-specific arrangement of aperture achieve.

Anna Joe

A microbially derived tyrosine sulfated peptide mimics a plant peptide hormone

Plant pathogens have developed numerous strategies to manipulate host cellular processes. In many cases, plants have evolved mechanisms to recognize and respond to these attacks resulting in robust immunity. Studies of Xanthomonas, a large genus of Gram-negative bacteria that infect numerous plant species, have provided tremendous insight into this ongoing arms race between pathogens and their hosts.
Rice receptor XA21 confers resistance to most strains of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo). We have recently identified the elicitor of XA21 as a small sulfated protein, which we named RaxX. Xoo strains lacking RaxX are able to evade XA21-mediated immunity. Sulfated, but not nonsulfated, RaxX triggers the hallmarks of the plant immune response in an XA21-dependent manner. RaxX shares remarkable similarity to peptides in tyrosine sulfated plant hormone PSY1 (plant peptide containing sulfated tyrosine 1). Here we show that a synthetic sulfated RaxX derivative comprising 13 residues, highly conserved between RaxX and PSY (RaxX13-sY), induces root growth in Arabidopsis and rice in a manner similar to that triggered by PSY. Analyses of multiple RaxX peptides identified residues that are required for activation of immunity mediated by the rice XA21 receptor but that are not essential for root growth induced by PSY. These findings suggest that RaxX serves as a molecular mimic of PSY peptides and that XA21 has evolved the ability to recognize and respond specifically to the microbial form of the peptide.

Jun Liu

The rice transcription factor OsbHLH19 is a central regulator of salicylic acid and jasmonic acid signaling

Phytohormones play fundamental roles in plant disease resistance. By transcriptome assays, we found that the OsbHLH family genes were substantially upregulated by Magnaporthe oryzae infection. One of the genes of the OsbHLH family, OsbHLH19, was not only highly induced by M. oryzae infection, but also by chitin treatments. Interestingly, resistance rice cultivars showed higher expression level of OsbHLH19 compared with susceptible rice cultivars upon pathogen infection. Overexpression of OsbHLH19 in rice plants led to enhanced disease susceptibility to M. oryzae; however, silencing the OsbHLH19 expression resulted in enhanced disease resistance, suggesting that OsbHLH19 plays a negative role in disease resistance to M. oryzae. In addition, WRKY45, the salicylic acid (SA) signaling marker gene, was significantly down regulated in OsbHLH19 overexpression lines, but the Jasmonic acid (JA) signaling was activated. OsbHLH19 is primarily located to the nucleus; mislocation of OsbHLH19 to cytoplasm abolished OsbHLH19-mediated disease response. Further, we find that OsbHLH19 interacts with OsMYC2, and competes for OsJAZs binding, thereby activating JA signaling. OsbHLH19 also interacts with OsNPR1, the SA signaling regulator, in the cytoplasm, and elevated OsNPR1 expression retains OsbHLH19 in the cytoplasm. Our data suggest that OsbHLH19 functions in nucleus to activate JA signaling; however, SA signaling activation induces OsNPR1 to retain OsbHLH19 in cytoplasm to suppress JA signaling, which eventually leads to enhanced disease resistance to M. oryzae in rice. We therefore describe a mechanism that how a transcription factor is involved in disease response via regulating SA and JA signaling in rice.

Narottam Dey

Molecular Genomics study for submergence tolerance and deep water trait in rice

Fifty indigenous submergence tolerant/ deep water rice lines were investigated for select out suitable lines to be used as donor parental population in submergence tolerant molecular breeding programme. Rice lines were subjected to Physiological, Biochemical, molecular study followed by expression study and development of miRNA linked molecular markers for sub1 loci. Fourteen days old healthy seedlings were studied for detailed physiological screening following the modified protocol and biochemical screening was done for total chlorophyll, protein, soluble and insoluble carbohydrates and enzymatic activity of invertase, alcohol dehydrogenase and pyruvate decarboxylase following the modified protocol. The seedlings were completely submerged in 90cm deep water in a dedicated screening tank for a period of 14 days. 29 days old seedlings after completion of two weeks of submergence were desubmerged and kept in open air for another week. Shoot length, internodal length, elongation rate were recorded at 7 days interval. Survival percentage was recorded and cross sections of the nodes were studied under microscope to record the amount of aerenchyma tissue at all the 7 days interval as specified above. Genotyping was done with 10 linked SSR loci located on rice chromosome 9. The Sub1A gene sequence was used for allele mining of sub1 loci across studied rice lines. Expression study was done for the selected line as recorded from physio-biochemical analysis. Expression behaviour of the studied gene was analysed in terms of relative expression to the reference gene as well as reference genotype. Sub1gene sequences was searched in psRNA target to find out whether this it is targeted by any miRNA or not. The single miRNA which was identified was osa-miR6248. Three strategies were taken to develop this miRNA linked molecular marker. The first one was pre-miRNA as a molecular marker, second was respective sequence target as marker and the third one was SSRs linked with respective premiRNA and targets as molecular marker. After considering detailed physio-biochemical and molecular analyses Bhashakalmi and Meghi were selected for their unique growth properties under submergence and also promising submergence tolerance characteristics. The different allelic forms detected for Sub1 loci were identified and the derived sequences were subjected to multiple sequence alignment. Sub1A gene of these two genotypes were subjected to quantitative PCR analysis and compared with FR13A and IR42. Expression behaviour of the studied genes was analyzed in terms of relative expression to the reference gene as well as reference genotype. All the different findings resulted out from this study are presented in this presentation.

Dong-Yup Lee

Plant Systems Biology: application to rice for understanding metabolic and regulatory characteristics under abiotic stresses toward crop improvement

Rice plants are exposed to a wide range of environmental stresses during their cultivation, that seriously affects the annual global rice production. Thus, a comprehensive understanding on how rice plants respond to these changing environments both at metabolic and gene regulation levels will provide a significant insight towards improved rice varieties. To do so, we employed systems biology approach, and initially developed a core mathematical model of rice which allows us to characterize cellular behavior and metabolic states under various abiotic stress conditions, such as i) photorespiratory pathway in rice leaves and identification of essential and lethal genes of the pathway, and ii) metabolically and transcriptionally regulated reactions and potential transcription factors involved in the regulation of coleoptile germination and elongation of rice seeds under anoxia. The core model was later expanded to reconstruct a fully compartmentalized genome scale metabolic model. Transcriptomics and metabolomics data were then systematically integrated with the model to identify the potential transcription factors, i) in leaf, root and panicle tissues at three different developmental stages in response to drought stress, and ii) the control of light-mediated signaling mechanisms. The information derived from the current in silico analysis in conjunction with multi-omics profiling can potentially guide for developing new breeding and/or engineering targets as crop productivity strategies. [This work was supported by Next-Generation BioGreen 21 Program (SSAC, No. PJ01109405), the Rural Development Administration, Republic of Korea]

Sichul Lee

OsASN1 overexpression increases grain quality and yield in rice grown under nitrogen-limitation

Nitrogen is a major limiting factor for crop yield in unfertilized soil. Crops with improved nitrogen utilization are needed to meet the growing food demand and to reduce environmental costs. This is especially true for rice, a primary food staple for most of the global population. Here, we report that Oryza sativa Asparagine Synthetase1 (OsASN1), a key enzyme for nitrogen mobilization in rice, is required for optimal crop performance of plants grown in both nitrogen-limiting conditions and in nitrogen-sufficient, conventional paddy fields. Transgenic plants overexpressing OsASN1 (OX) grown in conventional paddy fields produced grains with increased nutritional quality compared to wild type (WT). Importantly, under nitrogen-limited field conditions, OX plants displayed increased grain yield and nitrogen content compared to WT, associated with improved photosynthetic activity. Thus, modulation of OsASN1 provides a promising breeding strategy to improve nitrogen use efficiency, nutrient content and grain yield in rice.

Yuese Ning

Dissection of the ubiquitin E3 ligases-mediated disease resistance mechanism in rice against Magnaporthe oryzae

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most serious rice diseases. The ubiquitin-proteasome system (UPS) is one of the most important protein turnover mechanisms that regulate growth, development and responses to abiotic and biotic stresses. Among the three main kinds of UPS enzymes, E3 ubiquitin ligases (E3s) are highly flexible and diverse. Based on the subunit component, E3s can be divided into two types, single subunit type (HECT and RING/U-box) and multi-subunit type (CUL1-FBX, CUL3-BTB, CUL4-DWD and APC). The regulation mechanism of various E3s in the rice and M. oryzae interaction is still unclear. We found that the M. oryzae effector AvrPiz-t targets the single subunit type (RING-type) E3 ligase APIP6 to suppress PAMP-triggered immunity in rice. APIP6 interacts with and degrades OsELF3-2 to positively regulate immunity against M. oryzae in rice. Moreover, map-based cloning of a lesion mimic mutant demonstrates that the multi-subunit type (CUL3-BTB) E3 ligase OsCUL3a associates with programmed cell death and M. oryzae resistance in rice. OsCUL3a interacts with OsRBX1 and BTB-type protein OsNPR1 to form a multi-subunit CRL in rice, which promotes the degradation of OsNPR1. Taken together, these results indicate that both single and multi-unit E3 play important roles in rice immunity against M. oryzae.