Jianxin Shi

Shanghai Jiao Tong University | SJTU · Genetic and Developmental Biology

Male reproduction, an essential and vulnerable process in the plant life cycle, is easily disrupted by changes in surrounding environmental factors such as temperature, photoperiod, or humidity. Plants have evolved multiple mechanisms to buffer adverse environmental effects; understanding these mechanisms is crucial to increase crop resilience to a...

We express our deepest condolences on the passing of Prof. Dabing Zhang, our esteemed mentor, colleague, and friend. Prof. Zhang, a member of the Editorial Board of Seed Biology, passed away at the age of 56. He served as a Chair Professor in the School of Life Sciences & Biotechnology at Shanghai Jiao Tong University (SJTU), a Professor at the Uni...

Arabidopsis sepals coordinate flower opening in the morning as ambient temperature rises; however, the underlying molecular mechanisms are poorly understood. Mutation of one heat shock protein encoding gene, HSP70-16 , impaired sepal heat stress responses (HSR), disrupting lipid metabolism, especially sepal cuticular lipids, leading to abnormal flo...

In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been p...

Key message Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. Abstract The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN)...

A key to achieve the goals put forward in the UN’s 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is...

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GW...

[This corrects the article DOI: 10.3389/fpls.2022.1006735.].

A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is...

Key message Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Abstract Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deleti...

The thick cell wall and low astaxanthin productivity were two important bottlenecks limiting industrial production of astaxanthin via Haematococcus pluvialis. This study reports a strategy for increasing production and bio-accessibility of astaxanthin in H. pluvialis by screening and culturing red motile cells under high light condition. Compared w...

The vacuole is an important organelle with multiple functions in plants, and the tonoplast that wraps the vacuole also plays essential roles in intracellular trafficking and ion homeostasis. Previous studies found that tonoplast proton pumps regulate embryo development and morphogenesis through their effects on vacuole biogenesis and distribution,...

Key message The cloning and characterization of a novel C2H2 zinc finger protein that affects rice eating and cooking quality by regulating amylose content and amylopectin chain-length distribution in rice. Abstract One of the major objectives in rice breeding aims to increase simultaneously yield and grain quality especially eating and cooking qu...

Key message Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Abstract Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle hav...

Key message AtMYB31, a R2R3–MYB transcription factor that modulates wax biosynthesis in reproductive tissues, is involved in seed development in Arabidopsis. Abstract R2R3–MYB transcription factors play important roles in plant development; yet, the exact role of each of them remains to be resolved. Here we report that the Arabidopsis AtMYB31 is r...

γ‐oryzanol is the most studied component in rice (Oryza sativa L.) bran oil. It is not only associated with physiological processes of rice growth and development but also grain quality that is related to human health. Previous studies focused mainly on γ‐oryzanol composition and content in various rice cultivars, while its biosynthetic and regulat...

Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here, we report its genetic base using metabolite-based genome-wide association study (mGWAS) and metabolite-based quantitative traits locus (mQTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and...

Low temperature germination (LTG) is a key agronomic trait in rice ( Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover po...

The aerial surfaces of plants are covered by a layer of cuticular wax that is composed of long-chain hydrocarbon compounds for protection against adverse environmental conditions. The current study identified a maize (Zea mays L.) APETALA2/ethylene-responsive element-binding protein (AP2/EREBP)-type transcription factor, ZmEREB46. Ectopic expressio...

The reproductive development process of rice is not only important for basic developmental biology research, but also of great benefit to production practice. However, current understanding of the reproductive growth process is relatively limited, especially in the later stages of development. Here we report that OsGAMYBL2, a homologous gene of GAM...

Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association...

GDSL esterases/lipases (GELPs), present throughout all living organisms, have been a very attractive research subject in plant science due mainly to constantly emerging properties and functions in plant growth and development under both normal and stressful conditions. This review summarizes the advances in research on plant GELPs in several model...

Cytochrome P450 (CYP) catalyzes a wide variety of monooxygenation reactions in plant primary and secondary metabolisms. Land plants contain CYP703, belonging to the CYP71 clan, which catalyzes the biochemical pathway of fatty acid hydroxylation, especially in male reproductive tissues. Korean/Asian ginseng (Panax ginseng Meyer) has been regarded as...

Formins are actin-binding proteins that are key to maintaining the actin cytoskeleton in cells. However, molecular mechanisms controlling the stability of formin proteins in plants remain unknown. Here, we have identified six rice SIAH-type E3 ligases, named RIP1-6 (RMD Interacting Protein 1–6) respectively, with ubiquitination enzyme activity in v...

The actin cytoskeleton is crucial for plant morphogenesis, and organization of actin filaments (AF) is dynamically regulated by actin-binding proteins. However, the roles of actin-binding proteins, particularly type II formins, in this process remain poorly understood in plants. Here, we report that a type II formin in rice, Oryza sativa formin hom...

Trichomes that cover the epidermis of aerial plant organs play multiple roles in plant protection. Compared with a unicellular trichome in model plants, the development mechanism of the multicellular trichome is largely unclear. Notably, variations in trichome development are often accompanied by defects in the biosynthesis of cuticle and secondary...

Key message Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination. Abstract Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, ou...

Differentially expressed genes help in exploring plant defense mechanism under variable stress conditions. In current investigation, RNA sequencing was executed to explore the differential gene expression in resistant and susceptible varieties of Cotton (Gossypium hirsutum), upon infection with Aspergillus tubingensis. Comparative RNA-Seq of contro...

Abscisic acid (ABA) transport plays a crucial role in seed germination under unfavorable conditions such as cold stress. Heat shock protein 70 (HSP70) and voltage-dependent anion channel (VDAC) protein are both involved in cold stress responses in Arabidopsis. However, their roles in seed germination with regard to ABA signaling remains unknown. He...

Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from geneti...

Brown rot is a common and devastating disease of different fruits and vegetables. During 2018, a profound brown rot was observed on lemon (C itrus lemon L .) in Islamabad, Pakistan and adjacent areas. This study was designed to identify disease causing pathogen of this disease. Diseased lemon fruit were collected from the orchards and disease caus...

Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice ( Oryza sativa L.), wheat ( Triticum aestivum ), and barley ( Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interac...

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil...

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in...

Rapidly increasing industry has resulted in greater discharge of hazardous chemicals in the soil. In the current study, soil samples were collected from Nanjing mine (32*09' 19.29'' N 118*56'057.04'' E) and subjected to heavy metal analysis and microbe isolation. A total of 460 fungi were isolated, and five of these were yeast strains. Most of the...

Targeted nuclease based genome editing technology particularly clustered regularly interspaced short palindromic repeats (CRISPR) that allows to manipulate virtually almost any genomic sequences has greatly facilitated both basic and applied researches in plants. However, so far, very few of them has entered to the field and much less to the kitche...

Key message: The mutation of FAX1 (Fatty Acid Export 1) disrupts ROS homeostasis and suppresses transcription activity of DYT1-TDF1-AMS-MS188 genetic network, leading to atypical tapetum PCD and defective pollen formation in Arabidopsis. Fatty acids (FAs) have multiple important biological functions and exert diverse cellular effects through modul...

Key message A multiplex ligation-dependent probe amplification (MLPA)-based method was developed and successfully utilized to efficiently detect both CRISPR/Cas9-induced and naturally occurred mutations in rice. AbstractThe site-specific nuclease-based CRISPR/Cas9 system has emerged as one of the most efficient genome editing tools to modify multip...

Plant heat stress response (HSR) involves many heat shock proteins (HSPs), each might has distinct function. Thus, understanding of molecular bases of corresponding responses of each HSP in plant is essential for both basic and applied researches. While previous work focused dominantly on high temperature heat stress, studies on mild heat stress (a...

Stigma exsertion is an important agricultural trait that facilitates the application of heterosis in crop breeding. Although several quantitative trait loci associated with stigma exsertion have been fine mapped or cloned, the underlying genetic basis, particularly in legumes, remains unclear. In this study, we identified and characterized the exse...

The primexine formation and plasma membrane undulation are the crucial steps of pollen wall formation in many angiosperms. However, the molecular mechanism underlining these processes is largely unknown. In Arabidopsis, NEW ENHANCER OF ROOT DWARFISM1 (NERD1), a transmembrane protein, was reported to play pleiotropic roles in plant development inclu...

Cytochrome P450 monooxygenase 704B (CYP704B), a member of the CYP86 clan, was found to be needed in Arabidopsis and rice to biosynthesize precursors of sporopollenin through oxidizing fatty acids. In the present study, we cloned and characterized a CYP704B gene in Panax ginseng, named PgCYP704B1. It shared high sequence identity (98–99%) with CYP70...

Although Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has been widely used for basic research in model plants, its application for applied breeding in crops have faced strong regulatory obstacles, due mainly to a poor understanding the authentic output of this system, particularly in higher ge...

Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, genome-wide association analysis (G...

Haematococcus pluvialis is a kind of native bioresource, which accumulate high abundance of astaxanthin, one of the most important bioactive compounds, under various biotic and abiotic stress conditions particularly under high light. However, the global metabolic responses to high light in general and the relationship between primary metabolism and...

Astaxanthin produced by Haematococcus pluvialis is an economically valuable ketocarotenoid pigment that benefits the health of human being. Astaxanthin can be accumulated in H. pluvialis cells up to 3% under high light stress. In this study, by adding 1 mM potassium iodide (KI) into the culture media of H. pluvialis cells under high light condition...

Aspergillus tubingensis is an important pathogen of economically important crops. Different biotic stresses strongly influence the balance of metabolites in plants. The aim of this study was to understand the function and response of resistance associated metabolites which, in turn are involved in many secondary metabolomics pathways to influence d...

Rice flag leaves are major source organs providing more than half of the nutrition needed for rice seed development. The dynamic metabolic changes in rice flag leaves and the detailed metabolic relationship between source and sink organs in rice, however, remain largely unknown. In this study, the metabolic changes of flag leaves in two japonica an...

Degeneration of apical spikelets and reduced panicle fertility are common reasons for low seed-setting rate in rice (Oryza sativa). However, little is known about the underlying molecu- lar mechanisms. � Here, we report a novel degenerated panicle and partial sterility 1 (dps1) mutant that showed panicle apical degeneration and reduced fertility in...

The timely programmed cell death (PCD) of the tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development, including the deposition and patterning of the pollen wall. Although several genes involved in tapetal PCD and pollen wall development have been characterized, the underlying regulatory mechanism re...

In flowering plants, pollen wall is a specialized extracellular cell wall matrix surrounding male gametophytes and acts as a natural protector of pollen grains against various environmental and biological stresses. The formation of pollen wall is a complex but well‐regulated process, which involves the action of many different genes. However, genet...

Molecular characteristics including information of insertion site, flanking sequence, and copy numbers are the base for the safety assessment and subsequent monitoring of genetically modified organisms (GMOs), which has to be revealed thoroughly in a case-by-case manner. Although both polymerase chain reaction (PCR)-based and next-generation sequen...

Degeneration of apical spikelets and reduced panicle fertility are common reasons for low seed‐setting rate in rice ( Oryza sativa ). However, little is known about the underlying molecular mechanisms. Here, we report a novel degenerated panicle and partial sterility 1 ( dps1 ) mutant that showed panicle apical degeneration and reduced fertility in...

Haematococcus pluvialis, a commercial microalga, accumulates massive astaxanthin under biotic and abiotic stress conditions, particularly under high light conditions. Upon exposure to high light stress, the green motile cells rapidly differentiate into non-motile red cyst, which undergo dramatic morphology changes during subsequent encystment, incl...