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Fiuovtot Z*Tg) fiUoVtot z*tg) STATEMENTS 1) Comparative genomics provides a means to answer important questions about evolutionary history, includingorigi no fspecies ,adaptatio n tobioti can dabioti cfactor san dsurviva lfro mextinction . 2) Knowledge about adaptation to biotic and abiotic factors constitutes a basis for genetic therapy/remediation in a broad sense comprising areas such as agriculture, ecology, medicine and veterinary. 3) In situ (on-farm) conservation of genetic resources of wild species and crop landraces is essential to facilitate the evolutionary processes underlying biodiversity andcoul d bestrengthene d inth efutur e byth e development of programs coordinating the activities of farmers, governments and the biotechnology industries. 4) Bio-molecular techniques offer a fast and reliable way to control the quality of export/import agricultural productswithi nth einternationa lmarke t sanitarystandards . 5) Genetic engineeringo fforag e legumes includingth e introductiono fresistanc e topathogens , adaptationt o environmental conditions such as drought, enhanced nutritional feed-value, and preservation of feed- value understorag econdition swil lresul ti nincrease d livestockproduction . 6) Of the agricultural important mammals cow hasth e highest density ofmarker s associated with QTLsan d economic trait loci (ETLs). This offers the possibilityfo r positional cloning of these genes bycomparativ e genomics using the gene-rich human, mouse and rat genetic maps, which will markedly increase the opportunitiest o improve cattleproduction . 7) Biotechnology should be criticized, by similar standards as any other scientific, cultural or socialactivit y thatdrov e usi ntim efro mth eprehistori ccave s intoth e modem contemporarysociety . 8) "Y se quee nnuestra svRJa s seproduj o Elmilagr o inefablede lreflejo.. Ene lsilenci od e lanoch em ialm a Llegaa latuy acom ou ngra nespejo. " DelmiraAgustin i(1886-1914 , Uruguay). Fragmentfro mth epoe m"Intima "i nEllibrv Blanco (O.M. Bertanied.) , Montevideo 1907. In this thesis, the Medicago tmncatula Sym2-orthologous regionwa s clonedan d delimitated to 350 Kbp, providinga soli dbasi sfo rth eclonin go fth epe a Sym2gen e bycomparativ egenomics . 10) It is highly probable that the leucine-rich Cf4/Cf9-like pea cDNA RFLP marker PscLRR52-isolated inthi s thesis- is involved in Nod factor perception or /and signal transduction, and represents the pea Sym2 gene. Statementsfro mth e Ph.D.thesi sentitled : 'Medicago tmncatula, an intergenomicvehicl efo rth emap-base dclonin go fpe a(Pisum sativum) genes. Comparative structuralgenomi cstudie so fth epe a Sym2-Nod3 region.' Gustavo Salvador GualtieriGonzalez-Latorre . Wageningen,Ma y2 1 2001. Medicagotruncatula, an intergenomic vehicle for the map-based cloning of pea (Pisumsativum) genes Comparative structural genomic studies of the peaSym2-Nod3 region Gustavo S. Gualtieri Gonzalez-Lato rr e Promotor: prof.dr .A.H.J .Bisseling ,hoogleraa r Moleculaire Biologie Samenstelling promotiecommissie: prof.D .Coo k (University ofCalifornia ,USA ) dr.J.H .d eJon g(Wageninge n Universiteit) prof.dr .ir .M .Koornnee f (Wageningen Universiteit) prof.dr .W.J .Stiekem a(Plan t Research International; Wageningen Universiteit) prof.dr .S.C .d e Vries(Wageninge n Universiteit) „,joi?c — • r(,-2<i n Medicagotruncatula, an intergenomic vehicle for the map-based cloning ofpe a (Pisumsativum) genes Comparativestructura l genomicstudie so fth epe aSym2-Nod3 region Gustavo S.Gualtier i Gonzalez-Latorre Proefschrift terverkrijgin g van degraa dva ndocto r opgeza gva n derecto r magnificus van Wageningen Universiteit prof.dr . ir.L .Speelma n inhe topenbaa r teverdedige n opmaanda g2 1me i200 1 desnamiddag st evie r uur ind eAula . \jv^ £\ £ vxvA 8 Medicago truncatula, anintergenomi cvehicl e forth emap-base d cloning ofpe a (Pisum sativum) genes.Comparativ e structural genomic studies ofth epe aSym2-Nod3 region. G. Gualtieri ThesisWageninge n University, TheNetherland s With references - with summary inDutc h ISBN 90-5808-439-6 Contents CONTENTS Outline 7 Chapter1 The evolution of nodulation 11 Chapter2 Towards the cloning of the pea Sym2 gene by using 41 Medicago truncatula as intergenomic cloning vehicle: A region on M. truncatula chromosome 5 is highly microsyntenic toth epe aSym2-containin gregio n Chapter 3 Microsynteny between the Medicago truncatula Sym2- 63 orthologous genomic region and another genomic region both located onth e longar m ofchromosom e 5 Chapter4 Isolation of RFLP markers linked to the nodi 83 hypernodulation locus on pea linkage group I, and identification of orthologous genomic regions in Medicago truncatulaKYI Chapter5 Integration of FISH-pachytene and genetic maps of 103 Medicago truncatula Chapter6 Concluding remarks 123 References 129 Summary 135 Samenvatting 137 Resumen 139 Curriculum vitae 143 Acknowledgement 145 Outline OUTLINE Biological nitrogen fixation is a unique process that is only carried out by prokaryotes. In some cases microbes fix nitrogen in symbiotic association with specific groups of dicot plants. These prokaryotes produce the enzyme nitrogenase that reduces nitrogen gas into ammonia. Chapter 1 presents recent molecular phylogenetic studies of seed plants showing that all nodule-forming plants belong to a single clade named Rosid I. Within this clade four subclades out of six are able to form nodular symbioses. One of them contains the family Leguminosae that is nodulated exclusively by bacteria of the gram-negative genera Azo-, Brady-,Meso-aad Sino-Rhizobium, whileth e other three clades contain the families Rosaceae, Ulmaceae, Elaeagnaceae, Rhamnaceae, Betulaceae, Casuarinaceae, Myricaceae, Coriariaceae and Datiscaceae that interact with the gram-positive actinomycete Frankia and are collectively called actinorhizal plants. However, the tropical tree Parasponia belongs to the Ulmaceae, but can only be nodulated by rhizobia. Thus, molecular phylogenetic studies show that plants able to establish an endosymbiotic association leading to nitrogen fixing nodules are more related than what their morphological features indicate. Chapter 1 describes and compares legume and actinorhizal nodule ontogeny. It seems likely that the prenodule formed in actinorhizal symbioses is related to the nodule primordium formed in legume symbioses. Moreover, this comparison suggests that the mechanisms underlying nodule development are common to all nodule-forming plants. Furthermore, it is discussed that the nodulation process is(i npart? ) derivedfrom processe s that are widespread amonghighe rplants . One of the main questions addressed in this thesis, is whether microsynteny exists between legume species and this is analyzed bycomparativ e genomics studies. Chapter 2 isa structural comparative genomic study on two plants belonging to the Leguminosae: Pisum sativum bv viciae (pea) and Medicago truncatulaA1 7 line. The level of microsynteny of the pea "Sym2 region" and the orthologous Medicago region is studied. This chapter represents the beginning of a microsynteny-based positional cloning approach for the peaSym2 gene, which controls Nod factor structure-dependent strain-specific nodulation. A marker which is tightly linked to Sym2 was used to screen a M. truncatula A17 BAC library and three physically unlinked contigs (named cl, c2 and c3) were constructed and extended by chromosome walking to a final total size of about 600 Kbp. These contigs were mapped genetically and by FISH on M. truncatula A17 chromosome 5. RFLP analysis demonstrated that cl/c2 is the Medicago S_ym2-orthologous genomic region. Furthermore, some of these RFLP markers Outline revealed recombinations around the Sym2 locus and therefore delimitated the Sym2- orthologous region within cl/c2. Moreover, the potential of Medicago truncatula A17 as intergenomic cloning vehicle of pea genes located at microsyntenic regions is demonstrated by the isolation-from a pea root hair library-of the cDNA PscLRR52, which contains a LRR motif that is highly homologous to the LRR motives of the Cf4 and Cf9 [Licopersicon esculentum] disease resistance proteins. In Chapter 3, the distribution of several sequences in cl/c2 and c3 is studied through the construction of detailed contig molecular maps. This showed that the majority of the sequences located in cl/c2 do not occur c3. This demonstrates again that cl/c2 is the Sym2- orthologous region. However, c3 contains a sequence that ishighl y homologous to PscW62-l. In addition, the Sy»j2-linked RFLP markers Mtg3552 and Mtc411 from cl/c2, and the c2 genomic subclone Mtg2.4, are also present in both cl/2 and c3. Moreover, it was found that Mtg3552 and Mtg2.4, and PscW62-l and Mtc411, are physically clustered and that these clusters have a similar order in cl/c2 and c3, respectively. Thus, the colinearity of these marker clusters indicates that (a part of?) cl/c2 and c3 arose by genome duplication, rather than by independent evolution. Similar duplications have been described in grasses and in Brassicaceae. In Chapter 4 the RNA differential display mediated the isolation of the pea RFLP markers dd21.5 and Psc2.6 that are tightly linked to each other and located close to the nod3 hypernodulation locus that maps at a 2 cM distance from Sym2 in pea linkage group I. These two markers are probably as close to Nod3 as the cl markers Mtc831 and Mtc923 are from Sym2, because two recombinations map between dd21.5IPsc2.6 and Nod3, and Mtc831IMtc923 and Sym2. Moreover, since the Medicago Sy/w2-orthologous region was delimitated to about 350
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