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Comparative Genome Analysis of the Small-scale Duplication in Plants
DC Field | Value | Language |
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dc.contributor.advisor | 이석하 | - |
dc.contributor.author | 강양제 | - |
dc.date.accessioned | 2017-07-13T17:40:46Z | - |
dc.date.available | 2017-07-13T17:40:46Z | - |
dc.date.issued | 2013-02 | - |
dc.identifier.other | 000000010161 | - |
dc.identifier.uri | https://hdl.handle.net/10371/121036 | - |
dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 식물생산과학부 작물생명과학전공, 2013. 2. 이석하. | - |
dc.description.abstract | Mapping the genes against environmental changes is invaluable information for breeders to ensure the yield of cultivars, and become more important than ever before due to the global climate changes accompanying different biotic and abiotic stresses. However, the knowledge of the genes that provide resistance against such environmental stresses is still limited in crop plants.
Previous researches showed that the genes related to response to biotic stress and secondary metabolism in Arabidopsis were retained after small and large scale duplication events and the tandemly duplicated genes corresponded to gene ontology (GO) category of stress response had high probability of retention and suggested their role of adaptive evolution against environments. In this dissertation, nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes which are highly tandem-duplicated in G. max genome are suggested to contribute to soybean disease resistance by co-localization analysis with disease-related QTL and bacterial leaf pustule (BLP) treated transcriptome analysis. Moreover, genes underwent small scale duplication like tandem duplication and ectopic duplication were retrieved from 5 crop genomes and 2 non-crop genomes and investigated the QTL co-localization and the evolution rate by pair-wise calculation of Ks values in homologous gene groups, and we found the crop genome were commonly experienced recent tandem duplications while non-crop genome were not, which might implicate the domestication process could be influenced by tandem duplication process to optimize the adaptation to the environment and human needs. | - |
dc.description.tableofcontents | CONTENTS
GENERAL ABSTRACT i CONTENTS iii LIST OF TABLES vi LIST OF FIGURES viii ABBREVIATION x INTRODUCTION AND LITERATURE REVIEW 1 Whole genome assembly of plant genomes 1 NBS-LRR gene family in plant genome 3 Small scale duplication in genome 4 REFERENCES 6 CHAPTER 1 : Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean ABSTRACT 8 INTRODUCTION 10 MATERIALS AND METHODS 13 Data generation 13 Transcriptome data analysis 14 Validation of RNA-Seq experiments by qRT-PCR 14 RESULTS 16 Distribution of genome-wide NBS-LRR genes and disease resistance QTL 16 Recent duplication of NBS-LRR containing genomic regions 33 Transcriptome analysis of NBS-LRR genes 41 DISCUSSION 46 NBS-LRR chromosomal distribution 46 Recent duplication of the soybean genome and the redundancy of the disease resistance function 47 Transcriptome analysis of the NBS-LRR genes on the BLP-resistant NIL set 48 Conclusions 54 REFERENCES 55 CHAPTER 2 : Association Study of the Small-scale Duplication with Crop Domestication Process ABSTRACT 58 INTRODUCTION 60 MATERIALS AND METHODS 64 Retrieving tandemly duplicated gene clusters 64 QTL co-localization analysis of tandemly duplicated gene clusters 65 Calculation of synonymous substitution rate in tandemly duplicated gene cluster 65 Classification of tandemly duplicated gene clusters 66 RESULTS 67 Define the TDGs and IDGs from plant genomes 67 Gene ontology analysis and over-represented duplication timing of TDGs 67 GO analysis and the recent biased duplication of IDGs 69 Gene family analysis of TDGs 79 Commonly duplicated TDGs in both non-crop and crop genomes 80 DISCUSSION 87 REFERENCES 91 APPENDIX 95 | - |
dc.format | application/pdf | - |
dc.format.extent | 2462893 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | ko | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject.ddc | 633 | - |
dc.title | Comparative Genome Analysis of the Small-scale Duplication in Plants | - |
dc.type | Thesis | - |
dc.description.degree | Doctor | - |
dc.citation.pages | 124 | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부(작물생명과학전공) | - |
dc.date.awarded | 2013-02 | - |
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