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Characterization of Brassica Rapa Turnip Formation in Multiple Segregating Populations

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Characterization of Brassica Rapa Turnip Formation in Multiple Segregating Populations Characterization of Brassica rapa turnip formation in multiple segregating populations Peter Vos 830317-908-030 Laboratory of Plant Breeding, Wageningen University January-October 2009 Supervisors: Ningwen Zhang Guusje Bonnema Characterization of Brassica rapa turnip formation in multiple segregating populations Abstract In this study eleven F 2 populations were evaluated for turnip formation (TuF) and flowering time (FT). The goal was to select populations which form turnips with a wide range in size for studying the genetic basis of turnip formation. Besides the turnip formation FT is important because in previous studies FT and turnip formation are negatively correlated and QTLs for both traits are mapped in the same genomic region. The major finding on the FT-TuF correlation topic was that the correlation was present when the parents differ greatly in flowering time, on the other hand the FT-TuF correlation was absent when the parents did not differ in flowering time. In the evaluated populations a distinction can be made between the origin of the turnips in the populations. Populations with turnips from the Asian and European centers of variation were represented in this study. The phylogenetic relationship between different turnips suggests that different genes could underlie turnip formation in both centers of variation. This hypothesis is confirmed; in a population between turnips from both centers of variation other genomic regions correlate with turnip size than regions in populations with only the Asian turnips. This indicates that different genes underlie the same trait in different centers of variation. However this is only one population and therefore the conclusion is still fragile. Therefore new crosses have to be made between European turnips with RC-144 and PC-105 for comparison with the best populations in this study (VT-115 x RC-144 and VT-115 x PC-105). Keywords: Brassica rapa , Turnip formation, Flowering time, Segregating populations, Abbreviations: TuF = Turnip formation, FT = Flowering Time, VT = Vegetable Turnip, RC = rapid cycling, CC = Chinese cabbage, PC = Pakchoi, WO = Winter Oil, OR = Oil seed Rape, YS =Yellow Sarson 2 Characterization of Brassica rapa turnip formation in multiple segregating populations Table of contents ABSTRACT....................................................................................................................................... 2 1. INTRODUCTION ...................................................................................................................... 5 1.1. BOTANICAL DESCRIPTION ................................................................................................... 5 1.2. GENETIC RESEARCH IN BRASSICA RAPA ............................................................................... 6 1.3. PHYLOGENETICS................................................................................................................. 6 1.4. GENETIC MARKERS............................................................................................................. 7 1.5. MAPS AND POPULATIONS .................................................................................................. 8 1.6. FT-TUF CORRELATION......................................................................................................... 8 1.7. SCOPE OF THE THESIS ......................................................................................................... 9 2. MATERIAL & METHODS..........................................................................................................10 2.1. PLANT MATERIAL ..............................................................................................................10 2.2. EXPERIMENTAL DETAILS ....................................................................................................11 2.2.1. GERMINATION ..................................................................................................................11 2.2.2. BLOCK DESIGN ..................................................................................................................12 2.3. DNA ISOLATION ................................................................................................................12 2.4. MOLECULAR MARKER ANALYSIS ........................................................................................13 2.4.1. PCR PROGRAM FOR SSR MARKERS.....................................................................................13 2.4.2. LIGHTSCANNER .................................................................................................................14 2.5. PHENOTYPIC TRAIT SCORING .............................................................................................14 2.6. STATISTICAL ANALYSIS.......................................................................................................15 3. RESULTS ................................................................................................................................16 3.1. PHENOTYPIC DATA............................................................................................................16 3.2. LIGHTSCANNER .................................................................................................................18 3.3. CORRELATIONS AMONG TRAITS.........................................................................................19 3.4. MARKER ANALYSIS............................................................................................................20 4. DISCUSSION ..........................................................................................................................25 4.1. POPULATION 29 (VT-115 X PC-105) ....................................................................................25 4.2. POPULATION 36 (VT-115 X RC-144) ....................................................................................26 4.3. POPULATIONS 32 (VT-115 X CC-146) AND 48 (CC-168 X VT-9) ..............................................26 4.4. POPULATION 49 (VT-52 X VT-12)........................................................................................27 4.5. POPULATIONS 118 & 119 (VT-44 X WO-81), (WO-81 X VT-44) ..............................................28 4.6. POPULATIONS 27(VT-115 X OR-219), 30(VT-115 X YS-143), 34(PC-175 X VT-115) AND 45(CC-74 X VT-9) 28 4.7. TUF-FT CORRELATIONS ......................................................................................................28 3 Characterization of Brassica rapa turnip formation in multiple segregating populations 4.8. DIFFERENT QTLS UNDERLIE TUF IN TWO CENTERS OF VARIATION........................................29 5. CONCLUDING REMARKS AND FUTURE DIRECTION...................................................................30 ACKNOWLEDGEMENT.....................................................................................................................31 REFERENCES...................................................................................................................................32 APPENDIX 1 LIST OF ALL AVAILABLE MARKERS.................................................................................34 APPENDIX 2: DISTRIBUTION GRAPHS FLOWERING TIME (FT) IN ALL POPULATIONS............................35 APPENDIX 3 DISTRIBUTION GRAPHS TURNIP WIDTH OF ALL POPULATIONS. .....................................36 APPENDIX 4 DISTRIBUTION GRAPHS TURNIP WEIGHT ......................................................................37 APPENDIX 5 DNA ISOLATION PROTOCOL .........................................................................................38 4 Characterization of Brassica rapa turnip formation in multiple segregating populations 1. Introduction 1.1. Botanical description Brassica rapa is a species in the angiosperm family Brassicaceae. The Brassicaceae family consists of 338 genera and approximately 3710 species (Beilstein et al. 2008) of which several are agronomically important. In the Brassica genus six species are agronomically important. Three of them are diploid: Brassica rapa ( AA genome, 2n=20), containing three main morphotypes (turnip types, leafy types and oil types); Brassica nigra (BB genome 2n=16) (black mustard) and Brassica oleracea (CC genome 2n=18) including cabbages, broccoli, cauliflower and kohlrabi (above ground turnip). Three of those six are amphidiploids: Brassica juncea (AABB genome, 2n=36) (Indian or brown mustard and several leafy types); Brassica napus (AACC genome, 2n=38) including oilseed rape and the turnip forming Swede, and Brassica carinata (BBCC genome, 2n=34) (Ethiopian mustard). The relationships between these B rassica species and their genomes are summarized in the triangle of U (U 1935) shown in figure 1. Figure 1: Triangle of U, a schematic overview of the relation between six different Brassica species. Within those six species Brassica rapa is the species that was domesticated first. It has been cultivated for many years from central Asia to Europe and northern America (Gomez Campo 5 Characterization of Brassica rapa turnip formation in multiple segregating populations 1999). The crop is cultivated for the oil content (Yellow Sarson) and for vegetable purposes (Chinese cabbage, pakchoi, wutacai, turnip and broccoletto). 1.2. Genetic research in Brassica rapa Since all in the previous section mentioned B. rapa morphotypes (oil, leafy and turnip) can be crossed with each other, good genetic analysis of many morphological traits is feasible. Another advantage is genetic
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