The domestication of crops was a significant event in human history, which led to the emergence and prosperity of agricultural civilization. Maize is an important global food crop, and its domestication origin has long attracted the attention of both the biological and historical communities. The mainstream view in the past was that modern maize originated from the parviglumis type of teosinte. Recently, Yan Jianbing and his collaborators systematically collected and sorted various types of wild and cultivated maize resources, and comprehensively applied genomics, population genetics, and quantitative genetics methods, along with the use of archaeological findings. They found that modern maize also has the gene introgression of the mexicana type of teosinte, which has influenced many agronomic traits. A new model for the origin of modern maize has been proposed based on these findings.

Auxin plays an important role in plant growth and development and its signal transduction has always been the focus of attention in the field of plant biology. AUXIN BINDING PROTEIN 1 (ABP1)-TRANSMEMBRANE KINASE (TMK) molecular module is involved in the extracellular auxin perception. In recent years, ABP1 has been controversial as an auxin receptor. Recently, Tongda Xu’s team and Zhenbiao Yang’s team from Fujian Agriculture and Forestry University identified ABP1-LIKE PROTEIN (ABL) as the auxin binding proteins involved in the extracellular auxin perception. Different from traditional functional redundancy, ABL and ABP1 achieve functional compensation effect through protein structure similarity, and then form complex with TMK at the plasma membrane, acting as co-receptors of apoplastic auxin to mediate auxin driven rapid response. This study deeply dissects the mechanism of extracellular auxin sensing, which is a breakthrough in the field of auxin signaling transduction.

Plants can coordinate the growth direction of their various organs upon the gravity stimulus. In the process of plant gravitropism, gravity sensing and gravity signal transduction have always been the focus of attention in the field of plants. The classical “starch-statolith” hypothesis proposes that plants sense gravity through the sedimentation of amyloplasts that contain starch granules. In addition, previous studies have shown that LAZY proteins regulate plant gravitropism by mediating the asymmetric distribution of auxin. However, the molecular mechanism underlying how sedimentation of amyloplasts triggers gravity signal transduction and its coordination with LAZY proteins remains unclear. Recently, Professor Haodong Chen’s team from Tsinghua University reveals that gravistimulation induces the phosphorylation of LAZY proteins via MKK5-MPK3 kinase pathway in Arabidopsis, which modulates the phosphorylation of LAZY proteins. The phosphorylated LAZY proteins can enhance their interaction with the TOC proteins on the surface of amyloplasts, leading to the enrichment of LAZY proteins on the surface of amyloplasts and the polarity relocation on the new bottom of plasma membrane. This study illustrates the molecular mechanism underlying gravity signal transduction in plants and establishes the molecular connection between gravity sensing and LAZY mediated auxin asymmetric distribution, which is a major breakthrough in the field of plant gravitropism.

Aphids and the viruses transmitted by them cause some of the most devastating plant diseases across the globe. Once infected by aphids, plants can produce and release volatile organic compounds (VOCs), which are transmitted through air and elicit defense in neighboring plants (airborne defense, AD). However, the mechanisms underlying AD remained largely elusive. Dr. Yule Liu’s group at Tsinghua University, China, recently reports a new study and they identify a new signaling circuit, comprising methyl-salicylate (MeSA), salicylic-acid (SA)-binding protein-2 (SABP2), a transcription factor NAC2 and SA-carboxylmethyltransferase-1 (SAMT1) converting SA to MeSA, that mediate interplant communication and airborne defense against aphids and viruses. Furthermore, some virus-encoded virulence proteins could interact with NAC2 transcription factor to reduce the nuclear localization and promotes the degradation of NAC2, thereby suppressing the interplant AD and promoting viral transmission. This comprehensive study provides new mechanistic insights into airborne defense of plants and unravels an amazing aphid/virus co-evolutionary mutualism. It also sets the foundation for new approaches of using AD to control aphid and virus diseases in agriculturally-important plants.

Crop production is constantly threatened by various insect pests, revealing the mechanism underlying insect and host interaction is essential for environmentally-friendly pest management. Guangcun He and colleagues from Wuhan University identified and characterized a saliva protein BISP of the brown planthopper (BPH). In susceptible varieties, BISP targets OsRLCK185 and inhibits the basic defense. In varieties carrying the brown planthopper resistance gene Bph14, BPH14 directly binds to BISP and activates the host immune response but inhibits rice growth. BISP-BPH14 binds to the autophagic cargo receptor OsNBR1 and results in the degradation of BISP through the autophagic pathway, downregulating rice resistance against BPH and restoring the plant growth. This study illustrated the first insect salivary protein perceived by plant immune receptor, and revealed the molecular mechanism underlying the balance of immunity and growth in host by perceiving and regulating the protein level of insect effectors, which provides new ideas for developing high-yield insect resistant rice varieties.

Clubroot, Plasmodiophora brassicae (Pb) caused devastating disease, results in severe yield losses on cruciferous crops worldwide. Recently, Yu-hang Chen, Jian-Min Zhou and their colleagues from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences reported the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS in Arabidopsisis was transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. WTS encodes a small protein that is localized in the endoplasmic reticulum (ER). The cryo-EM structure analysis has revealed a pentameric architecture of WeiTsing with a central pore, which was previously unknown. Electrophysiological analysis has demonstrated that WeiTsing functions as a calcium-permeable cation-selective channel. The Pb-mediated activation of the WTS channels induces immune responses, including cell death. Brassica napus plants carrying the WTS transgene have exhibited robust resistance to Pb. These findings have identified a novel ion channel similar to resistosomes, which triggers immune signaling in the pericycle. This discovery provides a valuable tool for the development of elite crop varieties.

Saline-alkali stress is one of the main adverse environmental factors limiting agricultural production and crop yield. In recent years, great progress has been made in the dissection of the molecular mechanisms of plant’s responses to salt stress, but little is known concerning those for alkaline stress. Lack of the knowledge on alkaline tolerance has severely impeded the effort to improve saline and alkaline stress tolerance of crops through molecular designing and breeding. Recently, Professor Qi Xie at the Institute of Genetics and Developmental Biology of Chinese Academy of Sciences, teamed with Dr. Feifei Yu at China Agricultural University and Dr. Yidan Ouyang at Huazhong Agricultural University, made a breakthrough discovery towards the understanding of the molecular regulation of alkaline tolerance. They detected a major gene AT1, which negatively regulates alkaline tolerance, through sorghum genome-wide association study. The knockout of AT1 and its homologous genes increased the tolerance of sorghum, rice, millet and maize to alkali and increased the yield. AT1 encodes an atypical G protein γ subunit, which alters the cellular distribution of H₂O₂ via regulating the phosphorylation level of the aquaporins PIP2;1 to alleviate the alkali-induced oxidative stress in cells. This work reveals a new mechanism in the adaptation of crops to alkaline stress, which is of great significance to crop breeding for alkaline resistance.

Since the 1960s, the utilization of semi-dwarfing genes Rht-B1b and Rht-D1b has significantly improved the lodging resistance and harvest index of wheat (Triticum aestivum), leading to a doubling of global wheat production and triggering the “Green Revolution” in agriculture. Rht-B1b and Rht-D1b encode plant growth-inhibiting factors, DELLA proteins, which are negative regulatory factors in the gibberellin (GA) signaling pathway. Accumulation of DELLA proteins not only inhibits cell division and elongation, leading to a dwarf phenotype, but also suppresses photosynthesis and nitrogen use efficiency, resulting in semi-dwarf varieties requiring higher fertilizer inputs to achieve high yields. Addressing the challenge of “reducing fertilizer inputs while increasing efficiency” is a crucial issue for achieving green and low-carbon agriculture. Recently, Zhongfu Ni and his colleagues from China Agricultural University identified a novel “semi-dwarfing” regulatory module with potential breeding applications and demonstrated that reducing brassinosteroid (BR) signaling could enhance grain yield of wheat “Green Revolution” varieties (GRVs). They isolated and characterized a major QTL responsible for plant height and 1000-grain weight in wheat. Positional cloning and functional analysis revealed that this QTL was associated with a ~500 kb fragment deletion in the Heng597 genome, designated as r-e-z, which contains Rht-B1 and ZnF-B (encoding a RING E3 ligase). ZnF-B was found to positively regulate BR signaling by triggering the degradation of BR signaling repressor BRI1 Kinase Inhibitor (TaBKI1). Further experiments showed that deletion of ZnF-B not only caused the semi-dwarf phenotypes in the absence of Rht-B1b and Rht-D1b alleles, but also enhanced grain yield at low nitrogen fertilization levels. Thus, manipulation of GA and BR signaling provides a new breeding strategy to improve grain yield and nitrogen use efficiency of wheat GRVs without affecting beneficial semi-dwarfism, which will drive toward a new “Green Revolution” in wheat.

Wheat stripe rust, also known as yellow rust, is a disease caused by the fungus Puccinia striiformis f. sp. tritici (Pst) that can devastate wheat crops across the world. The most effective way to control rust diseases is by planting and breeding durable resistant wheat cultivars. The caveat of R gene-dependent disease resistance is the frequent loss of effectiveness due to pathogen mutations that allow evasion of detection by immune receptors. However, disruption of host baseline susceptibility by inactivating S genes could be adopted for broad-spectrum and durable disease resistance. A recent study finished by the research team at Northwest A&F University significantly advanced our understanding how wheat plants can be protected by a S gene and provided tools in the fight against a major disease. Upon infection, the fungus induces a receptor-like cytoplasmic kinase, TaPsIPK1, specifically interacting with the effector, PsSpg1, that promotes parasitism via enhancing kinase activity and nuclear entry of TaPsIPK1. TaPsIPK1 phosphorylates the transcription factor TaCBF1d for gene regulation. Phosphorylation of TaCBF1d switches its transcriptional activity on the downstream genes. Hence the enhanced TaCBF1d phosphorylation by TaPsIPK1 and PsSpg1 might reprogram target gene expression to disturb plant defense response and thus facilitate pathogen infection. CRISPR-Cas9 inactivation of TaPsIPK1 in wheat confers broad-spectrum resistance against Pst without impacting important agronomic traits in two-years of field tests. This is first study to reveal a new phosphorylation-transcriptional regulation mechanism triggered by PsSpg1-TaPsIPK1-TaCBF1d in wheat S genes to stripe rust, which provide a new strategy to develop cultivars with durable resistance by genetic modifications in crops.

The apoplast is the frontier area for plants to sense and respond to environmental stresses (including biotic and abiotic stresses). The pH of the apoplast is an important physiological parameter that is tightly regulated. Environmental stress (such as bacterial disease) can cause alkalinization of plant apoplast, but how does apoplast pH coordinate root growth and immune response? Its molecular regulation mechanism is still unclear. Recently, the team of Professor Hongwei Guo from the School of Life Sciences, Southern University of Science and Technology, and the team of Professor Jijie Chai from Tsinghua University-Max Planck Institute of Germany-University of Cologne used the model plant Arabidopsis as research materials, through genetic, cellular, biochemical and structural biology. By means of comprehensive methods, it was found that the small peptide-receptor complex on the cell surface can act as an apoplast pH sensor to sense and respond to the apoplast alkalinization of Arabidopsis root apex meristem cells induced by pattern triggered immunity (PTI). The results of this research have discovered the protein complex and response mechanism of plant root apex meristem apoplast pH sensing, as well as the coordination mechanism between immunity and growth, further understanding the biology reaction process of how plants balance growth and immune response.

Chinese scientists have made multiple breakthroughs in recent years in rice disease resistance studies, particularly in the areas of durable resistance and resistance-yield coordination. Most recently, a team led by Zuhua He and Weibing Yang at the CAS Center for Excellence in Molecular Plant Sciences made another major advance in our understanding of disease resistance and host-pathogen co-evolution in rice. They showed that the calcium sensor protein ROD1 directly enhances the activity of catalase protein CatB to remove reactive oxygen species during immune responses, preventing excessive immune responses and ensuring optimum rice plant growth. Remarkably, they also illustrated that a functionally attenuated variant of ROD1 is enriched in wild and domesticated Indica rice from tropical and subtropical regions and that this variant allows elevated resistance against sheath blight disease. Importantly, this variant is likely useful for breeding as it does not compromise rice growth and yield. Interestingly, they further demonstrated that an effector protein from the rice blast fungus structurally and functionally mimics ROD1 to suppress rice immunity. Thus, this study uncovers an immune regulatory axis defined by ROD1 and CatB that is at the center of rice-pathogen co-evolution.

Modern cultivated potato (Solanum tuberosum) is a clonally propagated autotetraploid, with highly heterozygous genome, complex genetic background, and severe inbreeding depression, making it difficult to combine eminent traits and resulting in a long breeding cycle and the dilemma of ‘genetic stagnation’ of potato hybrid breeding. Moreover, clonal propagation leads to low reproduction coefficient, high cost of storage and transportation, whereas tubers are easy to carry viruses and pests, which have hindered the development of potato industry for a long time. Recently a team led by Sanwen Huang in Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, successfully use genome design to develop the pure and fertile potato lines and thereby the hybrid F₁, reinvent potato from a clonally propagated tetraploid into a seed-propagated diploid. This work is a milestone in potato breeding, that starts a new era of genome design and rapid potato breeding.

It is an important event in the human history to domesticate wild plants into cultivated crops through selection of favorable genetic variations. Domesticated crops provide food to meet human needs and thereby promote the sustainable development of human civilization. At present, the global food security is becoming a serious challenge owing to the booming human population, the decrease of arable land, and the frequent occurrence of extreme weather. Based on the understanding of molecular mechanism underlying the domestication and important agronomic traits in crops, de novo domesticating wild plants into new crops, an approach combined with high-throughput genome sequencing and genome editing technology, will be one of effective strategies to face this challenge. Recently a team led by Prof. Jiayang Li in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, successfully de novo domesticated wild allotetraploid rice by optimizing the genetic transformation system, de novoassembling the wild allotetraploid rice (Oryza alta) genome, and editing several genes that control key domestication-related and agronomical traits, including seed shattering, awn, plant architecture, seed size, and heading date. This is a breakthrough study that not only demonstrated the possibility of rapid de novo domestication of wild allotetraploid rice into a staple cereal to strength global food security, but also provided new insights into the utilization of new ideocrops originating from de novo domestication of wild or semi-wild plants in the future.

Continuously exposed to a variety of environmental stresses, plants need to integrate internal and external information in order to achieve the purpose of adaption to environment. Among this process the perception and regulation of the energy state and soluble sugar level are of great importance. However, the molecular mechanisms underlying the integration of sugar signaling, nutrient metabolism and stress response in plants remain unclear. Recently, a team led by Prof. Yan Xiong from Fujian Agriculture and Forestry University (FAFU) have discovered that TOR kinase, the central player in metabolic signaling pathways, can directly bind and phosphorylate the core component of ethylene signaling EIN2 protein, forming a regulatory axis to coordinate TOR and ethylene signaling. The two kinases TOR and CTR1 precisely regulates distinct phosphorylation sites on EIN2, respectively, which makes EIN2 become a coordination hub of glucose signal and ethylene signal, and precisely control plant growth and development.

Innate immune system plays a crucial role to defend against pathogens attack and is classified into two layers, which include pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). The PTI and ETI are activated by cell-surface localized pattern-recognition receptors (PRRs) and mostly intracellularly-localized nucleotide-binding, leucine-rich repeat receptors (NLRs), respectively, with specific activation mechanisms, but largely overlapped downstream immune events and components. One of the top unanswered questions in the field of plant immunity is whether ETI and PTI are really distinct, considering the high similarity of the downstream of the recognition processes and components. Recently, a team led by Prof. Xiufang Xin, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, used the Arabidopsis thaliana and Pseudomonas syringae pathosystem to study the functional link between PTI and ETI, and demonstrated that PRRs and the co-receptor of PRRs contribute to ETI, and the production of reactive oxygen species (ROS) is the early signal event that connects PTI and ETI. They also showed that ETI enhances the transcript and protein levels of key components of PTI, and the increased PTI is crucial for full activation of ETI. This study provides mechanistic explanation to a long-lasting enigma in the field of plant immunity regarding the mechanistic connections of PTI and ETI, and the high similarity of these two layers of immunity. This work represents an important breakthrough in the field of plant immunity, and will have implications for the future molecular breeding in crops.

During sexual plant reproduction, pollen-stigma recognition is a critical step for the germination of compatible pollen to ensure successful fertilization and genetic stability of offspring. It is also the first barrier for interspecific hybridization in crop breeding. Thus, great efforts have been made in relevant investigations during past decades. However, how the compatible pollen is recognized by the stigma remains a mystery. Recently, Chao Li’s group from East China Normal University published their work inScience, which reveals that POLLEN COAT PROTEIN B-class peptides (PCP-Bs) could compete with stigma RALF23/33 for binding to the ANJ-FER complex on stigma surface, resulting in a decline of stigmatic reactive oxygen species (ROS) that facilitates compatible pollen hydration. This finding represents a breakthrough in the field.

Crop productivity relies heavily on inorganic nitrogen (N) fertilization, while excess application of N fertilizers results in detrimental effects on ecosystem and plant developmental process. Thus, the improvement of crop N use efficiency (NUE) is critical for the development of sustainable agriculture. Thus far, significant advances in understanding the regulation of NUE have been achieved in rice (Oryza sativa), one of the most important food crops. Several key transporter and regulatory genes involved in N uptake, translocation, and metabolism have been cloned and characterized in rice. However, the genetic mechanisms underlying the geographic adaptation of rice to the change of local soil N status remain elusive. Recently, a team led by Prof. Chengcai Chu, in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, evaluated the responses to N supplies of rice germplasm resources collected from different eco-geographical regions worldwide. By performing genome-wide association study on rice tillering response to N (TRN), OsTCP19 is identified as a repressor of TRN, and a 29 bp InDel polymorphism in its promoter determines TRN variations among the rice varieties. OsTCP19 regulates TRN by inhibiting the transcription of DLT, a tiller-promoting gene, whilst the transcription of OsTCP19 itself is controlled by a N responsive suppressor LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein. Notably, OsTCP19 haplotypes were selected among rice germplasms and correlated with local soil N content. This study not only reveals the genetic basis of geographic adaptation of cultivated rice to the changes of soil N environment, but also provides novel genetic candidates for effective breeding of higher NUE rice cultivars.

Mitogen-activated protein kinase (MAPK) cascade is an important and highly conserved cellular signal transduction pathway by delivery and amplification of upstream signals through protein kinase cascade phosphorylation in eukaryotes. In plants, MAPK signaling pathways not only mediate plant responses to environment, but also play crucial roles in regulating plant growth and development. A recent study from the Zhaojun Ding’s group of Shandong University uncovered a novel molecular mechanism of MPK14-mediated auxin signaling in lateral root development via ERF13- regulated very-long-chain fatty acids (VLCFAs) biosynthesis. This study reveals the molecular mechanism of the lateral root development from a new perspective, and further confirms the coupling between the vital phytohormone auxin and the ancient MAPKs module. Since lateral roots act as essential organs for plants in response to environment, deciphering the MAPK signaling pathway in regulation of lateral root development will provide a new strategy for how plants integrate development signals and environmental cues.

Pathogenic microbes employ specialized mechanisms to breach defense of host plants, causing diseases on plants and losses in agricultural production. Understanding mechanisms of pathogenesis offers new avenues for disease control. A team from Sichuan Agriculture University led by Xuewei Chen investigated mechanisms underlying the genera- tion of an infection structure called penetration peg, which is employed by many fungal pathogens such as the one causing blast disease on rice. They discovered that very-long-chain fatty acids are required for this process. They further demonstrated that a group of commercialized herbicides capable of inhibiting very-long-chain fatty acid biosynthesis in fungi can effectively inhibit pathogenesis of a broad spectrum of fungi, which brings new technology to control diseases and provides new ideas for new pesticides discovery.

Stem cells in plant shoot apical meristem maintain a high level of pluripotency, providing the source of all above-ground tissues and organs. Since plants cannot move to escape from various stresses, protection of plant stem cells from viruses and other pathogens is essential for plant growth and development. Although it has long been known that compared with other parts of the plant, the shoot apex containing the stem cell niche is against virus invasion and accumulation, the related mechanism is still elusive. A recent study from the group of Zhong Zhao at University of Science and Technology of China uncovered the mechanism of how plant stem cells in Arabidopsis are immune to virus infection through WUS-mediated innate immunity. WUS responses to the infection of cucumber mosaic virus, and represses virus accumulation in the central zone and peripheral zone. WUS directly represses the transcription of several S-adenosyl- L-methionine-dependent methyltransferase genes, resulting in disturbed rRNA processing and ribosome stability which affecting viral protein synthesis. This study reveals a conserved and broad-spectrum strategy of antiviral immunity in plant stem cells, which provides high values in both theory and application.

It is well-known that DELLA, AUX/IAA, JAZ and D53/SMXL act as repressor proteins that bind and repress transcription factors to suppress expression of hormone-responsive genes, while hormone molecules trigger signal transduction to induce degradation of these repressor proteins and eventually activate expression of hormone-responsive genes essential for various biological processes. The research team led by Dr. Jiayang Li recently reported that SMXL6, SMXL7 and SMXL8 (SMXL6,7,8) in strigolactone (SL) signaling pathway serve as dual-function repressor proteins which act as both repressors and transcription factors. They found that SMXL6,7,8 can function as transcription factors by directly binding to the promoters of SMXL6,7,8 genes and repressing their expression. In addition, they identified a large number of novel SL-responsive genes, and revealed molecular mechanisms underlying how SL regulates shoot branching, leaf elongation and anthocyanin biosynthesis. These important findings provide new insights into our understanding of plant hormone action, which are scientifically significant and agriculturally important.

Soybean (Glycine max) is an important oil and protein crop. The abundancy of genetic diversity within the species provides an essential resource for traits exploration and breeding improvement. However, one reference genome is inadequate for discovering all genetic diversity of a species. Pan-genome provides a new solution to overcome this limitation. Recently, Prof. Zhixi Tian’ Group and Prof. Chengzhi Liang’ Group from the Institute of Genetics and Develop- mental Biology, Chinese Academy of Sciences, selected 26 representative soybeans from 2 898 sequenced accessions. Together with three previously published genomes, they constructed a pan-genome and a graph-based genome of wild and cultivated soybean germplasm. The core, dispensable, and private genes as well as all the vast majority of genetic variations within this species were identified and characterized. These data comprehensively revealed allelic variations and gene fusion event of maturity gene E3, the haploid types of seed coat color gene I and their evolutionary relationship, and structural variations affecting gene expression and regional adaptation selection of ferric ion transporters. This study provide a new mode for crop genomics, and will facilitate genetic variations identification, traits exploration and germplasm innovation of soybean.

The Green Revolution represented by the breeding of semi-dwarf crops greatly promoted agriculture yield, but it also unfortunately led to the problem of low nitrogen use efficiency (NUE). The achievement of Green Revolution was mainly based on modification of gibberellin (GA) metabolic or signaling pathways in crops. A previous study has found that the central regulator of GA signaling pathway DELLA protein negatively regulates NUE through suppressing GRF4, an essential NUE regulator, which provided a resolution for improving NUE of semi-dwarf rice. A recent study further revealed a novel mechanism underlying the crosstalk between GA signaling and nitrogen response. The study revealed that NGR5 is a key gene controlling tiller number changes under different nitrogen conditions, which is inducible by nitrogen. Further investigation established that the NGR5 suppresses branching inhibitory genes, such as D14 and OsSPL14, through nitrogen-dependent recruitment of polycomb repressive complex 2 that promotes histone H3 lysine 27 tri-methylation in the regions habouring the branching suppressors. In addition to be responsive to nitrogen, NGR5 is also negatively regulated by GA and its receptor GID, and overexpression of NGR5 in the semi-dwarf background is thus able to significantly improve rice yields under low nitrogen conditions. This study not only uncovered a new mechanism of GA signaling, but also enlightens the new generation of Green Revolution by breeding high yield crops with enhanced NUE.

Horticultural plants include flowers, vegetables, fruit trees, some melon (such as watermelon (Citrullus lanatus), muskmelon (Cucumis melo)) and tea trees (Camellia sinensis), with a large number of species based on plant classification. Genomics and genetics researches for horticultural plants are of important theoretical value and economic significance. The development of genome sequencing technology and related bioinformatics tools greatly facilitate molecular biology researches of horticultural plants. In addition to its important ornamental value, the plant species ‘water lily’ has a very special position in evolutionary, belonging to an early angiosperm group. Recently, a high-quality genome map of an important flower plant, water lily, was generated. Through systematic analysis and genomic comparison of the water lily genome and other angiosperm genomes, the researchers thoroughly elucidated the evolutionary position and related evolutionary events of water lily. Based on the high-quality genomic sequences of these horticultural plants, researchers in horticultural plant science are expected to carry out in-depth molecular genetics research and identify functional genes underlying many traits such as flower organs, flower color, fragrance, and quality, which is expected to promote basic research and accelerate the creation of new varieties.

Increasing plant density is an important approach to boost crop yield, and leaf angle is one of the key factors affecting plant density. Recently, Feng Tian’s lab from China Agricultural University cloned and characterized two major QTLs (UPA1 and UPA2) regulating leaf angle in maize. The underlying genes are brd1 and ZmRAVL1, respectively, and both of them are involved in the brassinosteroid (BR) pathway to regulate leaf angle. UPA2 is located 9.5 kb upstream of ZmRAVL1 and is bound by DRL1. LG1, another leaf angle protein, directly activates the expression of ZmRAVL1. DRL1 and LG1 physically interact and the resulting complex in turn represses the LG1-activated expression of ZmRAVL1. The teosinte allele of UPA2 has a higher binding affinity with DRL1, resulting in the reduced ZmRAVL1 expression, which consequently down-regulates the brd1 expression and leads to the decreased brassinosteroid level, thereby reducing the leaf angle. The introgression of UPA2 teosinte allele into maize and the manipulation of ZmRAVL1 significantly increase maize yield with increased plant density. These findings have paved a new avenue for molecular breeding of high-yield maize varieties.

In rice breeding, ‘high yielding’ and ‘early maturing’ are negative-reciprocally regulated traits. A recent study identified a major maturity duration regulatory gene, Early flowering-completely dominant (Ef-cd), which encodes a long noncoding RNA. Ef-cd IncRNA overlaps with the antisense transcript of the OsSOC1 gene. Ef-cd positively regulates the expression of OsSOC1 and H3K36me3 deposition. Varieties and their derivatived hybrids harboring Ef-cd allele show 7-20 d early-maturation compared to their respective wild types at different latitudes, but without a concomitant yield penalty. Moreover, among 1 439 elite hybrid rice varieties, all of the hybrid cultivars with homozygous or heterozygous Ef-cd alleles mature significantly earlier. The mechanism of Ef-cd-promoted maturity without yield penalty is attributed to its facilitating nitrogen utilization and improving photosynthesis. Thus, Ef-cd may balance early maturating with stable grain yield, and can be used for molecular design breeding in rice.

The fungal pathogen Rhizoctonia solani causes banded leaf and sheath blight (BLSB) in maize (Zea mays) and sheath blight (ShB) in rice (Oryza sativa). R. solani has a wide range of host and severely threatens crop production. The lack of resistant resources against BLSB and the poor understanding of disease resistance mechanism hamper the development of effective approaches to control this fungal disease. Recently, Chinese scientists have made a breakthrough discovery that an F-box protein ZmFBL41 mediates the proteasomal degradation of cinnamyl-alcohol dehydrogenase ZmCAD to regulate BLSB and ShB disease resistance. By genome-wide association analysis, GRMZM2G 109140 (ZmFBL41) was identified as a major QTL candidate gene associated with BLSB disease resistance. ZmFBL41 protein is a member of SKP1-Cullin-F-box (SCF) E3 ubiquitin ligase complex which mediates the degradation of ZmCAD, thus reducing the accumulation of lignin and rendering maize more susceptible to R. solani. Interestingly, in the maize inbred line Chang7-2, the natural variation on two amino acids in ZmFBL41 ^Chang7-2 results in resistance against BLSB. Mechanistically, ZmFBL41 ^Chang7-2 fails to interact with and degrade its substrate ZmCAD, leading to the accumulation of lignin, which consequently enhances maize resistance. This study not only discovers a novel molecular mechanism underlying disease resistance of maize against R. solani, but also provides important theoretical basis and genetic resources for breeding maize and other crops with improved disease resistance.

Targeted base editing with CRISPR-Cas systems is a breakthrough in genome editing technologies and is widely used in studies of humans, animals and plants. Recently, Chinese scientists discovered that the cytosine base editor (CBE) including BE3 and HF1-BE3 but not the adenine base editor (ABE) has substantial promise for genome-wide off-targeted editing in rice. This discovery is of great significance to the application and further optimization of targeted base editing.

The most well established auxin signaling pathway is initiated from transport inhibitor response (TIR1)-mediated perception and degradation of Aux/IAAs, eventually leads to depression of auxin response factors (ARFs). A recent study from the Tongda Xu lab showed that high levels of auxin induced the cleavage of the plasma membrane localized transmembrane kinase receptor 1 (TMK1). The cleaved TMK1 C-terminus translocated to the nucleus and phosphorylated the nuclear localized non-canonical IAA32/34, which regulate the auxin signaling response by interacting with ARFs. The TMK1-IAA32/34-ARFs module, acting independently from the TIR1-dependent auxin signaling pathway, nicely interprets how the local auxin accumulation modulates asymmetric growth during apical hook development.

Nucleotide binding, leucine-rich repeat (NLR) immune receptors are a major family of plant resistance (R) proteins, which are also found in animals. NLRs turn on immune signaling by recognizing pathogen-specific effectors in plants. Although the first few plant NLR R genes were cloned more than 25 years ago, the activation mechanism remained elusive. No structure is available for the full-length plant NLRs despite attempts over the last 2 decades. Recently, studies from the Chai, Zhou and Wang labs, published in Science, solved the structure of zygote arrest 1 (ZAR1) before and after effector recognition, which fills a huge gap in NLR biology. This mini review briefly summarized these findings and related progresses, and highlighted further challenges in NLR-mediated immune signaling field.

Root-associated microbial communities in the soil play fundamental roles in plant nutrition uptake and fitness. However, how plants shape root microbial communities and how the microbes affect the fitness of their hosts remain elusive. Recently, Chinese scientists have made a breakthrough discovery that the nitrogen-use efficiency between indica and japonica rice varieties is associated with different root microbiota in rice. Nitrogen metabolism is greatly enriched in indica-enriched bacteria as compared with japonica-enriched bacteria. Rice NRT1.1B, a nitrogen sensor contributing to nitrogen use divergence between rice subspecies, is associated with the recruitment of these bacterial taxa. Inoculation of the japonica variety with indica-enriched bacteria can improve rice growth in organic nitrogen conditions in the SynCom experimental system. This work highlights the links between root microbiota and nitrogen use in rice and could be exploited to modulate the root microbiota that increase crop productivity and sustainability.

Astaxanthin, a red-colored ketocarotenoid, has stronger antioxidant activity than other carotenoids or vitamin E. It has been reported in anti-aging, improving immunity, preventing and treating several diseases and widely used in pharmaceuticals, nutraceuticals, and the aquaculture industry. However, β-carotene ketolase genes exist only in some species of microalgae, bacteria and yeast and not in most higher animals and plants. Humans consume astaxanthin mainly from some seafood, such as salmon, shellfish, and trout. Rice, as the most important food crop in the world, is the main grain of nearly half of the world and two thirds of China’s population. However, rice lacks carotenoid precursors, and the engineered biosynthesis of astaxanthin in rice has not been successful. Recently, Chinese scientists successfully engineered sophisticated β-carotene, keratin and astaxanthin biosynthesis in rice endosperm by the self-made multi-gene stacking expression system, which achieved precise synthesis from precursors and intermediate to final products regulated by a complex metabolic network.

Heterosis has been widely applied to improve the productivity and adaptability of crops. However, progeny of hybrid exhibits segregation, hybrid seed need to be produced using male sterile and restorer lines each year. Hybrid seed production is prohibitively expensive and the purity of hybrid seed is uncertain, that limit the extension of its large adoption. Recently, Chinese scientists obtained clonal F₁ seeds from hybrid rice by genome editing of some meiosis and fertilization related genes. Their work shed light on utilization and fixation of the heterosis by ‘one line’ method.

Programmed cell death (PCD) is an active and genetically controlled process that results in cell death in a multicellular organism. PCD plays important roles in plant development and defense and can be induced by increased reactive oxygen species (ROS) in mitochondria. Previous studies by Jiayang Li’s group in the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences identified a cell death mutant, mod1, in Arabidopsis. Although the authors suggested that signal communication between chloroplast and mitochondrion contributes to PCD in mod1, the underlying mechanisms remain elusive. Recently, by screening the suppressors of mod1, they cloned three new suppressor genes, plNAD-MDH, DiT1 and mMDH1, which encode a plastid-localized NAD-dependent malate dehydrogenase, a chloroplastic dicarboxylate transporter, and a mitochondrial malate dehydrogenase, respectively. Mutations in these three genes each can suppress ROS accumulation and PCD in mod1. Functional analyses of these genes demonstrated that malate is transported from chloroplasts to mitochondria and triggers ROS generation and PCD in plant. This study expands our knowledge of intracellular communications between organelles and provides new understanding of molecular mechanisms of PCD in plants, which is an important progress in this field.

Programmed cell death (PCD) plays important roles in regulating plant development and stress responses, and the reactive oxygen species (ROS) acts as the key regulator in PCD process. However, the underlying mechanism remains to be addressed. Recently, the Jiayang Li’s group from Institute of Genetics & Developmental Biology, Chinese Academy of Sciences has made great breakthroughs in the mechanism of PCD regulated by ROS. The group demonstrated that malate shuttling from the chloroplast to mitochondrion triggers ROS production and subsequent PCD in Arabidopsis. The study provides novel results for understanding the mechanism of PCD regulation.

Programmed cell death (PCD) is a fundamental biological process in plant development and is also related to plant response to environment stresses. Recently, Chinese scientists have made breakthroughs in understanding the molecular mechanisms of PCD signaling pathways in plants.

Cadmium (Cd) is a highly toxic heavy metal that threatens human health. Rice is one of food crops that can accumulate Cd in the grain to levels that are unsafe for human consumption. With increasing contamination of heavy metals in paddy soils in China, considerable proportions of rice grain produced in some areas of southern China exceed the 0.2 mg·kg^-1 Cd limit of the Chinese food standard, which causes widespread public concern. Molecular breeding of rice varieties that accumulate Cd in straw for removing Cd from paddy soil while producing safe grain is one of the strategies for phytoremediation of contaminated soils. Recently, Luo et al. identified a quantitative trait locus CAL1 in rice that specifically regulates the accumulation of Cd in leaves. CAL1 encodes a defensin-like protein that can chelate Cd in the cytosol and facilitates Cd secretion from xylem parenchyma cells into xylem vessels for long-distance transport. The chelation of Cd to CAL1 appears to prevent Cd from being loaded into the phloem for transport to rice grain. Thus, CAL1 does not affect the accumulation of Cd in rice grain. These findings shed light on understanding the molecular mechanism of Cd translocation and allocation in rice and provide a molecular tool to breed rice varieties that may be used to remove Cd from the soil without affecting grain Cd concentration.

Macleaya cordata is a traditional Chinese medicinal plant species from the Papaveraceae family and is considered a safe resource of antimicrobial feed additive for livestock for its production of antimicrobial-active constituents such as sanguinarine (SAN) and chelerythrine (CHE). Chinese scientists reported the de novo whole-genome sequencing of M. cordata, the first to be sequenced from the Papaveraceae family. They then used the tissue-specific transcriptome and metabolic profiling data to identify 16 candidate genes involved in the biosynthesis of SAN and CHE. Homologous cloning and substrate-feeding experiments were then applied to verify the biochemical functions of the 14 candidates. This research set up the foundation for further improvement of the biosynthesis, regulation and biosynthetic chemistry of benzylisoquinoline alkaloids and also provides a powerful tool for the dissection of metabolic pathway(s) in other species from the Papaveraceae family.

High-throughput sequencing technologies bring us the genomics age, consequently facilitates genome-wide association studies (GWAS) of complex traits in crops. But GWAS has not yet been successful in detecting the genetic basis of phenotypic variations in rice due to limited mapping resolution. Recently, chinese scientists have cloned a QTL for rice grain length and weight using GWAS combining with functional investigations and propelled the molecular dissection of rice QTL from genetics to genomics. Their study provided us not only a model for investigating rice complex traits and evolutionary changes using “omics” resources but also a valuable gene for rice breeding.

High temperature stress is a significant factor limiting rice growth and yield formation. DEAD-box RNA helicase plays a vital role in the processing of pre-rRNA and plant stresses response. Recently, Chinese scientists have great progress in the molecular mechanism of regulating thermo-tolerant of DEAD-box RNA helicase in rice.