雜交水稻（Oryza sativa L.）親本11個產(chǎn)量相關(guān)性狀配合力效應(yīng)與SNPLDB的關(guān)聯(lián)分析
發(fā)布時間：2024-06-02 09:48
雜交水稻籽粒產(chǎn)量高、營養(yǎng)價值好、對生物和非生物肋脅迫的抵抗力強。與常規(guī)品種相比,雜交水稻由于遺傳背景的多樣性,農(nóng)藝性狀優(yōu)良,使其能夠提高20%的產(chǎn)量。配合力分析是鑒定優(yōu)勢配組親本不可缺少的方法。在以往的研究中,曾用分子標(biāo)記檢測和發(fā)掘優(yōu)異一般配合力(general combining ability,GCA)的基因組資源。為了進一步獲得親本性狀GCA的有益等位基因,我們用構(gòu)建的單核苷酸多態(tài)性連鎖不平衡區(qū)段(single nucleotide polymorphism linkage disequilibrium block,SNPLDB)揭示 GCA 的遺傳基礎(chǔ)。相比以前的實驗,構(gòu)建的SNPLDB和親本性狀GCA效應(yīng)之間的關(guān)聯(lián)分析是用于鑒定GCA基因位點的一種新的和獨特的方法。在我們的研究中,通過對采用北卡羅來納交配設(shè)計Ⅱ1配制的48個秈稻一代雜種和78個粳稻一代雜種的表型分析,估算了 14個秈稻親本(8個CMS和6個恢復(fù)系)和19個粳稻親本(13個CMS和6個恢復(fù)系)的11個產(chǎn)量相關(guān)性狀的GCA效應(yīng)值。通過對親本基因組測序進行基因分型獲得基因型數(shù)據(jù)。應(yīng)用SAS/STAT軟件中標(biāo)記-性狀...
【文章頁數(shù)】：217 頁
【學(xué)位級別】：博士
【文章目錄】：
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
本文編號：3987170
【文章頁數(shù)】：217 頁
【學(xué)位級別】：博士
【文章目錄】：
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
本文編號：3987170
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