杂交水稻（Oryza sativa L.）亲本11个产量相关性状配合力效应与SNPLDB的关联分析
发布时间：2024-06-02 09:48
杂交水稻籽粒产量高、营养价值好、对生物和非生物肋胁迫的抵抗力强。与常规品种相比,杂交水稻由于遗传背景的多样性,农艺性状优良,使其能够提高20%的产量。配合力分析是鉴定优势配组亲本不可缺少的方法。在以往的研究中,曾用分子标记检测和发掘优异一般配合力(general combining ability,GCA)的基因组资源。为了进一步获得亲本性状GCA的有益等位基因,我们用构建的单核苷酸多态性连锁不平衡区段(single nucleotide polymorphism linkage disequilibrium block,SNPLDB)揭示 GCA 的遗传基础。相比以前的实验,构建的SNPLDB和亲本性状GCA效应之间的关联分析是用于鉴定GCA基因位点的一种新的和独特的方法。在我们的研究中,通过对采用北卡罗来纳交配设计Ⅱ1配制的48个籼稻一代杂种和78个粳稻一代杂种的表型分析,估算了 14个籼稻亲本(8个CMS和6个恢复系)和19个粳稻亲本(13个CMS和6个恢复系)的11个产量相关性状的GCA效应值。通过对亲本基因组测序进行基因分型获得基因型数据。应用SAS/STAT软件中标记-性状...
【文章页数】：217 页
【学位级别】：博士
【文章目录】：
ABSTRACT
摘要
LIST OF ABBREVATIONS
CHAPTER 1 LITERATURE REVIEW
1.1. RICE INTRODUCTION AND ITS IMPORTANCE
1.1.1. Rice
1.1.2. Morphology of rice plant
1.1.3. Production and consumption of rice
1.2. RICE BREEDING
1.2.1. Breeding methods
1.2.2. Hybrid rice breeding, a comparative analysis
1.3. MECHANISM OF PARENTAL SELECTION
1.3.1. Principle and utilization of combining ability in plant breeding
1.3.2. The GCA effect
1.4. MOLECULAR MARKER RESOURCES FOR GCA
1.4.1. Dissection of GCA with molecular markers
1.4.2. SNPs and its significance in rice breeding
1.4.3. The genotyping by sequencing method for SNP discovery
1.5. MARKER-TRAIT ASSOCIATION ANALYSIS IN RICE
1.5.1. Application of marker-trait association analysis in plant breeding
1.5.2. Association analysis using SNPLDBs
1.6. RESEARCH OBJECTIVE
CHAPTER 2 MATERIALS AND METHODS
2.1. PLANT MATERIALS AND HYBRIDS DEVELOPMENT
2.1.1. Nursery establishment
2.1.2. Transplantation
2.1.3. Pollination
2.2. PHENOTYPIC EVALUATION OF DEVELOPED HYBRIDS
2.3. TRAITS MEASUREMENT
2.4. STASTICAL ANALYSIS AND GENERAL COMBINING ABILITY CALCULATION
2.5. DNA ISOLATION
2.6. LIBRARY CONSTRUCTION AND SEQUENCING
2.7. SHORT READS MAPPING
2.8. SNP CALLING AND ANNOTATIONS OF IDENTIFIED SNPs
2.9. CONSTRUCTION OF SNPLDBS
2.10. ASSOCIATION ANALYSIS
CHAPTER 3 RESULTS
3.1. PERFORMANCES OF DEVELOPED HYBRIDS
3.2. GCA EFFECTS OF INDICA CMS AND RESTORER LINES
3.3. GCA EFFECTS OF JAPONICA CMS AND RESTORER LINES
3.4. MAPPING OF SHORT READS ONTO THE NIPPONBARE REFERENCE GENOME
3.5. DETECTION AND DISTRIBUTION OF SNPs IN INDICA CMS AND RESTORERLINES
3.6. DETECTION AND DISTRIBUTION OF SNPs IN JAPONICA CMS AND RESTORERLINES
3.7. ANNOTATION OF IDENTIFIED SNPs OF INDICA CMS AND RESTORER LINES
3.8. ANNOTATION OF IDENTIFIED SNPs OF JAPONICA CMS AND RESTORER LINES
3.9. ANALYSIS OF TRANSITIONS AND TRANSITIONS SUBSTITUTIONS
3.10. CONSTRUCTION AND CHARACTERIZATION OF SNPLDBs
3.11. ASSOCIATION ANALYSIS BETWEEN CONSTRUCTED SNPLDBs AND GCAEFFECTS
3.11.1. Days to heading
3.11.2. Plant height
3.11.3. Number of panicles per plant
3.11.4. Number of spikelets per panicles
3.11.5. Number of filled grain per panicles
3.11.6. Panicle length
3.11.7. Seed width
3.11.8. Seed thickness
3.11.9. Seed length
3.11.10. Thousand grain weight
3.11.11. Grain yield
3.12. SELECTION OF SUPERIOR ALLELES
3.13. ELITE PARENTAL LINES FOR DEVELOPING OF SUPERIOR HYBRIDCULTIVARS
CHAPTER 4 DISCUSSION
4.1. MATING DESIGN AND SIGNIFICANCE OF GCA EVALUATION TRIAL
4.2. SIGNIFICANCE OF GCA EVALUATION BY MARKERS
4.3. DISCOVERY OF GENOME-WIDE SNPs IN PARENTAL GENOMESOF HYBRID RICE USING GBS ASSAY
4.4. ANNOTATION OF IDENTIFIED SNPs
4.5. THE POSSIBLE USES OF SNPs
4.6. ADVANTAGE OF CONSTRUCTION OF SNPLDBs
4.7. ASSOCIATION ANALYSIS
4.8. GENE ONTOLOGY OF DETECTED GENES SITUATED WITHIN THE INTERVALSOF ASSOCIATED SNPLDBs
CHAPTER 5 CONCLUSION
5.1. BREEDING APPLICATION OF GCA EVALUATION
5.2. SIGNIFICANCE OF SNP DISCOVERY IN RICE
5.3. MINING OF SUPERIOR GCA ALLELES IN PARENTAL GENOMES BYASSOCIATION ANALYSIS
CHAPTER 6 MAJOR INNOVATION POINTS
REFERENCES
APPENDICES
ACKNOWLEDGEMENT
BIOGRAPHICAL DATA
PUBLICATIONS DURING THE PERIOD OF STUDY FOR PHD DEGREE
本文编号：3987170
【文章页数】：217 页
【学位级别】：博士
【文章目录】：
ABSTRACT
摘要
LIST OF ABBREVATIONS
CHAPTER 1 LITERATURE REVIEW
1.1. RICE INTRODUCTION AND ITS IMPORTANCE
1.1.1. Rice
1.1.2. Morphology of rice plant
1.1.3. Production and consumption of rice
1.2. RICE BREEDING
1.2.1. Breeding methods
1.2.2. Hybrid rice breeding, a comparative analysis
1.3. MECHANISM OF PARENTAL SELECTION
1.3.1. Principle and utilization of combining ability in plant breeding
1.3.2. The GCA effect
1.4. MOLECULAR MARKER RESOURCES FOR GCA
1.4.1. Dissection of GCA with molecular markers
1.4.2. SNPs and its significance in rice breeding
1.4.3. The genotyping by sequencing method for SNP discovery
1.5. MARKER-TRAIT ASSOCIATION ANALYSIS IN RICE
1.5.1. Application of marker-trait association analysis in plant breeding
1.5.2. Association analysis using SNPLDBs
1.6. RESEARCH OBJECTIVE
CHAPTER 2 MATERIALS AND METHODS
2.1. PLANT MATERIALS AND HYBRIDS DEVELOPMENT
2.1.1. Nursery establishment
2.1.2. Transplantation
2.1.3. Pollination
2.2. PHENOTYPIC EVALUATION OF DEVELOPED HYBRIDS
2.3. TRAITS MEASUREMENT
2.4. STASTICAL ANALYSIS AND GENERAL COMBINING ABILITY CALCULATION
2.5. DNA ISOLATION
2.6. LIBRARY CONSTRUCTION AND SEQUENCING
2.7. SHORT READS MAPPING
2.8. SNP CALLING AND ANNOTATIONS OF IDENTIFIED SNPs
2.9. CONSTRUCTION OF SNPLDBS
2.10. ASSOCIATION ANALYSIS
CHAPTER 3 RESULTS
3.1. PERFORMANCES OF DEVELOPED HYBRIDS
3.2. GCA EFFECTS OF INDICA CMS AND RESTORER LINES
3.3. GCA EFFECTS OF JAPONICA CMS AND RESTORER LINES
3.4. MAPPING OF SHORT READS ONTO THE NIPPONBARE REFERENCE GENOME
3.5. DETECTION AND DISTRIBUTION OF SNPs IN INDICA CMS AND RESTORERLINES
3.6. DETECTION AND DISTRIBUTION OF SNPs IN JAPONICA CMS AND RESTORERLINES
3.7. ANNOTATION OF IDENTIFIED SNPs OF INDICA CMS AND RESTORER LINES
3.8. ANNOTATION OF IDENTIFIED SNPs OF JAPONICA CMS AND RESTORER LINES
3.9. ANALYSIS OF TRANSITIONS AND TRANSITIONS SUBSTITUTIONS
3.10. CONSTRUCTION AND CHARACTERIZATION OF SNPLDBs
3.11. ASSOCIATION ANALYSIS BETWEEN CONSTRUCTED SNPLDBs AND GCAEFFECTS
3.11.1. Days to heading
3.11.2. Plant height
3.11.3. Number of panicles per plant
3.11.4. Number of spikelets per panicles
3.11.5. Number of filled grain per panicles
3.11.6. Panicle length
3.11.7. Seed width
3.11.8. Seed thickness
3.11.9. Seed length
3.11.10. Thousand grain weight
3.11.11. Grain yield
3.12. SELECTION OF SUPERIOR ALLELES
3.13. ELITE PARENTAL LINES FOR DEVELOPING OF SUPERIOR HYBRIDCULTIVARS
CHAPTER 4 DISCUSSION
4.1. MATING DESIGN AND SIGNIFICANCE OF GCA EVALUATION TRIAL
4.2. SIGNIFICANCE OF GCA EVALUATION BY MARKERS
4.3. DISCOVERY OF GENOME-WIDE SNPs IN PARENTAL GENOMESOF HYBRID RICE USING GBS ASSAY
4.4. ANNOTATION OF IDENTIFIED SNPs
4.5. THE POSSIBLE USES OF SNPs
4.6. ADVANTAGE OF CONSTRUCTION OF SNPLDBs
4.7. ASSOCIATION ANALYSIS
4.8. GENE ONTOLOGY OF DETECTED GENES SITUATED WITHIN THE INTERVALSOF ASSOCIATED SNPLDBs
CHAPTER 5 CONCLUSION
5.1. BREEDING APPLICATION OF GCA EVALUATION
5.2. SIGNIFICANCE OF SNP DISCOVERY IN RICE
5.3. MINING OF SUPERIOR GCA ALLELES IN PARENTAL GENOMES BYASSOCIATION ANALYSIS
CHAPTER 6 MAJOR INNOVATION POINTS
REFERENCES
APPENDICES
ACKNOWLEDGEMENT
BIOGRAPHICAL DATA
PUBLICATIONS DURING THE PERIOD OF STUDY FOR PHD DEGREE
本文编号：3987170
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