The wheat sucrose synthase gene TaSus1 is a determinant of grain number per spike

Some haplotypes of the sucrose synthase gene TaSus1 are associated with thousand-grain weight(TGW)in wheat(Triticum aestivum L.).However,no mutations have been identified within the gene to test this association.The effects of TaSus1 on grain number per spike(GNS)also are largely unknown.Our previous genome-wide association study identified TaSus-A1 as a candidate gene controlling fertile spikelet number per spike(FSN).In the present study,we generated two independent mutants for the three TaSus1 homoeologs by CRISPR/Cas9-mediated genome editing.The triple mutants displayed lower FSN,GNS,grain number per spikelet(GNST),and TGW than wild-type plants.In 306 hexaploid wheat accessions,two single-nucleotide polymorphisms in TaSus-A1 contributed differently to GNS.Introgression of the two alleles into a wheat genetic background confirmed their effects.The alleles differed in geographical distribution among the accessions.

Comparative Study on the Expression of Genes Involved in Carotenoid and ABA Biosynthetic Pathway in Response to Salt Stress in Tomato

Carotenoid biosynthetic pathway produces not only pigments that protect photosynthetic system against photo-oxidative damage, but also precursors of abscisic acid, the major hormone regulates stress responses. To understand the response of carotenoid biosynthetic pathway to salt stress, the expression of the genes involved in carotenoid and ABA biosynthesis were compared in cultivated tomato Solanum lycopersicon cv. Moneymaker and its relative wild genotype S. pimpinellifolium （PI365967） together with the contents of carotenoids and ABA. The results showed that 11 of the 15 genes investigated were up-regulated and four unaltered in Moneymaker after 5 h of salt stress; whereas only four genes were up-regulated, four unaltered, and seven down-regulated in PI365967 after stress. Further comparison revealed that 11 salinity-induced genes were expressed significantly lower in Moneymaker than in PI365967 under normal condition, and 8 of them were induced to similar levels after salt stress. In consistence, ABA level was doubled in Moneymaker but kept consistent in PI365967 after salt stress, though the contents of neoxanthin, violaxanthin, [3-carotene, lutein, and total carotenoids were kept unchanged in both species. Since it is known that PI365967 is more tolerant to salt stress than Moneymaker, we proposed that the constitutive high level of carotenoid and ABA biosynthetic pathway under normal growth condition could be benefit to PI365967 for establishing the early response to salt stress. In addition, CrtR-bl and CrtR-b2 that encode [3-carotenoid hydroxylases were the only genes in carotenoid biosynthetic pathway that were up-regulated by salt stress in both species. The CrtR-b2 gene was cloned from both species and no essential difference was found in the encoded amino acid sequences. Transformation of CrtR-b2 to tobacco improved the seed germination under salt stress condition, indicating that the hydrolysis of β-carotenoid is the target of transcriptional regulation of the carotenoid biosynthesis in both tomato cultivar and wild relative.

Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation

Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures.However,the accumulation of metabolites during cold acclimation(CA)in V.amurensis remains largely unknown.In this study,plantlets of V.amurensis and V.vinifera cv.Muscat of Hamburg were treated at 4℃ for 24 and 72 h,and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry.Most of the identified metabolites,including carbohydrates,amino acids,and organic acids,accumulated in the two types of grape after CA.Galactinol,raffinose,fructose,mannose,glycine,and ascorbate were continuously induced by cold in V.amurensis,but not in Muscat of Hamburg.Twelve metabolites,including isoleucine,valine,proline,2-oxoglutarate,and putrescine,increased in V.amurensis during CA.More galactinol,ascorbate,2-oxoglutarate,and putrescine,accumulated in V.amurensis,but not in Muscat of Hamburg,during CA,which may be responsible for the excellent cold tolerance in V.amurensis.The expression levels of the genes encodingβ-amylase(BAMY),galactinol synthase(GolS),and raffinose synthase(RafS)were evaluated by quantitative reverse transcription-PCR.The expression BAMY(VIT_02s0012 g00170)and RafS(VIT_05s0077 g00840)were primarily responsible for the accumulation of maltose and raffinose,respectively.The accumulation of galactinol was attributed to different members of GolS in the two grapes.In conclusion,these results show the inherent differences in metabolites between V.amurensis and V.vinifera under CA.

Chemical Constituents of Pedicularis longiflora var. tubiformis (Orobanchaceae), a Common Hemiparasitic Medicinal Herb from the Qinghai Lake Basin, China

Pedicularis longiflora var.tubiformis(Orobanchaceae)is an abundant parasitic herb mainly found in the Xiaopohu wetland of the Qinghai Lake Basin in Northwestern China.The species has an important local medicinal value,and in this study,we evaluated the chemical profile of its stems,leaves and seeds using mass spectrometry.Dried samples of stems,leaves and seeds were grinded,weighted,and used for a series of extractions with an ultrasonic device at room temperature.The chemical profiles for each tissue were determined using Gas Chromatography-Mass Spectrometry(GC-MS)and Liquid Chromatography-Mass Spectrometry(LC-MS).Twenty-seven amino acids and organic acids were identified and quantified from stems,leaves and seeds.The content of amino acids detected in leaves and seeds was higher than the amount found in stems.Six fla-vonoids were also detected,including isoorientin,orientin,luteolin-7-O-glucoside,luteolin,apigenin and tricin.The concentrations of luteolin-7-O-glucoside,luteolin and tricin were the highest and more concentrated in leaves,while that of orientin was the lowest and mainly found in stems.Soluble monosaccharides and oligosaccharides below tetramer were also examined,and our analyses detected the presence of arabitol,fructose,galacturonic acid,glucose,glucuronic acid,inositol,sucrose,and trehalose.This is the first study to identify and quantify the main components of amino acids,organic acids,flavonoids and soluble sugars from stems,leaves and seeds of P.longiflora var.tubiformis.Eight of the amino acids detected are essential for humans,highlighting the medicinal importance of this species.Results shown here can be used as a reference case to develop future studies on the chemical constituents of Pedicularis herbs and other medicinal plants from the Tibetan region.

Progeny selections of coffee cultivar'Mundo Novo'with potential for the specialty coffee market

Coffee is one of the most popular beverages in the world with a global market worth over$USD 100 billion.In Brazil,the Arabica coffee(Coffea arabica)cultivar'Mundo Novo'is one of the most planted cultivars due to its high yield,growth vigor and stability.However,this traditional cultivar is generally not considered a good production source for specialty coffee.Exploring intra-cultivar variation and selecting'Mundo Novo'progenies with superior sensory quality may provide a viable option for coffee producers targeting the rapidly expanding specialty coffee market.The present study analyzed cup quality attributes,agronomic characteristics and genetic identities of 14 genotypes selected from the putative progenies of'Mundo Novo'and assessed their potential as specialty coffee in Brazil.Beverage quality was assessed using chemical and sensory analysis according to the methodology proposed by the Specialty Coffee Association(SCA)in six selected genotypes.High sensory quality,with sensory scores above 80 points was observed which qualified them in the very good and excellent quality categories.Genetic identities of the 14 selections were verified using 96 SNP markers,based on 57 reference cultivars from the coffee collection of EPAMIG(Empresa de Pesquisa Agropecuária de Minas Gerais),Brazil.Multivariant and Bayesian clustering analysis generated consistent results and confirmed that all the 14 selections were progenies of'Mundo Novo'.Among them,the top three genotypes(SGAB 1,SGAB 7 and SGAB 8)were selected as promising genotypes,either for future genetic improvement or for direct use in the production of specialty coffee.

An overview of the endogenous and environmental factors related to the Coffea arabica flowering process

The transition of vegetative meristems to a reproductive state followed by floral development and flowering is a complex process regulated by many regulatory pathways that integrate(epi)genetic and environmental factors to guarantee the reproductive success in angiosperms.In woody and perennial species,such as coffee trees,the extended life cycle reflects adaptive strategies,i.e.,two-year cycle,sequential flowering and bud latency during the winter,that ensure reproductive success in a variable environment.The dynamics of coffee flowering integrate multiple stimuli to induce morpho-physiological changes,especially during the reproductive phase.We discussed diverse stimuli which are directly and indirectly associated with molecular pathways related to the reproductive meristem transition and floral development until anthesis.Here,we propose to redefine some concepts regarding coffee floral development,such as:i)a summary of genes possibly involved in the flowering pathways;ii)a new classification of buds by position in the node(B1-B4)to avoid misunderstandings with the uneven developmental stages;iii)comparative ABC model to Arabidopsis and tomato to allow evolutionary discussions of whorls development in Coffea sp.From this,we expect to collaborate to drive future studies towards coffee breeding and production,for example,improving floral bud activation,controlling the flowering time,anthesis synchronization to produce more homogeneous ripening fruits,reducing abortion or early flower openings,and increasing fruitification.Moreover,we think that the explored relationship between physiological and molecular approaches during the coffee flowering may be extended to understand other tropical perennial species,especially those with asynchronous flowering behavior,and to understand evolutive aspects in Rubiaceae.

Plant regeneration in the new era:from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways.Like animal regeneration,cell totipotency and pluripotency are the molecular basis of plant regeneration.Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration.Specifically,plant hormones,cell division,epigenetic remodeling,and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells.Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species,with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity.Conducting multi-omics studies at the single-cell level,tracking plant regeneration processes in real-time,and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration,improve crop regeneration efficiency,and contribute to future crop design.

The molecular regulation of cell pluripotency in plants

Plants have a remarkably regenerative capability to replace the damaged organs or form the new organs and individuals both in vivo and in vitro,which is fundamental for their developmental plasticity and the agricultural practices.The regenerative capacities of plants are highly dependent on the totipotency or pluripotency of somatic cells,whose fates are directed by phytohormones,wounding,and other stimuli.Recent studies have revealed that the two types of cellular reprogramming are involved in the acquisition of cell pluripotency during plant in vitro and in vivo regeneration programs.This review focuses on the recent advances of the cellular origin,molecular characteristic,and genetic and epigenetic regulations of cell pluripotency acquisition in plants,highlighting the molecular frameworks of cellular reprogramming activated by diverse stimuli and their possible potentials in regeneration-based plant biotechnologies.

Toward a Molecular Understanding of Plant Hormone Actions

Plants rely on a diverse set of small-molecule hormones to regu- late every aspect of their biological processes including develop- ment, growth, and adaptation. Since the discovery of the first plant hormone, auxin, hormones have always been at the frontier of plant biology.

Unlocking the power of tandem repeat variations to fine-tune rice phenotypes

The diversity of crop phenotypes is shaped by numerous genomic variants.For staple cereals like rice,lots of functional variants,including quantitative trait locus(QTLs),have been identified and used to improve various crop traits(yield,quality,architecture,etc.).To breed ideal crop cultivars for agricultural production,we need more and more precise modulation of phenotypes to obtain desirable traits.Over the past decade,genome editing techniques have enabled us to precisely change crop genome sequences,and also functional variants[1],[2],[3].

SIZ1-Mediated SUMOylation of TPR1 Suppresses Plant Immunity in Arabidopsis

Plant immune responses are tightly regulated to ensure their appropriate deployment. Overexpression of TOPLESS-RELATED 1 (TPR1), a SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 (SNC1)-interacting protein, results in autoimmunity that reduces plant growth and development. However, how TPR1 activity is regulated remains unknown. Loss of function of SIZ1, a (SUMO) E3 ligase, induces an autoimmune response, partially due to elevated SNC1 levels. Here we show that SNC1 expression is upregulated in Arabidopsis thaliana siz1-2 due to positive-feedback regulation by salicylic acid. SIZ1 physically interacts with TPR1 and facilitates its SUMO modification. The K282 and K721 residues in TPR1 serve as critical SUMO attachment sites. Simultaneous introduction of K282R and K721R substitutions in TPR1 blocked its SUMOylation, enhaneed its transcriptional co-repressor activity, and increased its association with HISTONE DEACETYLASE 19 (HDA19), suggesting that SUMOylation of TPR1 represses its transcriptional co-repressor activity and inhibits its interaction with HDA19. In agreement with this finding, the simultaneous introduction of K282R and K721R substitutions enhanced TPR1 mediated immunity, and the tpr1 mutation partially suppressed autoimmunity in siz1-2. These results demonstrate that SIZ1-mediated SUMOylation of TPR1 represses plant immunity, which at least partly contributes to the suppression of autoimmunity under nonpathogenic conditions to ensure proper plant development.

Physiological and Molecular Features of Puccinellia tenuiflora Tolerating Salt and Alkaline-Salt Stress

Saline-alkali soil seriously threatens agriculture productivity; therefore, understanding the mechanism of plant tolerance to alkaline-salt stress has become a major challenge. Halophytic Puccinellia tenuiflora can tolerate salt and alkaline-salt stress, and is thus an ideal plant for studying this tolerance mechanism. In this study, we examined the salt and alkaline-salt stress tolerance of P. tenuiflora, and analyzed gene expression profiles under these stresses. Physiological experiments revealed that P. tenuiflora can grow normally with maximum stress under 600 mmol/L NaCl and 150 mmol/L Na 2 CO 3 （pH 11.0） for 6 d. We identified 4,982 unigenes closely homologous to rice and barley. Furthermore, 1,105 genes showed differentially expressed profiles under salt and alkaline-salt treatments. Differentially expressed genes were overrepresented in functions of photosynthesis, oxidation reduction, signal transduction, and transcription regulation. Almost all genes downregulated under salt and alkaline-salt stress were related to cell structure, photosynthesis, and protein synthesis. Comparing with salt stress, alkaline-salt stress triggered more differentially expressed genes and significantly upregulated genes related to H ＋ transport and citric acid synthesis. These data indicate common and diverse features of salt and alkaline-salt stress tolerance, and give novel insights into the molecular and physiological mechanisms of plant salt and alkaline-salt tolerance.

A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis

Light and chloroplast function is known to affect the plant immune response; however, the underlying mechanism remains elusive. We previously demonstrated that two light signaling factors, FAR-RED ELONGATED HYPOCOTYL 3（FHY3）and FAR-RED IMPAIRED RESPONSE 1（FAR1）, regulate chlorophyll biosynthesis and seedling growth via controlling HEMB1 expression in Arabidopsis thaliana. In this study, we reveal that FHY3 and FAR1 are involved in modulating plant immunity. We showed that the fhy3 far1 double null mutant displayed high levels of reactive oxygen species and salicylic acid（SA） and increased resistance to Pseudomonas syringae pathogen infection. Microarray analysis revealed that a large proportion of pathogen-related genes, particularly genes encoding nucleotide-binding and leucine-rich repeat domain resistant proteins, are highly induced in fhy3 far1. Genetic studies indicated that the defects of fhy3 far1 can be largely rescued by reducing SA signaling or blocking SA accumulation, and by overexpression of HEMB1, which encodes a 5-aminolevulinic acid dehydratase in the chlorophyll biosynthetic pathway.Furthermore, we found that transgenic plants with reduced expression of HEMB1 exhibit a phenotype similar to fhy3 far1.Taken together, this study demonstrates an important role of FHY3 and FAR1 in regulating plant immunity, through integrating chlorophyll biosynthesis and the SA signaling pathway.

QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F_2 Population

Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controlling grain size and weight,we developed a near isogenic line F_2(NIL-F_2)population,which was derived from a residual heterozygous plant in an F_7 generation of recombinant inbred line(RIL).With the completion of more than 30×whole genome re-sequencing of the parents,two DNA bulks for large and small grains,a total of 58.94 Gb clean nucleotide data were generated.A total of455 262 single nucleotide polymorphisms(SNPs)between the parents were identified to perform bulked QTL-seq.A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5.We designated the major QTL in the candidate region as q TGW5.3.Then,q TGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F_2 population.Furthermore,recombinants and the progeny tests delimited the candidate region of q TGW5.3 to 1.13 Mb,flanked by HX5009(15.15 Mb)and HX5003(16.28 Mb).A set of NILs,selected from the F_2 population,was developed to evaluate the genetic effect of q TGW5.3.Significant QTL effects were detected on grain length,grain width and 1000-grain weight of H12-29 allele with 1.14 mm,-0.11 mm and 3.11 g,which explained 99.64%,95.51%and 97.32%of the phenotypic variations,respectively.

Molecular basis of heading date control in rice

Flowering time is of great significance for crop reproduction,yield,and regional adaptability,which is intricately regulated by various environmental cues and endogenous signals.Genetic approaches in Arabidopsis have revealed the elaborate underlying mechanisms of sensing the dynamic change of photoperiod via a coincidence between light signaling and circadian clock,the cellular time keeping system,to precisely control photoperiodic flowering time,and many other signaling pathways including internal hormones and external temperature cues.Extensive studies in rice(Oryza sativa.),one of the short-day plants(SDP),have uncovered the multiple major genetic components in regulating heading date,and revealed the underlying mechanisms for regulating heading date.Here we summarize the current progresses on the molecular basis for rice heading date control,especially focusing on the integration mechanism between photoperiod and circadian clock,and epigenetic regulation and heading procedures in response to abiotic stresses.

Coordinative regulation of plants growth and development by light and circadian clock

The circadian clock,known as an endogenous timekeeping system,can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth.The synchronization of internal clock with external environmental information needs a process termed entrainment,and light is one of the predominant entraining signals for the plant circadian clock.Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses,including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development.Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system,especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs.We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.

Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives

Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.

aunalysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Dear Editor Salvia miltiorrhiza Bunge （Danshen） is a medicinal plant of the Lamiaceae family, and its dried roots have long been used in traditional Chinese medicine with hydrophilic phenolic acids and tanshinones as pharmaceutically active components （Zhang et al., 2014; Xu et al., 2016）. The first step of tanshinone biosynthesis is bicyclization of the general diterpene precursor （E,E,E）-geranylgeranyl diphosphate （GGPP） to copalyl diphosphate （CPP） by CPP synthases （CPSs）, which is followed by a cyclization or rearrangement reaction catalyzed by kaurene synthase-like enzymes （KSL）. The resulting intermediate is usually an olefin, which requires the insertion of oxygen by cytochrome P450 mono-oxygenases （CYPs） for the final production of diterpenoids （Zi et al., 2014）. While the CPS, KSL, and several early acting CYPs （CYP76AH1, CYP76AH3, and CYP76AK1） for tanshinone biosynthesis have been identified in S. miltiorrhiza （Gao et al., 2009; Guo et al., 2013, 2016; Zi and Peters, 2013）, the majority of the overall biosynthetic pathway, as well as the relevant regulatory factors associated with tanshinone production, remains elusive （Figure 1B）.

Contribution of Genomics to Gene Discovery in Plant Abiotic Stress Responses

Sustaining agricultural production under adverse environ- mental conditions, such as drought and high salinity, rep- resents a major challenge. The discovery of key genes and signal transduction pathways underlying plant responses to environmental stress will play an important role in devel- oping strategies for the genetic improvement of crops to address this challenge. Crop functional genomics has greatly contributed to the identification of abiotic stress-related genes. Current advances in genomic technologies now pro- vide effective and high-throughput methods for identifying stress-related genes at a genome-wide level, especially with the availability of the complete genomic sequence of several model and crop plant species. The development of genetic database resources has allowed bioinformatic approaches to identify stress-tolerant gene families across species based on homology and synteny. Additionally, genome-wide associa- tion studies （GWAS） for complex trait loci in crops have facili- tated the discovery of critical stress-related genes and their favorable alleles.

TATA-box binding protein-associated factor 2 regulates grain size in rice

Grain size,characterized by a combination of grain length,width,and thickness,is one of the major determinants of yield in rice.The present study identified TATA-box binding protein-associated factor 2(TAF2)as an essential component regulating transcription and determining grain size in rice.Map-based cloning showed that a G/T substitution in TAF2 resulted in a naturally occurring mutant called reduced grain size and plant height 1(rgh1).The mutants,with weak edited rgh1 alleles,exhibited a small grain phenotype with reduced grain length and width,while the severe knockout mutant(rgh1-2s)was dwarf and completely sterile.Allelic test performed between rgh1 and several edited alleles confirmed that the mutation in TAF2 caused the rgh1 phenotype.GUS staining showed that TAF2 was mainly expressed in the vascular bundles of roots,stems,leaves,and grains.The cytological analysis revealed that reduced cell division in the glumes resulted in the small grain phenotype of rgh1.Further RNA-sequencing detected altered expression of genes involved in the basic biological processes in rgh1 mutant.These findings provide novel insights into the TAF2-mediated genetic mechanism regulating grain size in rice.