Identification of key genes regulating the synthesis of quercetin derivatives in Rosa roxburghii through integrated transcriptomics and metabolomics

Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.

PbrChiA:a key chitinase of pear in response to Botryosphaeria dothidea infection by interacting with PbrLYK1b2 and down-regulating ROS accumulation

Pear ring rot,caused by the pathogenic fungi Botryosphaeria dothidea,seriously affects pear production.While the infection-induced reactive oxygen species(ROS)burst of infected plants limits the proliferation of B.dothidea during the early infection stage,high ROS levels can also contribute to their growth during the later necrotrophic infection stage.Therefore,it is important to understand how plants balance ROS levels and resistance to pathogenic B.dothidea during the later stage.In this study,we identified PbrChiA,a glycosyl hydrolases 18(GH18)chitinase-encoding gene with high infection-induced expression,through a comparative transcriptome analysis.Artificial substitution,stable overexpression,and virus induced gene silencing(VIGS)experiments demonstrated that PbrChiA can positively regulate pear resistance as a secreted chitinase to break down B.dothidea mycelium in vitro and that overexpression of PbrChiA suppressed infection-induced ROS accumulation.Further analysis revealed that PbrChiA can bind to the ectodomain of PbrLYK1b2,and this interaction suppressed PbrLYK1b2-mediated chitin-induced ROS accumulation.Collectively,we propose that the combination of higher antifungal activity from abundant PbrChiA and lower ROS levels during later necrotrophic infection stage confer resistance of pear against B.dothidea.

Genome-wide identification and characterization of the PbrATG family in Pyrus bretschneideri and functional analysis of PbrATG1a in response to Botryosphaeria dothidea

The pear is an economic fruit that is widely planted around the world and is loved by people for its rich nutritional value. Autophagy is a self-protection mechanism in eukaryotes, and its occurrence often accompanied by the degradation of damaged substances in cells and the recycling of nutrients. Autophagy is one of the mechanisms through which plants respond to environmental stress and plays an important role in plant development and stress resistance. Functional studies of autophagy-related genes (ATGs) have been performed on a variety of plant species, but little information is available on the ATG family in pear (Pyrus bretschneideri Rehd). Therefore, we analyzed the evolutionary dynamics and performed a genome-wide characterization of the PbrATG gene family. A total of 28 PbrATG members were identified.Phylogenetic analysis showed that PbrATGs were more closely related to ATGs of European pear and apple. Evolutionary analysis revealed that whole-genome duplication (WGD) and dispersed duplication events were the main driving forces of PbrATG family expansion.Expression analysis of different pear tissues showed that all the genes were expressed in different pear tissues, and different PbrATGs are expressed at different times and in different locations. Moreover, all PbrATGs also responded to different abiotic stresses, especially salt and drought stress, which elicited the highest expression levels. Pear seedlings were subsequently infected with Botryosphaeria dothidea (B.dothidea). The results showed that different PbrATGs had different expression patterns at different infection stages. According to the gene expression data, PbrATG1a was selected as a key autophagy gene for further analysis. Silencing of PbrATG1a reduced the resistance of pear to B. dothidea, which resulted in increased lesions, reactive oxygen species (ROS) contents, antioxidant enzyme activity, and gene expression levels in the silenced pear seedlings after B. dothidea inoculation. In this study, a comprehensive bioinformatic analysis of ATGs was conducted, and the functions of PbrATGs in pear development and in response to stress were elucidated, which laid a foundation for further study of the molecular mechanism of autophagy and a new strategy for pear resistance breeding.

Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

Betalain has received increased attention because of its high nutritional value and crucial physiological functions.Based on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic engineering.Synthesis of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of carrot.In this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated transformation.Betanin can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension culture.However,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine feeding.The p YB:CDD-transgenic lines can synthetize betanin in whole plants.The betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative analysis.These betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

The genome sequence of celery(Apium graveolens L.),an important leaf vegetable crop rich in apigenin in the Apiaceae family

Celery(Apium graveolens L.)is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients,such as apigenin and terpenoids.Here,we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data,achieving~189-fold genome coverage,from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length.The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes.Repetitive DNA sequences represent 68.88%of the genome sequences,and LTR retrotransposons are the main components of the repetitive sequences.Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery,which could have contributed to its large genome size.The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance,flavonoid biosynthesis,terpenoid metabolism,and other important cellular processes.The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery.The whole-genome sequences of celery have been deposited at CeleryDB(http://apiaceae.njau.edu.cn/celerydb).The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.

Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics

Mitogen-activated protein kinase(MAPK)cascade signal transduction modules play crucial roles in regulating many biological processes in plants.These cascades are composed of three classes of hierarchically organized protein kinases,MAPKKKs,MAPKKs and MAPKs.Here,we analyzed gene retention,phylogenetic,evolution and expression patterns of MAPK cascade genes in Brassica rapa.We further found that the MAPK branches,classes III and IV,appeared after the split of bryophytes and green algae after analyzing the MAPK cascade genes in 8 species,and their rapid expansion led to the great size of the families of MAPKs.In contrast,the ancestral class I subfamily of MAPKK gene families have been highly conserved from algae to angiosperms.For the MAPKKK family,the MEKK and Raf subfamily share a common evolutionary origin,and Raf plays a major role in the expansion of the MAPKKK gene family.The cis-elements and interaction network analyses showed the important function of MAPK cascade genes in development and stress responses in B.rapa.This study provides a solid foundation for molecular evolution analyses of MAPK cascade genes.

The Variation of Stone Cell Content in 236 Germplasms of Sand Pear(Pyrus pyrifolia)and Identification of Related Candidate Genes

Stone cells have been described to substantially influence pear fruit quality,as lignin and cellulose are the main components of stone cells.However,there are limited studies on the relationship between the variation and molecular basis of stone cells,lignin and cellulose content among different pear varieties.Here,to reveal the variation of stone cell content within different cultivated species,we collected 236 germplasms of sand pear(Pyrus pyrifolia)at 50 days after flower blooming(DAFB),the key stage of stone cell formation.In our results,we measured the content of stone cells,lignin and cellulose and found that these contents ranged from2.82%to 29.00%,8.84%to 55.30%and 11.52%to 30.55%,respectively.Further analysis showed that the variation coefficient of stone cell,lignin and cellulose content was 39.10%,28.03%and 16.71%,respectively.Additionally,a significant correlation between stone cell,lignin and cellulose content were detected,and the correlation coefficient between the contents of stone cell and lignin(0.912)was higher than between the contents of stone cell and cellulose(0.796).Moreover,the average lignin content(29.73%)was higher than the average cellulose content(18.03%)in stone cells in pear fruits,indicating that lignin is the main component of stone cell in pears.Finally,on the basic of the transcriptome data,we identified 10 transcription factors belonging to bHLH,ERF,MYB,and NAC transcript families,which might be involved in lignin formation in stone cells.qRT-PCR experiments verified coincident trends between expression of candidate genes and stone cell content.This research laid foundation for future studies on genetic variation of stone cells in pear fruits and provided important gene resources for stone cell regulation.

Involvement of long non-coding RNAs in pear fruit senescence under high-and low-temperature conditions

Pear fruit senescence under high-and low-temperature conditions has been reported to be mediated by microRNAs.Long non-coding RNAs(lncRNAs),which can function as competing endogenous RNAs that interact with microRNAs,may also be involved in temperature-affected fruit senescence.Based on the transcriptome and microRNA sequencings,in this study,3330 lncRNAs were isolated from Pyrus pyrifolia fruit.Of these lncRNAs,2060 and 537 were responsive to high-and low-temperature conditions,respectively.Of these differentially expressed lncRNAs,82 and 24 correlated to the mRNAs involved in fruit senescence under high-and low-temperature conditions,respectively.Moreover,three lncRNAs were predicted to be competing endogenous RNAs(ceRNAs)that interact with the microRNAs involved in fruit senescence,while one and two ceRNAs were involved in fruit senescence under high-and low-temperature conditions,respectively.A dual-luciferase assay showed that the interaction of an lncRNA with a microRNA disrupts the action of the microRNA on the expression of its target mRNA(s).Furthermore,four alternative splicing-derived lncRNAs interacted with miR172i homologies(Novel_88 and Novel_69)to relieve the repressed expression of their target and produce an miR172i precursor.Correlation analysis of microRNA expression suggested that Novel_69 is likely involved in the cleavage of the pre-miR172i hairpin to generate mature miR172i.Taken together,lncRNAs are involved in pear fruit senescence under high-or low-temperature conditions through ceRNAs and the production of microRNA.

Genome-wide identification of the mitogen-activated protein kinase kinases in pear and their functional analysis in response to black spot

The mitogen-activated protein kinase(MAPK)cascade is crucial to plant growth,development,and stress responses.MAPK kinases(MAPKK)play a vital role in linking upstream MAPKK kinases(MAPKKK)with the downstream MAPK.Black spot is one of the most serious fungal diseases of pear which is an important part of the fruit industry in China.The MAPKK genes have been identified in many plants,however,none has been reported in pear(Pyrus bretschneideri).In order to explore whether MAPK gene of pear is related to black spot disease,we designed this experiment.The present study investigated eight putative PbrMAPKK genes obtained from the Chinese white pear genome.The phylogenetic analysis revealed that PbrMAPKK genes were divided into A,B,C,and D groups.These PbrMAPKK genes are randomly distributed on 7 out of 17 chromosomes and mainly originated from the whole-genome duplication(WGD)event.The expression analysis of PbrMAPKK genes in seven pear tissues and the leaves of susceptible and resistant varieties after Alternaria alternata infection by quantitative real-time PCR(qRT-PCR)identified seven candidate genes associated with resistance.Furthermore,virus-induced gene silencing(VIGS)indicated that PbrMAPKK6 gene enhanced resistance to pear black spot disease in pear.

Theanine, a tea-plant-specific non-proteinogenic amino acid, is involved in the regulation of lateral root development in response to nitrogen status

Glutamine synthetase type I(GSI)-like proteins are proposed to mediate nitrogen signaling and developmental fate by synthesizing yet unidentified metabolites.Theanine,the most abundant non-proteinogenic amino acid in tea plants,is the first identified metabolite synthesized by a GSI-like protein(CsTSI)in a living system.However,the roles of theanine in nitrogen signaling and development are little understood.In this study we found that nitrogen deficiency significantly reduced theanine accumulation and increased lateral root development in tea plant seedlings.Exogenous theanine feeding significantly repressed lateral root development of seedlings of tea plants and the model plant Arabidopsis.The transcriptomic analysis revealed that the differentially expressed genes in the roots under theanine feeding were enriched in the apoplastic pathway and H2O_(2) metabolism.Consistently,theanine feeding reduced H2O_(2) levels in the roots.Importantly,when co-treated with H2O_(2),theanine abolished the promoting effect of H2O_(2) on lateral root development in both tea plant and Arabidopsis seedlings.The results of histochemical assays confirmed that theanine inhibited reactive oxygen species accumulation in the roots.Further transcriptomic analyses suggested the expression of genes encoding enzymes involved in H2O_(2) generation and scavenging was down-and upregulated by theanine,respectively.Moreover,the expression of genes involved in auxin metabolism and signaling,cell division,and cell expansion was also regulated by theanine.Collectively,these results suggested that CsTSI-synthesized theanine is likely involved in the regulation of lateral root development,via modulating H2O_(2) accumulation,in response to nitrogen levels in tea plants.This study also implied that the module consisting of GSI-like protein and theanine-like metabolite is probably conserved in regulating development in response to nitrogen status in plant species.

Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato

Photosynthesis is involved in the essential process of transforming light energy into chemical energy.Although the interaction between photosynthesis and the circadian clock has been confirmed,the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear.Here,we propose a first computational model for circadian-clock-controlled photosynthesis,which consists of the light-sensitive protein P,the core oscillator,photosynthetic genes,and parameters involved in the process of photosynthesis.The model parameters were determined by minimizing the cost function(δ=8.56),which is defined by the errors of expression levels,periods,and phases of the clock genes(CCA1,PRR9,TOC1,ELF4,GI,and RVE8).The model recapitulates the expression pattern of the core oscillator under moderate light intensity(100μmol m^(-2) s^(-1)).Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low(62.5μmol m^(-2) s^(-1))and normal(187.5μmol m^(-2) s^(-1))intensities.When exposed to low light intensity,the peak times of clock and photosynthetic genes were shifted backward by 1–2 hours,the period was elongated by approximately the same length,and the photosynthetic parameters attained low values and showed delayed peak times,which confirmed our model predictions.Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.

AgMYB1,an R2R3-MYB factor,plays a role in anthocyanin production and enhancement of antioxidant capacity in celery

Celery is rich in nutrients and cultivated worldwide.Anthocyanins are natural plant pigments with high antioxidant capabilities in the human diet.The accumulation of anthocyanins in celery results in the purple skin color of petioles.Here,an R2R3-MYB transcription factor(TFs),AgMYB1,was cloned from purple-skin celery.Phylogenetic analysis revealed that AgMYB1 belongs to the anthocyanin branch.Sequence alignment showed that AgMYB1 contains multiple anthocyanin-related motifs.Consistent with the activating role in anthocyanin production,AgMYB1 showed higher transcriptions in purple celery compared with non-purple celery.Transient expression of AgMYB1 in tobacco leaves promoted the accumulation of anthocyanins and produced red pigments in leaves.Heterologous expression of AgMYB1 in Arabidopsis activates anthocyanin production and generates dark-purple plants.The enhancement of anthocyanin biosynthetic genes transcripts and glycosylation capacities in transgenic Arabidopsis verified the activating roles of AgMYB1 at the gene and protein level,respectively.The antioxidant capacity of transgenic Arabidopsis was also increased compared to wild type Arabidopsis.Additionally,yeast two-hybrid assay proved that AgMYB1 interacted with bHLH TFs to regulate anthocyanin biosynthesis.Our results show that the overexpression of single R2R3-MYB gene,AgMYB1,without coexpression of other TFs,can improve anthocyanin production and antioxidant capacity in transgenic plants.This study presents new information for anthocyanin regulatory mechanisms in purple celery and provides a strategy for cultivating plants with high levels of anthocyanins.

Comparative genomic analysis of N6-methyladenosine regulators in nine rosaceae species and functional characterization in response to drought stress in pear

N 6-methylated adenine(m6 A)is an emerging epigenetic marker in eukaryotic organisms that plays an important role in biological functions and in enriching genetic information.m6 A exerts these functions via the dynamic interplay among m6 A writers,erasers,and readers.However,little is known about the underlying mechanisms of m6 A in plant growth and stress responses.Here,we identified 276 masked m6 A regulators from nine Rosaceae species(Pyrus bretschneideri,Pyrus betulifolia,Pyrus communis,Malus domestica,Fragaria vesca,Prunus avium,Prunus mume,Prunus persica,and Rubus occidentalis).We classified and named these genes in more detail based on phylogenetic and synteny analysis.The expansion of m6 A regulators in Maloideae was dated back to the recent whole-genome duplication(WGD)in Rosaceae.Based on the expression pattern analysis and gene structure analysis of m6 A regulators,m6 A was shown to be a significant factor in regulating plant development and resistance.In addition,PbrMTA1-silenced pear plants displayed significantly reduced drought tolerance and chlorophyll content,as well as increased electrolyte leakage and concentrations of malondialdehyde and H2 O2.

Evaluation of the early defoliation trait and identification of resistance genes through a comprehensive transcriptome analysis in pears

Early defoliation,which usually occurs during summer in pear trees,is gradually becoming a major problem that poses a serious threat to the pear industry in southern China.However,there is no system for evaluating the responses of different cultivars to early defoliation,and our knowledge of the potential molecular regulation of the genes underlying this phenomenon is still limited.In this study,we conducted field investigations of 155 pear accessions to assess their resistance or susceptibility to early defoliation.A total of 126 accessions were found to be susceptible to early defoliation,and only 29 accessions were resistant.Among them,19 resistant accessions belong to the sand pear species(Pyrus pyrifolia).To identify the resistance genes related to early defoliation,the healthy and diseased samples of two sand pear accessions,namely,the resistant early defoliation accession‘Whasan’and the susceptible early defoliation accession‘Cuiguan’,were used to perform RNA sequencing.Compared with‘Cuiguan’,a total of 444 genes were uniquely differentially expressed in‘Whasan’.Combined with GO and KEGG enrichment analyses,we found that early defoliation was closely related to the stress response.Furthermore,a weighted gene co-expression network analysis revealed a high correlation of WRKY and ethylene responsive factor(ERF)transcription factors with early defoliation resistance.This study provides useful resistant germplasm resources and new insights into potentially essential genes that respond to early defoliation in pears,which may facilitate a better understanding of the resistance mechanism and molecular breeding of resistant pear cultivars.

Genome-wide identification of the MATE gene family and functional characterization of PbrMATE9 related to anthocyanin in pear

Plant multidrug and toxic compound extrusion(MATE) genes play an important role in the process of detoxification, plant morphogenesis, and anthocyanin accumulation. However, whether the MATE gene family functions in pear peel coloration is still unknown. To evaluate and identify the MATE gene family members which are involving in anthocyanin accumulation and coloration in pear. In this study, 85 MATE genes were identified in the reference pear genome of ‘Dangshansuli’ through genome-wide identification. Based on gene structure and phylogenetic tree analysis, the MATE family was divided into five subfamilies. RNA sequencing and quantitative real-time polymerase chain reaction(qRTPCR) indicated that the expression patterns of PbrMATEs were tissue-specific. 28.24%(24) of PbrMATE genes were expressed in the fruits, and44.71%(38) of PbrMATE genes were expressed in the leaves. Additionally, we found that the expression levels of PbrMATE9, PbrMATE26,PbrMATE50, and PbrMATE69 in debagged fruits with red peel were significantly higher than those in bagged fruits without red peel, according to our bagging/debagging treatment of ‘Mantianhong’. The expression pattern of PbrMATE9 was consistent with the variation trend in anthocyanin content, suggesting that it might play an important role in anthocyanin accumulation in response to light exposure. Subcellular localization showed that PbrMATE9 was a membrane protein. More strikingly, the transient overexpression of PbrMATE9 promoted anthocyanin accumulation in the peel of pear, and the expression of structural genes(PbrCHI, PbrANS, PbrDFR, and PbrUFGT) in the anthocyanin biosynthesis pathway also increased significantly. Through co-expression network analysis, the transcription factors were identified, such as WRKY, COL,GATA, and BBX, which might be involved in the regulation of PbrMATE9. The study has enriched the genetic resources and improved the understanding of the regulation network of anthocyanin accumulation in pear.

Elimination of the yellow pigment gene PSY-E2 tightly linked to the Fusarium head blight resistance gene Fhb7 from Thinopyrum ponticum

Fhb7 is a major gene that was transferred from Thinopyrum ponticum to chromosome 7D of wheat(Triticum aestivum)and confers resistance to both Fusarium head blight(FHB)and Fusarium crown rot(FCR).However,Fhb7 is tightly linked to the PSY-E2 gene,which causes yellow flour,limiting its application in breeding.To break this linkage,marker K-PSY was developed for tagging PSY-E2 and used with Fhb7 markers to identify recombination between the two genes.Screening 21,000 BC1F2 backcross progeny(Chinese Spring ph1bph1b*2/SDAU 2028)revealed two Fhb7^(+)wheat-Tp7el_(2)L lines,Shannong 2–16and Shannong 16–1,that carry a desired truncated Fhb7^(+)translocation segment without PSY-E2.The two lines show levels of resistance to FHB and FCR similar to those of the original translocation line SDAU 2028,but have white flour.To facilitate Fhb7 use in wheat breeding,STS markers were developed and used to isolate Fhb7 on a truncated Tp7el_(2) translocation segment.Near-isogenic lines carrying the Fhb7^(+)segment were generated in the backgrounds of three commercial cultivars,and Fhb7^(+)lines showed increased FHB and FCR resistance without yield penalty.The breakage of the tight linkage between Fhb7 and PSY-E2 via homoeologous recombination provides genetic resources for improvement of wheat resistance to FHB and FCR and permit the large-scale deployment of Fhb7 in breeding using marker-assisted selection.

CmMYB3-like negatively regulates anthocyanin biosynthesis and flower color formation during the post-flowering stage in Chrysanthemum morifolium

Color fading caused by a decrease in anthocyanin accumulation during the post-flowering stage significantly affects postharvest quality of chrysanthemum.However,the underlying mechanism by which anthocyanin accumulation decreases during the post-flowering stage still unclear,which greatly restricts design of molecular breeding in chrysanthemum.Here,a chrysanthemum SG7 R2R3 MYB transcription factor(TF),CmMYB3-like,was identified to have a function in regulating anthocyanin biosynthesis during the post-flowering stage.Quantitative real time PCR(qRT-PCR)assays showed that the expression of CmMYB3-like was gradually downregulated when anthocyanin content increased during the flowering stage and was significantly upregulated during the post-flowering stage.Genetic transformation of chrysanthemum and dual-luciferase assays in N.benthamiana leaves showed that CmMYB3-like suppressed anthocyanin accumulation by inhibiting the transcription of CmCHS and CmANS directly and that of CmF3H indirectly.However,overexpression or suppression of CmMYB3-like did not affect the biosynthesis of flavones or flavonols.Genetic transformation of chrysanthemum revealed that the overexpression of CmMYB3-like inhibited anthocyanin accumulation,but its suppression prevented the decrease in anthocyanin accumulation during the post-flowering stage.Our results revealed a crucial role of CmMYB3-like in regulating the color of petals during the post-flowering stage and provided a target gene for molecular design breeding to improve the postharvest quality of chrysanthemum.

E3 ubiquitin ligase PbrATL18 is a positive factor in pear resistance to drought and Colletotrichum fructicola infection

The Arabidopsis Toxicos en Levadura(ATL)protein is a subfamily of the E3 ubiquitin ligases,which exists widely in plants and is extensively involved in plant growth and development.Although the ATL family has been identified in other species,such as Arabidopsis,Oryza sativa,and grapevine,few reports on pear ATL gene families have been reported.In this study,92 PbrATL genes were identified and analyzed from the Pyrus breschneideri genome.Motif analysis and phylogenetic tree generation divided them into nine subgroups,and chromosome localization analysis showed that the 92 PbrATL genes were distributed in 16 of 17 pear chromosomes.Transcriptome data and quantitative real-time polymerase chain reaction(qRT-PCR)experiments demonstrated that PbrATL18,PbrATL41,and PbrATL88 were involved in both pear drought resistance and Colletotrichum fructicola infection.In addition,Arabidopsis thaliana overexpressing PbrATL18 showed greater resistance to drought stress than the wild type(WT),and PbrATL18-silenced pear seedlings showed greater sensitivity to drought and C.fructicola infection than the controls.PbrATL18 regulated plant resistance by regulating chitinase(CHI),phenylalanine ammonia-lyase(PAL),polyphenol oxidase(PPO),catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD)activities.This study provided a reference for further exploring the functions of the PbrATL gene in drought resistance and C.fructicola infection.

Genome-wide analysis of the WRKY transcription factor gene family in Gossypium raimondii and the expression of orthologs in cultivated tetraploid cotton

WRKY proteins are members of a family of transcription factors in higher plants that function in plant responses to various physiological processes.We identified 120 candidate WRKY genes from Gossypium raimondii with corresponding expressed sequence tags in at least one of four cotton species,Gossypium hirsutum,Gossypium barbadense,Gossypium arboreum,and G.raimondii.These WRKY members were anchored on 13 chromosomes in G.raimondii with uneven distribution.Phylogenetic analysis showed that WRKY candidate genes can be classified into three groups,with 20 members in group I,88 in group II,and 12 in group III.The88 genes in group II were further classified into five subgroups,groups IIa–e,containing 7,16,37,15,and 13 members,respectively.We characterized diversity in amino acid residues in the WRKY domain and/or other zinc finger motif regions in the WRKY proteins.The expression patterns of WRKY genes revealed their important roles in diverse functions in cotton developmental stages of vegetative and reproductive growth and stress response.Structural and expression analyses show that WRKY proteins are a class of important regulators of growth and development and play key roles in response to stresses in cotton.

Comparison of the Δ^(12) fatty acid desaturase gene between high-oleic and normal-oleic peanut genotypes

△^12 fatty acid desaturase gene has been targeted as a logical candidate controlling the high oleate trait in peanut seeds. By RT-PCR method, the full-length cDNAs of △^12 fatty acid desaturase gene were isolated from peanut （Arachis hypogaea L.） genotypes with normal and high ratio of oleic to linoleic acid, which were designated AhFAD2B and AhFAD2B＇, respectively. Sequence alignment of their coding regions revealed that an extra A was inserted at the position ＋442 bp of AhFAD2B＇ sequence of high oleic acid genotypes, which resulted in the shift of open reading frame and a truncated protein AhFAD2B＇, with the loss of one histidine box involved in metal ion complex required for the reduction of oxygen. Analysis of transcript level showed that the expression of △^12 fatty acid desaturase gene in high oleic acid genotype was slightly lower than that in normal genotype. The enzyme activity experiment of yeast （Saccharomyces cerevisiae） cell transformed with AhFAD2B or AhFAD2B＇ proved that only AhFAD2B gene product showed significant △^12 fatty acid desaturase activity, but AhFAD2B＇ gene product did not. These results suggested that the change of AhFAD2B＇ gene sequence resulted in lower activity or deactivation of △^12 fatty acid desaturase in high oleic acid genotype.