Angiosperm fertilization has been a hot topic in the field of sexual plant reproduction. In recent years, great advances have been made in the studies on some critical steps, such as pollen tube guidance, polytubey block, and fertilization recovery system. However, most of these known mechanisms are synergid cell-based for ensuring successful double fertilization, the counterpart system based on central cell remains poorly understood. A recently published paper from Hongju Li’s lab revealed that the central cell could also secrete peptides as pollen tube attractants to guide the pollen tube entering embryo sac to ensure double fertilization. Interestingly, this mechanism is not synergid-dependent. Thus, the authors revealed a novel fertilization recovery system and bridged a gap in understanding the mechanism underlying double fertilization.

Life science is entering into the era of big data due to the rapid development of high-throughput omics technology. Multi-omics data such as genome, transcriptome, proteome, metabolome have greatly facilitated dissecting the complex and sophisticated regulatory networks of organisms. Recently, a collaborative team led by Lin Li, Fang Yang and Jianbing Yan from Huazhong Agricultural University constructed the first multi-omics integrative network map of maize. This map comprises over 30 000 genes and 2.8 million network edges at the levels of genome, transcriptome, translatome, and proteome, finally forming 1 412 regulatory modules. Using the integrative network map, the research team successfully predicted and confirmed five new functional genes regulating the development of tiller, lateral organ, and kernel in maize. Based on the integrative map and machine learning, the research team identified 2 651 maize flowering time genes that are enriched in eight candidate subnetworks. The biological functions of 20 flowering candidate genes were further validated using CRISPR/Cas9 gene editing technology and EMS mutants. Furthermore, evolutionary analysis of the integrative network map showed that the two subgenomes of maize had undergone a progressive functional differentiation from the levels of co-expression, co-translation to interactome. The construction of the multi-omics integrative network map represents an important breakthrough in maize functional genomics, which provides a new tool for cloning new genes, identifying novel molecular regulatory pathways, and revealing maize genome evolutionary features. This multi-omics integrative network map is a new key to decode maize functional genomics.

Optimal Balance between high yield and stress tolerance is the goal of breeding, which is related to the strategy in choice of both ways. The questions such as which negative regulators of stress tolerance affect yield and how they function are important issues for breeding. Over the past century, owing to the breeding of high-yield varieties, the maize yield has been tremendously increased, but this is accompanied with the increased sensitivity to environmental stresses, and the genetic mechanisms underlying this phenomenon remains elusive. This restricts the breeding of maize cultivars with both high yield and stress tolerance. Both yield traits and stress tolerance are complex quantitative traits, determined by the expression and regulation of a large number of genes. Small RNAs (sRNAs) are important gene expression regulators, and they are generated in large quantities from the maize genome. But the mechanisms underlying their regulation on crop stress responses and yield traits remain largely elusive. Recently, the group of Prof. Mingqiu Dai, collaborated with the groups of Prof. Lin Li and Prof. Feng Li at Huazhong Agricultural University, identified about ten-thousands of drought-responsive sRNAs and eQTLs associated with the expression of these sRNAs, by analyzing the sRNAome and transcriptome of a maize panel consisting 338 natural inbred lines grown under different environment conditions. They cloned an eQTL hotspot named DRESH8, which is a Transposable Element-mediated Inverted Repeat (TE-IR) in a length of about 21.4 kb. Genetic and molecular evidence showed that DRESH8-derived siRNAs directly inhibit the expression of the drought-resistant genes via a post-transcriptional silencing mechanism, and indirectly inhibit the expression of negative regulators of yield-related traits, thus negatively regulating drought response and positively regulate yield-related traits. Further analysis demonstrated that DRESH8 was selected during maize domestication and improvement. Their findings suggest that DRESH8 is a key genetic locus that balances maize yield and drought tolerance, and that IR-mediated balance between maize yield and drought resistance may be a universal mechanism. This study thus revealed a key genetic mechanism underlying balancing crop yield and environmental stress resistance at a genome-wide level, and provided a large number of valuable IR loci for breeding new maize varieties with both high yield and stress tolerance via genetic engineering approaches in the future.

Domestication of wild plants was crucial for human settlement and the development of civilization, which arose independently in many different geographic areas on different wild species. However, these crops underwent variant domestication process displaying the ‘domestication syndrome’ with a common suite of traits. The systematical analysis of convergent selection at genome level may provide important information and genetic resources for crop breeding. Recently, a team led by Xiaohong Yang and Jiansheng Li from Chinese Agricultural University and Jianbing Yan from Huazhong Agricultural University reported the genetic basis of convergent selection between maize and rice at both single gene and whole genome levels. Particularly, they found the maize KRN2 and rice OsKRN2 genes experienced convergent selection and regulated grain number and yield in a similar pathway. Moreover, they identified a large number of orthologous gene pairs that underwent convergent selection during maize and rice evolution, which were enriched in certain pathways including starch metabolism, sugar and coenzyme synthesis. This significant work not only cloned KRN2/OsKRN2 orthologous gene pairs with great value in maize and rice breeding, but also revealed the convergent selection between maize and rice at the genome level, providing critical foundations for studying the molecular basis of domestication syndrome and their applications in breeding practices.

Phosphorus is a macronutrient essential for plant growth and development, however, phosphate (Pi), the major form of phosphorus absorbed by plants, is quite limiting in soil. To cope with this nutritional stress, plants have evolved an array of adaptive responses, which are largely regulated by changing gene expression in response to Pi deficiency. The transcription factor, PHR1 plays a key role in regulating plant transcriptional response to Pi deficiency. Besides, most land plants can form symbiosis with arbuscular mycorrhizal (AM) fungi, through which plants can obtain Pi from soil more effectively. Recently, the research group of Ertao Wang of Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, reported that a PHR-centered gene regulatory network plays an essential role in promoting plant-AM symbiosis. Therefore, PHR not only functions in maintaining plant Pi homeostasis, but also in communicating with beneficial microorganisms in the environments, which provides another route for plants to obtain Pi from soil.

RNAs can be classified into protein-coding RNAs and non-coding RNAs (ncRNAs). Small non-coding RNAs (sRNAs) are generated by Dicer-LIKEs (DCLs) and RNA Dependent RNA Polymerases (RDRs). They are associated with different ARGONAUTE (AGO) effector complexes and play important regulatory roles in diverse biological processes. 21 nt microRNAs (miRNAs) and 24 nt small interfering RNAs (siRNAs) are the most abundant classes of sRNAs in plants. The mechanisms of their biogenesis and functions are well studied. However, the functions of other less abundant sRNAs remain largely unknown. A recent study from Prof. Hongwei Guo's group at Southern University of Science and Technology showed that a class of 22 nt siRNAs is produced by RDR6 and DCL2 when plants are under certain stress conditions, especially upon nitrogen deficiency. These 22 nt siRNAs are loaded into AGO1 and mediate translational repression of target mRNAs including nitrate reductase structural genes NIA1/2, thereby minimizing energy consumption. This work elegantly shows that plants deploy 22 nt siRNAs to achieve a deliberate balance between growth and defense in response to environmental stress.

Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease on wheat not only because of severe yield loss, but also contamination of the grain with deadly mycotoxin. A recent study significantly advanced our understanding how wheat plants can be protected by resistance genes and provided tools in the fight against a major disease. A team led by Prof. Kong in Shandong Agricultural University successfully identified an important FHB resistance gene, Fhb7, and illuminated a mechanism by which this gene might have evolved in plants and a mechanism by which the resistance protein overcome the pathogen. This is an elegant study that not only opens new window to our understanding of plant-pathogen co-evolution, but also allows us to better utilize the rich gene resources of Thinopyrum elongatum for effective breeding of FHB resistance and other traits in wheat.

Microtubules (MTs) are an essential component of the cytoskeleton in eukaryotic cells. Similar to other living organisms, for MTs, the organization and dynamics are critical for the normal growth and development of plants but are also responsible for environmental responses. Recently, Chinese scientists have made groundbreaking discoveries in illustrating the underlying mechanisms of MTs in precise regulating the dynamic organization of cortical arrays in plants.

Domestication, improvement, divergence and introgression are the major stages in the history of tomato breeding. During this period, both fruit weight and quality of tomato were significantly changed; however, the variation in metabolites and the genetic basis remain unknown. Recently, researchers revealed the metabolome changes in tomato breeding by using a multi-omics dataset. The content of 46 steroidal glycoalkaloids (SGAs) declined during tomato domestication, and 7 major loci were identified for 44 of 46 compounds. Pyramiding of these high-value loci significantly reduced the SGAs content. The linkage drag of fruit weight genes and nearby genes might result from altered metabolite profiles during the selection for larger fruits, and the selection for one trait might affect other traits. This work systematically analyzed the effects of selection on crop metabolites by a multi-omics approach, which lays the foundation for tomato quality improvement.

Cold (chilling or freezing) stress affects the growth and geographical distribution of plants, and it is one of the main factors that restricts crop yield and quality. Plants respond to cold signals by activating a series of effectors to adapt to cold stress. MAP protein kinase family plays a crucial role in plant response to environmental stresses, but it remains unclear whether they are directly involved in perception, transduction or/and networks in cold signaling. Recently, three research groups in China highlight the important role of MAP kinase in cold signaling transduction in Arabidopsis thaliana and rice, respectively. Low temperature activates MPK kinase that phosphorylates the ICE1 protein. Stability of ICE1 is controlled by MAP kinase mediated ICE phosphorylation, thus regulating freezing and chilling tolerance in plants. Their studies have advanced our understanding of the ICE1-mediated network of plant cold responses, which is an important breakthrough in the field. The outcome of these studies would provide a powerful theoretical basis for future molecular design breeding in crops.

Flowering is an important process for plants to switch from vegetative to reproductive phase. Vernalization is a process whereby plants acquire the ability to flower after exposure to a prolonged cold temperature. In Arabidopsis, inhibitor-type transcription factor FLOWERING LOCUS C (FLC) is a critical point in vernalization-mediated flowering pathway. Previous studies in Arabidopsis thaliana revealed that two homologous epigenome readers, VAL1 and VAL2, re- cognize a cis DNA element in the nucleation region for Polycomb group (PcG) silencing at the key floral repressor FLC, engaging Polycomb group proteins to induce epigenetic silencing of FLC by histone 3 lysine trimethylation (H3K27me3) during vernalization. This silencing is maintained in subsequent growth and development under normal temperature, namely vernalization memory. How to delete vernalization memory in the next generation to de novo activate FLC expression, preventing the offspring from flowering before or during winter, is not clear. Recently, Chinese scientist have found that a seed-specific transcription factor LEAFY COTYLEDON1 (LEC1) functions in deleting vernalization memory and reactivating the expression of FLC in the pro-embryo by resetting the chromatin states from the silenced state (marked by H3K27me3) to an active state (H3K36me3). This study provides important understanding of molecular and genetic mechanisms for flowering control by vernalization, and a novel strategy to genetically manipulate crop flowering times for the benefit of agricultural production, which is a great breakthrough of this field.

Nitric oxide, as a small active particle, is involved in many physiological activities of animals and plants. In protein posttranslational modifications, NO is mainly in the form of (NO)-based S-nitrosylation. Methylation, as another protein transcription modification, also has an important role in DNA damage and mRNA translation. Although these two areas have many published articles in recent years, there are few reports of the interaction between the two approaches. Recently, Chinese scientists have found that NO can positively regulate the activity of PRMT5, an enzyme that catalyzes Arg symmetric demethylation, through S-nitrosylation at Cys-125. The Arabidopsis prmt5-1 mutant shows severe deve- lopmental defects and hypersensitivity in stress responses. A PRMT5^C125S transgene with non-nitrosylatable mutation at Cys-125 in a prmt5-1 background shows recovered developmental defects but not the stress responses. Furthermore, S-nitrosylation at Cys-125 of PRMT5 was found involved in regulating Arg symmetric demethylation induced by NaCl. The study led to a new direction of protein S-nitrosylation and protein methylation modification, which opened up new research fields and set a new example for research in this field.

With improved transgenic technology, there is great potential for bio-fortification of crops. For complex agronomic traits controlled by multiple genes, single gene transformation is insufficient, and multi-gene engineering is limited to technical factors. Regulation and expression of metabolic modification and a series of related genes is more difficult to break through. Recently, Chinese scientists successfully engineered sophisticated anthocyanin biosynthesis in rice endosperm, which suggests the potential utility of the TransGene Stacking II System for synthetic biology and improving agronomic traits in crops.

The investigations on molecular mechanism of male and female gametophyte interaction have been a hot topic and frontier in the field of sexual plant reproduction. However, due to the great difficulties, many essential questions still remain to be answered. How does the pollen tubes sense the signals from female gametophyte is one of the suspense questions. Recently, Chinese scientists have presented a clear answer to the question and open a new window to seek the mechanism that regulates male gametophyte response to the female gametophyte and ensures successful fertilization.

Grain size and number of spikelets are major factors controlling rice yield. The miR396-GRF module plays multifaceted roles in the growth and development of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Recently, Chinese scientists have revealed novel insights into the role of miR396-GRF modules in controlling grain size and number of spikelets in rice.

To elucidate the molecular mechanism of phytohormones has always been the research frontier and the hot spot in biology, while how to regulate the plant architecture of crops remains a key task of the green revolution. Recently, Chinese scientists have made breakthrough progresses in the signaling pathway of the new phytohormones strigolactones, as well as in their molecular mechanisms for plant architecture regulation in rice. The findings have been awarded “2014 Top 10 Science Breakthrough Progresses in China”.

Tomato and cucumber are both nutritious and delicious vegetables, which are widely cultivated in the world. Recently, Chinese scientists have made breakthrough advances toward our understanding on the molecular mechanisms of how tomato was domesticated and how bitterness was regulated in cucumber.

Plants have evolved sophisticated and fine-tuned mechanisms in response to various stresses. Recently, Chinese scientists have made breakthrough advances toward our understanding on the molecular mechanisms of sensing cold signals in rice, the artificial selection of the sensor during rice domestication, and the regulatory role of phosphorylation in cold signaling in Arabidopsis.