Documente Academic
Documente Profesional
Documente Cultură
Helaine Carrer
Dept. Biological Sciences/ESALQ/USP
> 15.000 farmers > US $1.2 billion 200 million of plants 930 mil ha (81% SP) 22 % of SP agriculture production 504 protected nurseries
Challenges to Citrus Genetic Breeding Botany Juvenility - patterns to differentiate fruit - patterns of growing - limited production Apomixy - genetic e phenotipic fixation - clonal propagation - difficulty to hybridization Sterility - impediment to recombination
Genetics
Incompatibility pre and pos zygotic - obstacle to recombination Heterozygose - hybrid character fixed by apoximy - high F1segregation Long cycle of selection - trees, perennial - Important epigenetic factors - environmental factors X phenotypes
Agronomy
Fruit Quality - complex characteres - environmental effect (herdability) Propagation - vegetative Resistance to biotic and abitotic factors - complex inheritance
Caused by Xylella fastidiosa Damage: US$ 70 million (cuts, renovation and insect control) Sweet orange: highly susceptible Tangerines and hybrids: tolerant or resistance
Caused by Citrus leprosis virus (CiLV) Damage: around US$ 100 million to control the vector (Brevipalpus phoenicis) Sweet orange: highly susceptible Tangerines and hybrids: tolerant in the field
Tristeza
Caused by Citrus tristeza virus (CTV) Damage: virus is endemic Sweet orange: susceptible and highy susceptible depending on the rootstock Tangerines and hybrids: tolerant Poncirus trifoliata: resistence
Caused by Guignardia citricarpa Damage: avoid fruit exportation Sweet orange: suceptible C. latifolia (Tahiti lime): tolerant
4% 1% 6% 3% 22% 3%
Laranja doce e hbridos Tangerinas e hbridos Limes e hbridos Limo Cravo e hbridos Limo Volkameriano Toranjas e hbridos Outros gneros e espcies
Laranja azeda e hbridos Limas cidas, doces e hbridos Cidras e hbridos Limo Rugoso e hbridos Pomelos e hbridos Trifoliatas e hbridos
CitEST Program
Main goal: Integration
Citrus breeding: Evaluating new scion and rootstock hybrids in the field for disease resistance Citrus genetic: Validation and saturation (SSR and SNPs based on sequence data) of genetic linkage maps from hybrid populations Citrus genome: ESTs database of Citrus species under different stress conditions Functional genomics: expression analysis of genes of citrus and their pathogens
C. sinensis C. reticulata P. trifoliata C. aurantium C. aurantifolia C. latifolia C. limonia C.limettiodes C. sunki Total
32,121 18,873 12,873 5,607 4,327 4,883 5,945 4,540 2,652 91,821
Only 5ends were sequenced Valid reads = >400 bp and Phred quality >20 Redundancy = [1 - (# Unigenes / # Reads)] # Unigenes = # Contigs + # Singlets Sequencing Efficiency = # Valid Reads / # Submitted Reads Total of sequenced reads = 286,559
#Sequenced reads
MB sequenced
MB unigenes
Coverage of the genome n (%) (*) 8.03 4.51 2.96 1.27 0.92 1.08 1.23 1.03 0.54
106601 52679 32637 8439 8219 8756 11045 8188 5216 241780
91.06 44.39 27.18 7.17 6.74 7.56 8.87 7.58 4.33 204.89
29.47 16.56 10.85 4.65 3.38 3.97 4.51 3.79 1.96 79.13
Only 5ends were sequenced Valid reads = >400 bp and Phred quality >20 Redundancy = [1 - (# Unigenes / # Reads)] # Unigenes = # Contigs + # Singlets Sequencing Efficiency = # Valid Reads / # Submitted Reads Total of sequenced reads = 286,559
In silico analysis
Transcription factor
Snif1 (535 reads)
Snf1 (sucrose non-fermenting-1) plays a major role in regulating gene expression in eukaryotic cells. This family of regulatory proteins is represented by sucrose nonfermenting-1 (Snf1) protein kinase in Saccharomyces cerevisiae, AMPactivated protein kinases (AMPKs) in mammals and SnRKs (Sucrose non-fermenting-1-related protein kinases) in higher plants
Citrus sinensis; CR: Citrus reticulata; C1: leaf cDNA; C3: fruit cDNA; 100: non-infected; 101: infected with Xylella fastidiosa; 102: 30 days after X. fastidiosa infection; 700: stadium 1 of the fruit; 701: stadium 2 of the fruit; 703 stadium 4 of the fruit.
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LTREHHQFFLYQMLRALKYMHTANVYHRDLKPKNILANANCKLKVCDFGLARVAFSDTPMTVFWTDYVATRWYRAPELCGSFFSKYTPAIDIWSIGCIFAEVLT LTPEHYQFFLYQLLRGLKYIHTANVFHRDLKPKNILANADCKLKICDFGLARVAFNDTPTAIFWTDYVATRWYRAPELCGSFFSKYTPAIDIWSIGCIFAELLT -----------------------NVFHRDLKPKNILANADCKLKICDFGLARVSFTDTPSAIFWTDYVATRWYRAPELCGSFFSKDAYLQNC---------------------------PRSSYKANVFHRDLKPKNILANADCKLKICDFGLARVSFTDTPSAIFWTDYVATRWYRAPELCGSFFSKYTPAIDIWSIGCIFAELLT LTPEHHQFFLYQLLRALKYIHSANVFHRDLKPKNILANADCKLKICDFGLARVSFTDTPSAIFWTDYVATRWYRAPELCGSFFSKYTPAIDIWSIGCIFAELLT ---STASISCINFFEDSSISIQQMLFIGDLKPSNLLLNANCDLKICDFGLARPTS----ENEFMTEYVVTRWYRAPELL-LNSSDYTAAINVWSVGCIFMELMN LTNDHCQYFLFQLLRGLKYLHSANILHRDLKPGNLLVNANCDLKICDFGLARTSNG---KNQFMTEYVVTRWYRAPELL-LCCDNYGTSIDVWSVGCIFAELLG LSEEHCQYFLYQILRGLKYIHSANVLHRDLKPSNLLLNANCDLKICDFGLARVTS----ETDFMTEYVVTRWYRAPELL-LNSSDYTAAIDVWSVGCIFMELMD LSEEHCQYFLYQLLRGLKYIHSANVIHRDLKPSNLLLNANCDLKICDFGLARPTS----ENEFMTEYVVTRWYRAPELL-LNSSDYTAAIDVWSVGCIFMELMN FSEAEVRNWCFQVFQGLAYMHQRGYFHRDLKPENLLVSKDT-IKIADFGLAREIN----SRPPFTEYVSTRWYRAPEVL-LQSYLYSSKVDMWAMGAIMAELIT FSEGEIRSFMSQMLQGLAHMHRNGYFHRDLKPENLLVTNDV-LKIADFGLARELS----SMPPYTEYVSTRWYRAPEVL-LQSSSYTPAIDMWAVGAILAELFT LTDDHCQYFLYQLLRGLKYIHSANVLHRDLKPSNLLLNANCDLKICDFGLARTTS----ETDFMTEYVVTRWYRAPELL-LNCSEYTAAIDIWSVGCIFMEIMQ LTREHYQFFLYQLLRALKYIHTADVYHRDLKPKNILANANCKLKICDFGLARVAFNDTPTTIFWTDYVATRWYRAPELCGSFFSKYTPAIDIWSIGCIFAEVLT LTDDHCRYFLYQLLRGLKYVHSANVLHRDLKPSNLLLNANCDLKIGDFGLARTTS----ETDFMTEYVVTRWYRAPELL-LNCSEYTAAIDIWSVGCILGEIMT LTREHHQFFLYQMLRALKYMHTANVYHRDLKPKNILANANCKLKVCDFGLARVAFSDTPMTVFWTDYVATRWYRAPELCGSFFSKVWVAQC------------LT EH QFFLYQLLRGLKYIHSANVFHRDLKP NLLLNANC LKICDFGLARVT FWTEYVATRWYRAPELL L S YT AIDIWSVGCIFAELLT
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(468) C21(454) C10(308) C68(350) C15 (54) C3(112) C109 (22) C64 (81) C91(135) C6 (1) C18 (50) C83 (17) CS00-C1-102-049-B10-CT.F(117) CS00-C1-102-062-D10-CT.F (30) CR05-C3-700-109-C06-CT.F(123) CS00-C1-102-037-B06-CT.F(120) CR05-C3-701-058-D03-CT.F (98) Consensus(468)
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VHRDIKCANILVDANGS-------VKLADFGLAKATK------------LNDVKSCRGTAFWMAPEVIN-----NKNKGYGLPADIWSLGCTVLEMLTSQIPYA VHRDIKGANILVDPNGR-------VKLADFGMAKHIAG-----------HSCPLSFKGSPYWMAPEVIKNSS------GCNLAVDIWSLGCTVLEMATAKRPWS VHRDIKGANILVDPSGR-------VKLADFGMAKHITG-----------QSCPLSIKGSPYWMAPEVIKNSN------GWYLAVDI-----------------VHRDIKGGNILLTDQGE-------VKLGDFGVAAQLTRT----------MSKRNTFIGTPHWMAPEVIPESR-------YDGRV-------------------MHRDIKSENILIDLERKKADGKPVVKLCDFDRAVPLRSFLHTCCIAHRGIPAPDVCVGTPRWMAPEVLRAMHKPN---LYGLEVDIWSYGCLLLELLTLQVPYM IHRDLKSSNLLVDKHWT-------VKVGDFGLSRLKHET----------YLTTKTGKGTPQWMAPEVLRNEP-------SDEKSDVYSFGVILWELATEKIPWD MHRDIKGANILVDNKGC-------IKLADFGASKQAT------------VSGDNSMKGTPYWMAPEVICQT-------GHSYSADIWSVGCTVIEMATGKPPWS IHRDIKGANLLVDASGV-------VKLADFGMAKHLTG-----------LSYELSLKGSPNWMAPEVIKAVMQKDGNPKLALAVDIWSLGCTVIEMLTGKPPWS ------------------------LIYFQFTCCIKLTG-----------LSYELSLKGSPYWMAPEVMQADIQKDGNHRVALLADIWSLGCTVIEMLTGKPPWS IHRDIKGANLLVDASGV-------VKLADFGIGKHLTG-----------LSYELSLKGSPYWMAPEVMQADIQKDGNHRVALLADIWSLGCTVIEMLTGKPPWS VHRDIKCANILVDASGS-------VKLADFGLAKATT------------MNDLKSCKGTPFWMAPEVVN-----SKNDGYGLTADIWSLGCTVLEMLTRRPPYS IHRDLKPENILLFSLDDDVM----LKIADFGLSCTL-----------HPGNYAEKVCGSPIYMAPEVLQFQRYDEKVDMWSVGAILFELLNGYPPFSGRDNVQV VHRDLKSSNLLVDKNWT-------VKVGDFGLSSLKNAT----------YLTAKSGRGTPQWMAPEVLRSEP-------SNEKSDVFSFGVILWELVTASIPWN IHRDLKPENILLSGLDDDVM----LKIADFGLSCSTL----------YPGNYAEKVCGSPLYMAPEVLQFQRYDEK---------------------------VHRDIKGANILVDPHGE-------IKLADFGMAKHMTS-----------CASMLSFKGSPYWMAPEVVMNTN------GYSLTVDIWSLGCTVLEMATFKTTMD IHRDIKGANILTTKEGL-------VKLADFGVATKLTEA----------DVNTHSVVGTPYWMAPEVIEMSG-------VCAASDIWSVGCTVIELLTCVPPYY VHRDIKGANILVD G VKLADFGLAK LT LS SLKGSPYWMAPEVI L ADIWSLGCTVIEMLT K PW
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(658) C38(629) C28(406) C84(252) C46(302) C16(245) C13(141) C55(141) C65(214) C33 (72) C51(141) C70(147) C49 (47) C39 (96) C79 (80) C99 (95) C23(136) C45 (67) C1(128) C22 (117) C80(145) C12 (181) CR05-C1-100-052-F01-CT.F (1) LT33-C1-003-057-A10-CT.F (36) CS00-C3-702-066-C07-CT.F(130) CS00-C1-100-106-A10-EU.F (3) Consensus(658)
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LHTSHPTIVHRDLKSPNLLVDKN----WVVKVCDFGLSRIKHH---TYLSSKSTAGTPEWMAPEVLRNEPANE--------KCDVYSFGVILWELATLSVPWKG LHQNN--IIHRDLKTANLLMDEN----GVVKVADFGVARVQA----QSGVMTAETGTYRWMAPEVIEHKPYDY--------KADVFSFGIALWELLTGELPYAG VHRLG--LIHRDLKSDNLLIFSD----KSIKIADFGVARIEV----QTEGMTPETGTYRWMAPEMIQHRPYTQ--------KVDVYSFGIVLWELVTGMLPFQN LHQNN--IIHRDLKAANLLMDEN----EVVKVADFGVARVKA----QSGVMTAETGTYRWMAPEVIEHKPYDH--------KADVFSFGIVLWELLTGKLPYEY LHRNN--IIHRDLKAANLLMNEN----GVVKVADFGVARVQA----QYGVMTAETGTYRWMAPEVIEHQPYNH--------RADVFSFGIVLWELVTGKLPYDD LHSHG--IIHRDLKPENLLLTEDL---KTIKLADFGLAREES----LTEMMTAETGTYRWMAPELYSTVTLRQGEKKHYNHKVDSYSFAIVLWELLHNKLPFEG LHANG--IIHRDLKPDNLLLTPDQ---KSLKLADFGLAREET----VTEMMTAETGTYRWMAPELYSTVTLRQGEKKHYNNKVDVYSFGIVLWELLTNRLPFEG VHGLG--FIHRDLKSDNLLISAD----KSIKIADFGVARIEV----QTEGMTPETGTYRWMAPEMIQHRPYTQ--------KVDVYSFGIVLWELITGLLPFQN LHSQG--ILHRDLKSENLLLGED----MCVKVADFGISCLES----QCGSAKGFTGTYRWMAPEMIKEKRHTK--------KVDVYSFGIVLWELLTALTPFDS LHANG--IIHRDLKPDNLLLTPDQ---KSLKLADFGLAREET----VTEMMTAETGTYRWMAPELYSTVTLRQGEKKHYNNKVDVYSFGIVLWELLTNRLPFEG LHSKT--IVHRDVKTENMLLDAN----RTLKIADFGVARVEAQ---NPRDMTGETGTLGYMAPEVLDGKPYNR-----K---CDVYSFGICLWEIYCCDMPYPD LHSKT--IVHRDVKTENMLLDAN----RTLKIADFGVARVEAQ---NPRDMTGETGTLGYMAPEVPTSLFAIP-----Q---RRFSALLLLSC----------IHSQG--VIHRDLKPENVLIDQE----FHLKIADFGIACEEV----YCDALSDDPGTYRWMAPEMIKHKSYGR--------KVDVYSFGLILWEMVAGTIPYEE LHQRN--IIHRDLKTANLLMDTH----NVVKVADFGVARFQN----KGGVMTAETGTYRWMAPEVINHQPYDQ--------KADVFSFAIVLWELVTAKVPYDS LHSKN--IVHFDLKCDNLLVNLKDPSRPICKVGDFGLSKIKR----NTLVSGGVRGTLPWMAPELLSGSSSKVS------EKVDVFSFGIVLWEILTGEEPYAN LHSKN--IVHFDLKCENXLVNLRDPQRPICKVGDFGLSRIKR----NTLVSGGVRGTLPWMAPELLNGSSNRVS------EKVDVFSFGISMWEILTGEEPYAD LHSKN--IVHFDLKCDNLLVNLKDPIRPICKVGDFGLSKIKR----NTLVTGGVRGTLPWMAPELLNGSSSKVS------EKVDVFSFGIVLWEILTGEEPYAN LHRRNPPIVHRDLKSPNLLVDKK----YTVKVCDFGLSRLKAN---TFLSSKSAAGTPEWMAPEVLRDEPSNE--------KSDIYSFGVILWELATLQQPWGN LHEQN--VVHRDIKCANILVDASG----SVKLADFGLAKATT-----MNDVKSCKGTAFWMAPEVVNLKKDGYG------LTADIWSLGCTVLEMLTRRHPYSH LHGKN--IVHFDLKCENLLVNMRDPQRPVCKIGDLGLSKVKQ----QTLVSGGVRGTLPWMAPELLSGKSHMVT------EKIDVYSFGIVMWELLTGDEPYAD LHSIG--LLVLNLKPSNLLLSEHD----QLVLGDFGIPYLLLGRSLSDSDMALRLGTPNYMAPEQWEPEVRGPIS-----FETDTWGFGCSIMEMLTGIQPWFG ----------------NLLVDKN----WVVKVCDFGLSRMKHN---TFLSSRSTAGTAEWMAPEVLRNEPSDE--------KCDVYSFGVILWELCTMQQPWGG LHGKN--IVHFDLKSDNLLVNLRDPHRPICKVGDLGLSKVKC----QTLISGGVRGTLPWMAPELLNGSSSLVS------EKVDVFSFGIVLWELLTGDEPYAD LHTSTPTIVHRDLKSPNLLVDKN----WNVKVSDFGLSRLKHN---TFLSSKSTAGTPEWMAPEVLRNEPSNE--------KCDVYSFGVILWELATLKLPWIG MCVHRMKIVHRDLKSANCLVNKH----WTVKICDFGLSRIITD---SPMRDSSSAGTPEWMAPELIRNEPFTE--------KCDIFSLGVIMWELCTLNRPWEG LH IVHRDLK DNLLV VKVADFGLARI Q MTG GT WMAPEVL K DVYSFGIVLWELLTG LPY
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Snf1: Alignment of part of the N-terminal catalytic domain and the T-loop domain of CitEST contigs and singletons encoding putative SnRKs, SNF1 and other SnRKs 18 contigs and two singletons
T-loop
Phylogenetic relationship between members of the SnRK families. Alignment of N-terminal catalytic and T-loop domains amino acid sequences was performed using AlignX (Vector NTI program).
MACROARRAY RT-PCRq
Category
Putative Function
Number of genes inGenes with differentialGenes with differential the membrane expression (%) expression (%) > 2x
genes R
97
58,76 60 78,94 66,66 52,94 0 66,66 66,66 85,71 66,66 75 100 100 60 0
genes requeridos pelos genes R 10 MAPK MAP2K MAP3K MAP4K SNF1 NADPH oxidase SOD Nitrato redutase fenilalanina-amnia liase chorismate mutase isochorismate sintase PR-protenas canais de clcio 19 3 51 4 18 6 7 3 4 3 2 10 2
Category
Putative Function
Number of genes inGenes with differentialGenes with differential the membrane expression (%) expression (%) > 2x
C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26
Chalcone sintase Glutationa transferases Glutationa peroxidase peroxidases catalases canais de on-potssio metacaspases lipoxigenases cido cinmico 4-hidroxilase Epoxide hydrolase stress inducible protein
2 2 2 5 5 4 3 5 2 2 2
50 0 0 40 80 25 33,33 20 0 0 0
Genes de C. sinensis com expresso diferencial significativa 4,3 3,8 -log10(probt) 3,3 2,8 2,3 1,8 1,3 -4 -3 -2 -1 0 1 2 3 4 5 log2 das diferenas estimadas
273 genes analyzed: 171 (62.63%) showed significant differential expression at the level of 5% probability
Categorias % do total de genes com expresso diferencial % dos genes com expresso diferencial > do que 2 vezes
Of these 171 differential expression genes, 80 showed significant differential expression greater than 2 times, 38 of these genes were induced and 42 were repressed
Porcentagem
9 genes analyzed: 5 genes induced in the macroarray were validated by RT-PCRq 3 of the 4 genes repressed in the macroarray were validated by RT-PCRq
5 4 3 2 1 0 -1 -2 -3 -4 -5 -6
Genetic Transformation of Rangpur Lime (Citrus limonia Osbeck) with gene bO (bacterio-opsin) gene
Rangpur Lime rootstock represents 70% of the total cultivated area tolerance to citrus tristeza virus, water stress Low resistance to Phytophthora spp
pEL154
PCR analysis
Southern Blot
Northern Blot
Protein immunoblot analysis of bO-His expressing 1: non-transformed tobacco plant 2: transgenic tobacco expressing His-tagged bO 3: non transformed Rangpur lime 4: Transgenic Rangpur lime line 2 5: Transgenic Rangpur lime line 1
Variations in size of lesions by Phytophthora nicotianae A: Non-transformed B: Transgenic line 2 C: Transgenic line 1
Acknowledgements: Francisco de Assis Alves Mouro Filho ESALQ/USP Beatriz M. J. Mendes CENA/USP Fernando A. Azevedo Centro Apta Citros Marcos Machado Centro Apta Citros Antonio de Goes UNESP/Jaboticabal Eric Lam Rutgers University Michael A. Lawton Rutgers University
Thank you
Helaine Carrer hecarrer@esalq.usp.br
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