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Cytogenetic and Molecular Studies on Tomato Chromosomes Using Diploid Tomato and Tomato Monosomic Additions in Tetraploid Potato

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Cytogenetic and Molecular Studies on Tomato Chromosomes Using Diploid Tomato and Tomato Monosomic Additions in Tetraploid Potato CYTOGENETIC AND MOLECULAR STUDIES ON TOMATO CHROMOSOMES USING DIPLOID TOMATO AND TOMATO MONOSOMIC ADDITIONS IN TETRAPLOID POTATO Song-Bin Chang Promotor: Prof. dr. ir. E. Jacobsen - Hoogleraar in de Plantenveredeling Co-promotoren: Dr. J. H. de Jong - Universitair hoofddocent, Laboratorium voor Erfelijkheidsleer Dr. P. Lindhout - Universitair hoofddocent, Laboratorium voor Plantenveredeling Promotiecommissie: Prof. dr. ir. M. Koornneef (Wageningen Universiteit ) Prof. dr. A.H.J. Bisseling (Wageningen Universiteit) Prof. dr. A.G.M. Gerats (Katholieke Universiteit Nijmegen) Prof. dr. R.A. Wing (University of Arizona, Tucson AZ, USA) Dit onderzoek werd uitgevoerd binnen de onderzoekschool Experimentele Plantenweten- schappen (EPW) Song-Bin Chang CYTOGENETIC AND MOLECULAR STUDIES ON TOMATO CHROMOSOMES USING DIPLOID TOMATO AND TOMATO MONOSOMIC ADDITIONS IN TETRAPLOID POTATO Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit Prof. dr. ir. L. Speelman in het openbaar te verdedigen op woensdag 9 Juni 2004 des namiddags te 3:30 uur in de Aula The work presented in this thesis was carried out at the Laboratory of Genetics, Wagenin- gen University, the Netherlands. This research was financially supported by my parents and myself. Subject headings: Fluorescence in situ Hybridization (FISH), multi-colour FISH, AFLPs, repeat bar-coding, physical mapping, jointless-2, tomato monosomic additions. With references - With summaries in English, Dutch and Chinese ISBN 90-8504-027-2 To my parents and brothers Contents Chapter General introduction 7 Chapter 2 Production of alien chromosome additions and their utility in 7 plant genetics Chapter 3 AFLP fingerprinting in a full set of monosomic additions con- 37 taining tomato chromosomes in 4x potato background Chapter 4 FISH mapping and molecular organization of the major repeti- 5 tive DNA classes of tomato Chapter 5 Localization of jointless-2 gene in the centromeric region of to- 75 mato chromosome 2 based on high resolution genetic and phys- ical mapping Chapter 6 Physical mapping of BACs on tomato chromosome 6 at pachy- 89 tene and DNA fibres using multi-colour FISH Chapter 7 General discussion 05 Chapter 8 Summary (English, Dutch, Chinese) 3 Chapter 9 Acknowledgements 23 5 General Introduction 7 Tomato (Lycopersicon esculentum, 2n=2x=24) is an excellent model for genetic and molecu- lar studies in the Solanaceae family. It is a self-pollination crop, can produce relatively large amount seeds and has a rather short generation time. Tomato also has a relatively small genome size, . pg = 950 Mb/C, and the twelve pairs of chromosomes at pachytene can easily be identified and show a well-differentiated morphology making it an outstanding species for cytogenetic research (Ramanna and Prakken, 967; Khush and Rick, 968; Sher- man and Stack, 995; Peterson et al., 999; Zhong et al., 998). In addition, well-saturated ge- netic maps based on various L. esculentum x L. pennellii/ pimpinellifolium F2 populations are available (Tanksley et al., 992; Haanstra et al., 999). In addition, tomato has been used for a variety of cell and tissue techniques and its protoplasts were used for several somatic hybridisations with related species (Melchers et al., 978; Wolters et al., 994). Furthermore, tomato is an important economic crop and therefore draws attraction to relevant studies for human favours. Attribute to those outstanding features is the recently initiated Interna- tional Solanaceae Genome Project (SOL) to study diversity and adaptation aspects, which has chosen tomato as the Solanaceae model species for genome sequencing (http://www. sgn.edu/Solanaceae-project/). In spite of all fundamental genetic and cytogenetic research so far, many questions still remain unanswered. We do not know how single copy sequences and repetitive sequences are organised in the genome and where hey are located on the chromosomes with respect to heterochromatin and euchromatin regions. One way to simplify such questions is to re- duce the number of chromosomes under study. Here we show how monosomic additions, in which a single tomato chromosome is added to a tetraploid potato, can be used to map mo- lecular markers that are non-polymorphic in the tomato chromosome for cytogenetic as- signment to the alien tomato chromosome. We also discuss how such monosomic additions are eminent for positioning tomato specific repetitive sequences, to study homo(eo)logous recombination and to evaluate the heterologous expression of alien genes. Since the tomato has well-differentiated chromosomes at pachytene showing conspicuous distal euchromatin and pericentromeric heterochromatin (Ramanna and Prakken, 967), we can use this heterochromatin pattern to identify all chromosomes in the complement and to map single copy and repetitive DNA sequences. Peterson et al. (999) gave an over- view of DNA contents and physical lengths of all 24 chromosome arms. Chromosome has the longest complement and largest euchromatin block while chromosome 2 is the shortest one. Fluorescent in situ hybridisation (FISH) technique provides an advanced tool to visualise physical positions of repeats or single-copy sequences on mitotic chromosomes, higher resolution pachytene complements and even on extended DNA fibres. The three major aim in my thesis are i) to discuss the significance of alien additions for the study of the tomato genome and to show its use for mapping molecular markers on the chromosomes, ii) FISH mapping and analysing repetitive sequences and iii) positioning sin- gle copy sequence in Bacterial Artificial Chromosomes (BACs) on pachytene chromosomes 8 by FISH. Production and analyses of alien additions Alien additions are useful not only for genomic studies but also for breeders to introduce desirable germplasm from related species into the crop. In the offspring families aneuploids individuals could thus be isolated containing only a single alien chromosome added to the full complement of the recipient parent. Monosomic additions can be selected on the basis of specific alien traits (Fernandez and Jouve, 988; Gao and Jung, 2002; Jena and Khush, 989; Littlejohn and Pienaar, 995; Mesbah et al., 997; Morgan, 99; Reamon Ramos and Wricke, 992; Riera-Lizarazu et al., 996; Shigyo et al., 997), molecular markers (Friebe et al., 2000; Garriga-Caldere et al., 997; Kaneko et al., 2000; Jorgensen et al., 996; van Heus- den et al., 2000; Hernandez et al., 2002; Riera-Lizarazu et al., 996; Mesbah et al., 997a; Gao et al., 200) and karyotype analysis (de Jong et al., 985) to demonstrate the presence of an extra chromosome. Alien chromosomes in interspecific hybrids, backcross derivatives and monosomic addi- tions can best be studies by genomic in situ hybridization (GISH) or genome painting, a fluorescence in situ hybridization protocol using total genomic donor DNA as probe and non-labelled DNA from the recipient parent as competitor (Schwarzacher et al., 989). Ex- amples of GISH for establishing the number of alien chromosomes in intergeneric back cross families are demonstrated in tomato to potato (Jacobsen et al., 995), Oat to maize (Ri- era-Lizarazu et al., 996), Beta corolliflora in beet (Gao et al., 200) and Solanum brevidens to potato (Dong et al., 200) and S-genome in wheat (Belyayev et al., 200). The maintenance of monosomic additions is important because the transmission rate of alien chromosome from parents to offspring vary by plants, genotypes, genders and even by different chromosomes. Transmission rates are generally far higher through the female than the male line, and vary greatly between and among the monosomic addition sets (Mul- tani et al., 994; Li et al., 2003). In the monosomic additions with Solanum lycopersicoides chromosomes to tomato, transmission rate of chromosome 0 was 24%, whereas hardly any transmission of chromosome 6 could be found (Chetelat et al., 998). Ali et al. (200) ana- lyzed the transmission values of tomato monosomic additions and found of chromosome 9 it ranged 0 – 32%, whereas it varied from 4 – 88% in chromosome 6 between the different families. The primary use of alien additions is to transfer desirable genes to a crop. An example is of special interest to produce aneuploids carrying genes for apomixes. Since meiosis is skipped, offspring is almost identical to the mother. Therefore, monosomic additions and other aneuploids can be maintained for breeding purposes (Kindiger et al., 996; Morgan et al., 998; Gao and Jung 2002). Alien additions also provide a unique system to investigate heterologous gene expression of genes on an alien chromosome in the genetic background of a wide relative (Muehlbauer et al., 2000) and to study their dependence of genes on other 9 chromosomes of the donor species, and the effect of different genetic background of the recipient species, but little experiments have been carried out so far (Hu et al., 996). As for studying chromosome pairing at meiosis, monosomic and disomic additions are the par- ticularly suitable materials (Schwarzacher, 997; Mikhailova et al., 998; Martinez-Perez et al., 999; Maestra et al., 2002). The correlation between specific alleles and molecular markers or repeat fingerprints and the presence of an alien chromosome not only helps to identify the alien chromosome in the monosomic addition, but also allows assigning loci or linkage groups on chromosomes. The identification and characterization of the alien chromosome are often based on RFLP, or other molecular marker assay in combination with chromosome banding or
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