Genetic Evolution Analysis on Wild Isolates of Citrus Tristeza Virus Originated in China Based on Coat Protein Genes Sequences

The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.     

Phylogenetic Analysis of Citrus tristeza virus Isolates of Wild Type Citrus in China

The genetic variation and phylogenetic relationships of Citrus tristeza virus （CTV） isolates collected from Chinese wild type citrus were analyzed by comparing the sequences of nine genomic regions （p23, p20, p13, p18, p25, p27, POL, HEL and k17） with the CTV isolates of cultivated citrus from different countries. The results showed that the divergence pattern of genomic RNA of the CTV isolates from wild type citrus was similar to that of other isolates from cultivated citrus, the 3′ proximal region was relatively conserved, and the 5′ proximal region had greater variability. The nine genomic regions of CTV isolates analyzed were found to have been under purifying selection in the evolution process. Phylogenetic analysis showed that the eleven Chinese wild CTV isolates were located at different clades and did not relfect their geographical origins, suggesting genetic diversity among the Chinese wild CTV populations. These results will aid in the understanding of molecular evolution of the Chinese CTV populations.     

Characterization of Citrus tristeza virus Isolates by Indicators and Molecular Biology Methods

Citrus tristeza virus （CTV） exists in citrus as a large number of distinct strains differing in biological characters. The control strategies such as mild strains cross protection （MSCP） require a clear understanding of the characterization of CTV. For better understanding of the structure of CTV population and the relationship between molecular and biological characterization, 72 CTV samples collected from five provinces in China were studied, using biological indexing, p25/Hinf I restriction fragment length polymorphism （RFLP）, multiple molecular markers, and bidirectional RT-PCR assay. The mixture of severe stem pitting isolates was found to be dominant in the field. CTV isolates with p25/Hinf Ⅰ RFLP group 3 and p23/BD-PCR group Ⅰ, Ⅲ were the main cause of epidemics, and most CTV isolates were found to be the mixture of T30 and VT genotypes. More accurate identification of strain mixtures in the field and better understanding of the biological traits of the isolates may be achieved by applying the three molecular detection methods simultaneously.     

Preliminary Studies on CPG/Hinf Ⅰ RFLP Groups of Citrus tristeza virus Infected Sweet Oranges in China

Citrus tristeza virus （CTV） causes economically important losses to the citrus industry worldwide. Mild strain cross protection （MSCP） against tristeza has hardly been practised due to mixed infection of different CTV-strains and little background of its molecular biology in China. For better cognition on CTV, 192 sweet orange samples collected from eight provinces （Chongqing, Sichuan, Fujian, Hunan, Guangxi, Yunnan, Guangdong and Jiangxi） were tested by direct tissue blot immuno-assay （DTBIA）, and 158 of them were tested positively, which therefore were subjected to coat protein gene （CPG）/Hinf Ⅰ restriction fragment length polymorphism （RFLP） analysis. Sample bulks were compared between Chongqing and Fujian by some statistical data, including ratios of single infection and mixed infection to local samples, proportions of CTV isolates with single RFLP groups, and rates of each RFLP group. The simplified analysis of samples from the other six provinces were then conducted. This study suggests that CTV isolates with CPG/Hinf Ⅰ RFLP groups Ⅲ and Ⅰ are the main epidemic ones in China, and mixed infection of CTV in fields are popular. Based on observation of severity of stem-pitting symptom in field trees, CTV isolates with CPG/Hinf Ⅰ RFLP groups Ⅲ and Ⅰ caused severe stem-pittings in sweet oranges in China.     

Preliminary Studies on Species and Distribution of Citrus Viroids in China

Citrus viroids are the small but economically important RNA pathogens. For investigating their occurrence and distribution in China, 65 viroid samples collected from 8 major citrus cultivated regions were evaluated using one-step or multiplex onestep RT-PCR and biological indexing for specifically detection of Citrus exocortis viroid （CEVd）, Citrus bent leaf viroid （CBLVd）, Hop stunt viroid （HSVd）, Citrus viroid-Ⅲ （CVd-Ⅲ） and Citrus viroid-Ⅳ （CVd-Ⅳ）. The results showed that there were at least 4 kinds of citrus viroids （CEVd, CBLVd, HSVd, and CVd-Ⅲ） on citrus trees in China. Most of the infected citrus plants harbored more than one viroid species, and two plants were infected with up to 4 citrus viroids. Sweet orange was more frequently infected by viroids than other citrus varieties. It is the preliminary report on the species and distribution of citrus viroids in China.     

Yield Estimation Model of Citrus Based on Spectral Data and Agronomic Parameters

With the development of precision agriculture, the research that applies Remote Sensing technology, especially hyperspectral remote sensing, to realize crop management, monitoring and yield estimation, has been concerned. Nowadays, the growth-monitoring and yield-estimating methods in rice, wheat and other annual crops develop rapidly with some achievements having already been put into service. But the yield estimation research on perennial economic crops is few. Taking peren- nial citrus trees as the research object, using ASD spectrometer to collect citrus canopy spectral, this article studied and analyzed the citrus of veget＆tion index and its relationship on yield, synthetically considered the influence of the agriculture pa- rameters on crop yield, and finally constructed the citrus yield estimation model based on the spectral data and agronomic parameters. Through the Significance Test and Samples＇ Test, olutained that the model＇s fitting degree was R=0.631, F= 13.201, P〈0.01 and the error rate of estimating accuracy was controlled in the range 3%-16%, proving that the model has statistical signification and reliability. It concluded that hyperspectral acquired from citrus canopy has substantial potential for citrus yield estimation. This study is an application and exploration of Hyperspectral Remote Sensing technology in the citrus yield estimation.     

The Mining of Citrus EST-SNP and Its Application in Cultivar Discrimination

Single nucleotide polymorphisms （SNPs） are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in cultivar identification and genetic diversity studies. The objective of this study was to identify SNP markers useful for discrimination of citrus cultivars, since large numbers of expressed sequence tags （ESTs） of sweet orange are available from the National Center for Biotechnology Information （NCBI）. We now have the opportunity to discover SNP markers suitable for determining the haplotypes with which to distinguish very closely related cultivars and to assess genetic diversity within or between related species of citrus. SNPs and small insertions/deletions （Indels） from ESTs of sweet orange and satsuma were identified by the in silico SNP discovery strategy. 55 296 EST sequences of sweet orange and 2 575 of satsuma retrieved from the NCBI repository were mined for potential SNPs. Cleaved amplified polymorphic sequences （CAPS） and sequencing approaches were used to validate putative SNPs in a sample of 30 citrus accessions. A total of 3 348 putative SNPs were identified based on the abundance of sequences and haplotype cosegregation. Of these 3 348 SNPs, the transitions, transversions and Indels ratios were 47.9, 36.1 and 16.0%, respectively. The SNPs occurred on average at a frequency of 1 per 164 bp in the coding region of citrus. 14 SNPs were randomly selected and genotyped according to 30 citrus accessions including 23 accessions of sweet orange; 11 SNPs displayed polymorphism with an average polymorphism information content （PIC） of 0.20 among 30 citrus accessions. The genetic diversity present in sweet orange was low, so the 14 SNP markers failed to discriminate different cultivars of sweet orange, but they did succeed in distinguishing accessions of inter-species of citrus. In this study, SNPs were mined from EST sequences of sweet orange and satsuma, which displayed potential capability as molecular markers to discriminate inter-species accessions of citrus. It is anticipated that these putative SNPs could be applied in citrus genetics research and breeding.     

Analysis of Major Carotenoid Composition and Its Content of Citrus Fruit

a-carotene, β-carotene, lycopene, β-cryptoxanthin, zeaxanthin and lutein content of fruits in53 citrus cultivars were determined using HPLC. In both peel and pulp of citrus fruit, the major carotenoidswere lutein, zeaxanthin and β-cryptoxanthin. β-carotene content was relatively low and extremely low was theamount of or-carotene. Among the 53 cultivars tested, lycopene was detected only in pulp of Cara Cara navelorange. Carotenoid content in both peel and pulp of citrus fruit was the highest in Citrus reticulata Blanco andlowest in Citrus grandis Osbeck. Consequently, as far as the health protection value is considered, fruit ofCitrus reticulata Blanco ranks probably higher than other citrus fruits. In fruit of most Citrus retieulatavarities, β-cryptoxanthin was the main carotenoid component in pulp and its amount approximated that of lu-tein in peel. Content of lutein, zeaxanthin and β-cryptoxanthin in peel was about 2.5 - 15 times that in pulp onthe basis of fresh weight. Thus peel was inferred to be the principal location for the carotenoid stock in citrus fruit.     

Pathotypes and Genetic Diversity of Chinese Collections of Elsino？ fawcettii Causing Citrus Scab

Two scab diseases are currently recognized on citrus：citrus scab, caused by Elsino？ fawcettii, and sweet orange scab, caused by E. australis. Although these pathogens are economically important, there is no molecular data on these species in China. Here we use internal transcribed spacer sequence data to report on host-speciifcity and genetic relationships among 46 isolates collected from the main citrus varieties grown across China. All strains isolated were E. fawcettii. Based on pathogenicity testing on 9 different citrus species, isolates were divided into 11 pathotypes （SM, FBHR, SJCR, SPOJCR, SR, SOJG, SPOJC, SRGC, Lemon and two unnamed pathotypes）. SM is a new pathotype, and two isolates did not ift into any of the known pathotypes of E. fawcettii. Inter-simple sequence repeat （ISSR-PCR） assays separated the E. fawcettii isolates into 10 subgroups;the groupings basically corresponded to the pathogenicity test.     

柑橘衰退病毒基因RNAi载体的构建

基于转化病毒基因介导抗性,通过在植物表达载体p CAMBIA 2301上插入启动子–内含子–终止子的方式,构建一种含有发夹结构的、通用型强的RNAi载体骨架结构;以柑橘衰退病毒(citrus tristeza virus,CTV)的p25、p20和p23基因保守序列为模板设计正向片段和反向片段,先后与骨架载体连接,成功构建了3个RNAi载体(分别命名为ds2301–p25、ds2301–p20和ds2301–p23),并将载体ds2301–p23注射入墨西哥莱蒙叶片。制作p23基因的地高辛标记探针,用Northern杂交检测是否有si RNA产生。结果表明:用Northern杂交可以检测到p23特异的si RNA,在墨西哥莱蒙叶片中瞬时表达的农杆菌ds2301–p23可以发生RNAi,表达有效的si RNA。本研究中构建的骨架载体可以广泛用于RNAi载体的构建,含有柑橘衰退病毒基因片段的3个载体可以用于基因功能分析及具有CTV抗性的柑橘种质资源获得。     

Detection of Thrips Defect on Green-Peel Citrus Using Hyperspectral Imaging Technology Combining PCA and B-Spline Lighting Correction Method

In order to find an effective method of detecting thrips defect on green-peel citrus, a defect segmentation method was developed using a single threshold value based on combination of characteristic wavelengths principal component analysis （PCA） and B-spline lighting correction method in this study. At first, four characteristic wavelengths （523, 587, 700 and 768 nm） were obtained using PCA of Vis-NIR （visible and near-infrared） bands and analysis of weighting coefficients; secondarily, PCA was performed using characteristic wavelengths and the second principal component （PC2） was selected to classify images; then, B-spline lighting correction method was proposed to overcome the influence of lighting non-uniform on citrus when thrips defect was segmented; finally, thrips defect on citrus was extracted by global threshold segmentation and morphological image processing. The experimental results show that thrips defect in citrus can be detected with an accuracy of 96.5% by characteristic wavelengths PCA and B-spline lighting correction method. This study shows that thrips defect on green-peel citrus can be effectively identified using hyperspectral imaging technology.     

柑桔衰退病毒基因组学研究进展

柑桔衰退病毒(CTV)是柑桔普遍存在的一种重要病毒病害,因其自身基因变异和寄主的不同而产生不同的症状,给防治CTV带来一定困难.为防治柑桔衰退病,需要研究CTV本身的相关特征.从CTV的基因组学上的特征综述了国内外在CTV基因组学最新的科研进展.     

应用抑制性差减杂交技术筛选锦橙CTV应答基因

【目的】探讨易感柑橘衰退病病毒（Citrus tristeza virus,CTV）品种锦橙CTV应答分子机理,筛选和分析CTV应答基因。【方法】以嫁接CTV强毒株TRL514的锦橙阳性材料叶片为试验方（Tester）,用嫁接无毒枝条的CTV阴性锦橙叶片为驱动方（Driver）,构建CTV侵染的锦橙的正向差减文库。【结果】随机挑选850个阳性克隆测序,其中742条测序成功,去除载体片段和接头序列后得到有效EST 692条。将所有EST序列对应到柑橘的预测基因组转录物,共涉及137个柑橘基因。应用BLAST2GO对这些特异性表达的基因进行功能归类和KEGG分析。结果表明,受CTV侵染的影响,锦橙能量代谢相关基因上调明显,与光合器官碳固定、氮代谢、淀粉和蔗糖代谢等途径相关的EST出现频率较高。另外,与抗逆防御以及苯基丙氨酸合成、类苯基丙烷代谢、类胡萝卜素合成等与植物防御素类物质合成密切相关的代谢途径相关基因较多。【结论】由于CTV的侵染,CTV易感品种锦橙基础代谢改变明显,须通过增强能量代谢和提高自身防御能力来维持自身生长和发育。     

柑橘衰退病毒分子生物学研究进展

柑橘衰退病毒(Citrus tristeza virus，CTV)是对世界柑橘生产具有严重为害的重要病原物之一。近年来，CTV的分子生物学研究取得了很大的进展。本文综合有关文献，主要就CTV的基因组结构与功能、复制与表达及其分子诊断等方面进行综述。同时，本文简要指出了目前CTV分子生物学研究中存在的问题，并对研究前景做了简要展望，认为关于CTV的弱毒株系构建、弱毒系交叉保护机理、抗病毒基因工程等还有待进一步深入研究。     

Comparison of PCR, DIA and Pathogenicity Assay for Detection of Xanthomonas axonopodis pv. citri, the Causal Agent of Citrus Bacterial Canker Disease

Polymerase chain reaction (PCR) approach based on newly designed primers, JYF5/JYR5, was applied for specific detection of Xanthomonas axonopodis pv.citri(Xac). The efficiency and reliability of PCR method were compared with dot immunobinding assay (DIA) and classical pathogenicity test techniques for detecting suspensions of pure cells of Xac and soaking sap of citrus tissues. Detection sensitivity of PCR was about 4.5 cells or 1.56 pg target DNA per reaction which was higher than that of DIA (ca.450 cells per dot).These three techniques (PCR assay, DIA and Pathogenecity test) could always detect Xac from symptomatic citrus samples. Different performances were obtained from citrus materials without symptoms, and the positive detection frequency was PCR, DIA and pathogenicity test.     

四川安岳柑橘衰退病病原鉴定及序列分析

[目的]探明引起四川安岳柑橘衰退病的病原。[方法]利用RT-PCR、克隆、测序等技术对四川安岳地区的柑橘类果树进行柑橘衰退病毒(CTV)检测,并对其外壳蛋白(CP)全序列进行了分析。[结果]81个疑似CTV侵染的样品中共有18个检测呈阳性,检出率为22.2%,表明安岳地区柑橘类果树衰退病由CTV引起。基于CP全序列同源性比较及进化分析表明,危害该地区柑橘类果树的CTV分属5个组群,亲缘关系较复杂。[结论]为安岳地区CTV的防控与防治提供了理论依据。     

Effects of INA on postharvest blue and green molds and anthracnose decay in citrus fruit

As a synthetic functional analog of salicylic acid, 2,6-dichloroisonicotinic acid(INA) is effective in inducing the host disease resistance of a plant against a pathogen. The effects of INA on controlling postharvest blue and green molds and anthracnose decay and defense-related enzymes on citrus fruits were investigated, and the ascorbic acid of naturally infected citrus flavedo was also measured. Results showed that 1.0 mmol L~(–1) INA treatments significantly reduced blue and green molds and anthracnose decay development on both wound-inoculated fruit and naturally-infected fruit compared with the control fruit. The treatment effectively enhanced the β-1,3-glucanase(GLU), chitinase(CHI), phenylalanine ammonia-lyase(PAL) and peroxidase(POD) activities and the polyphenol oxidase(PPO) in flavedo. The results presented here suggest that INA might be used as a chemical fungicide substitution to control postharvest diseases in citrus fruits.