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Meiotic Recombination and Its Implications for Plant Breeding Meiotic recombination and its implications for plant breeding T.G. (Erik) Wijnker Thesis committee Promotors Prof. dr. J.H.S.G.M. de Jong Personal chair at the Laboratory of Genetics, Wageningen University Prof. dr. ir. M. Koornneef Personal chair at the Laboratory of Genetics, Wageningen University and Director at the Max Planck Institute for Plant Breeding Research (MPIZ) Cologne, Germany Co-promotor Dr. R.H.G. Dirks Research manager at the Rijk Zwaan Breeding Company, Fijnaart. Other members Prof. dr. ir. E. Jacobsen, Wageningen University, Wageningen Prof. dr. H. Puchta, University of Karlsruhe, Karlsruhe, Germany Dr. A. Schnittger, University of Strasbourg, Strasbourg, France Prof. dr. M.E. Schranz, Wageningen University, Wageningen This research was conducted under the auspices of the Graduate School Experimental Plant Sciences (EPS) Meiotic recombination and its implications for plant breeding T.G. (Erik) Wijnker Thesis at Wageningen University Submitted in fulfillment of the requirements for the degree of doctor Prof. dr. M.J. Kropf, by the authorityin the presence of the Rector of the Magnificus Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 6 February 2013 at 4 p.m. in the Aula. T.G. (Erik) Wijnker Meiotic Recombination and its implications for plant breeding With references, with summaries in Dutch and English Thesis, Wageningen University, Wageningen, NL (2013) ISBN 978-94-6173-440-2 Contents General introduction Chapter 1 7 Whole-genome sequencing of (non–)crossover sites reveals that meiotic Chapter 2 recombination targets structurally open chromatin in Arabidopsis thaliana 23 Supplementary Figures 51 Supplementary Tables 67 CDKA;1 shapes the recombination landscape in Arabidopsis thaliana Chapter 3 89 Supplementary Discussion 116 Supplementary Figures 119 Chromosome evolution in Solanum traced by cross-species BAC-FISH Chapter 4 125 Supporting Information 146 Managing meiotic recombination in plant breeding Chapter 5 155 Reverse breeding: a novel breeding approach based on engineered meiosis Chapter 6 171 Reverse breeding in Arabidopsis thaliana generates homozygous parental Chapter 7 lines from a heterozygous plant 187 Supplementary Figures, Tables and Note 200 General discussion Chapter 8 213 Summary Samenvatting Acknowledgements - 234 Curriculum Vitae 241 Publications 248 Graduate School EPS Education Statement 249 250 Genesis Het was de zesde dag. Adam stond klaar. Hij zag de eiken met hun volle greep in het niets. Macht is een kwestie van vertakkingen. hij had de bergen gezien, opbergruimtes van alleen maar zichzelf, hoge leegstaande kelders. En herten. Met poten zo dun als stethoscopen stonden ze te luisteren aan de borst van de aarde, en zodra ze iets hoorden, liepen ze weg, de uitvinding van het pizzicato met zich meenemend, verten in. Herten. En hij had de zee gezien, het laden en het lossen van drukte, waar je rustig van werd. En de lege, hetzerige gebaren van de wind, van kom mee, kom mee, en niemand volgde. En diepte, afgronden waar je moeilijk van werd. En zwijgen, want dat deed het allemaal, en te groot zijn. En toen zei God: en nu jij. Nee, zei Adam. H. de Coninck (In: ‘De hectaren van het geheugen’, 1985) Chapter 1 General introduction 7 Chapter 1 Meiosis generates variation duction evolved in complex organisms (Eukaryotes) to facilitate this adaptation by ac tivelyLife evolves changing by adaptingallele combinations continuously on to chromosomes. its ever-changing A greater environment. part of this Sexual variability repro- - homologous pairing, crossover formation and balanced segregation of recombinant chromosomesis generated in creates the highly novel specialised alleles and novelprocess allele of meiosis.combinations The unique on chromosomes. combination As of a major driving force of all this genetic variation, meiosis can be placed at the very heart of evolution, domestication, and also of plant breeding. The key to the creation of new crop varieties lies in the systematic exploration of genetic variation and the selection of new phenotypes. While meiotic recombination provides plant breeders with count less numbers of allele combinations, the unpredictability of such variation leads to time - consuming breeding practices (Dirks et al. ery as well as methods of selection. Only if 2009;we are Wijnker able to and understand de Jong 2008). the mechanisms Improving governingbreeding thus meiotic requires recombination, improving bothwe will the be processes able to control of variation meiotic generation recombination, and discov and- variation during meiosis, determine what patterns underlie this variation and to what extentmanage this it for can breeding help improving purposes. the I managementwill therefore of raise variation questions for plant of how breeding. plants generate As explained above, meiosis plays a pivotal role in creating novel genetic variants/ genotypes by recombining variation that before existed in different genotypes. It does so in two consecutive divisions and along few entirely different processes. It generates new allele and chromosome combinations, while reducing the somatic chromosome number by half during gamete production (Gerton and Hawley 2005). This is achieved in centromeresa controlled sequence until the ofmetaphase unique events of the starting second with division. an S-phase Following in which duplication, chromosomes plants are duplicated, generating two sister-chromatids that remain joined together at their mosomal DNA (Pawlowski et al. et al. atesproduce homology about 100-500search and double recombination. strand breaks At (DSBs)the same along time, the chromosomes whole length progressively of their chro- 2003; Sanchez-Moran 2007), a process that initi- for homologous chromosomes to join together along their entire lengths. This joint tri condense while assembling proteinaceous lateral axes that subsequently serve as a base - partiteWhile proteineous chromosomes structure begin isto knownsynapse, as DSBs the synaptonemal are processed complex and repaired (SC) (Moses through 1968; ho Westergaard and von Wettstein 1972). - Whilemologous mostly recombination leading to genuine (HR). This repair, is a HR specific in meiosis DNA repairalso generates pathway true in which reciprocal DNA exre- pair proteins use homologous DNA sequences as template for DSB repair (Puchta 2005). when a chromatid is repaired by joining one end of it to the other end of a homologous- changes between non-sister chromatids. These so-called meiotic crossovers originate 8 General Introduction somes (i.e., the chromatids) thus consist of new allele combinations of both homologues. While(non-)sister the paired chromatid, homologues thus generating disjoin, their a recombinant SC disassembles chromatid. and homologues Recombinant remain chromo to- gether only at sites of their crossovers, which are now microscopically visible as chias mata in cell complements at late meiotic prophase I (diplotene to metaphase I). Here we- see evidently that homologues are joined by at least one chiasma, which is essential for- proper orientation of the bivalents on the metaphase I divisional plane. Shortly later, at undergo a second division in which sister centromeres disjoin, similar to mitosis. The tetradanaphase stage I, themarks half-bivalents the end of meiosis, (homologues) when the segregate meiocyte equally contains to theirfour spores poles, thatand eachthen carry half the chromosome number of the parent. These spores can then further develop establishing the somatic chromosome number. Crossoverinto gametes recombination (like pollen ensuresand egg that cells) the that dual can roles then of meiosisfuse with are one properly another, executed: thus re- • crossovers form chiasmata that are important for joining homologous chromosome division and reduce the chromosome number of the cell to half (the reductional divi sion).together, enabling them to segregate equally to opposite poles at the first meiotic • crossovers generate new variation directly by creating new allele combinations on- chromosomes, while facilitating random chromosome assortment. Meiosis generates novel genetic combinations in a highly regulated way, but interest ingly, the precise outcome of the genetic content of their daughter cells is always differ - tion and independent chromosome assortment, depends on the number and position of- theent bycrossover the reshuffling sites (intrachromosomal of alleles during meiosis. recombination) The total and genetic the number blending of bychromosomes recombina- crossover incidence varies between bivalents, chromatids, cells, sexes, individuals and (interchromosomal recombination). While the chromosome number is normally fixed, species (Baudat et al. ucts are identical. 2010; Lenormand and Dutheil 2005). As a result, no meiotic prod- Meiosis and breeding While the generation of random variation is pivotal to breeders, it also poses them with tough challenges because meiotic recombination, which is essential for generating fa vourite combination of valuable traits, also produces allele combinations that are un desired and hence useless in the breeding program. Plant breeders found a way of deal- - - inbred families and doubled haploids (Forster et al. inbredsing with still this formby preserving crossovers specific at meiosis, allele the combinations identical homologues in (near) homozygotes ensure that suchno new as allele combinations will be generated. Plant breeders 2007). produce Although and hold the vast homologues collections
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