普通野生稻主效粒型QTL的遗传剖析
发布时间：2021-06-27 10:16
籽粒大小是影响粒重的重要农艺性状之一,在水稻中其对籽粒品质和产量有着重要的影响。然而,在作物中籽粒大小调控机制尚不完全明确。在本研究中,为了阐明水稻籽粒大小、粒型和粒重的遗传机制,我们通过利用大粒品系中恢8015和普通野生稻杂交、回交手段,构建了一个染色体片段渗入系（BC4F6）。在杭州和陵水两地、四代,利用分子辅助选择（marker-assisted selection,MAS）和全基因关联分析（Genome wide association study,GWAS）进行群体构建与水稻籽粒大小QTLs分析。在杭州和陵水两地,利用集群分离分析法（Bulk sergeant analysis,BSA）构建遗传图谱和水稻籽粒大小QTLs鉴定。在第3号染色体着丝粒附近鉴定到了与籽粒大小密切相关的QTL簇,其中存在6个相关QTL位点。其中,来自大粒亲本中恢8015、分别控制粒长、长宽比及千粒重的四个QTL qGL3.1、qLWR3.1、qTGW3和qTGW3.1,其贡献率分别为80.91%、63.43%、24.40%和41.23%。其中qGL3.1和q...
【文章来源】：中国农业科学院北京市
【文章页数】：132 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
LIST OF ABBREVIATIONS
CHAPTER 1 INTRODUCTION
1.1 GENERAL INTRODUCTION
1.2 LITERATURE REVIEW
1.2.1 What is grain size
1.2.2 Genetic analysis of grain size and weight
1.2.3 What are quantitative trait loci(QTL)
1.2.4 Genetic mapping of quantitative trait loci in rice
1.2.5 Identification of QTL
1.2.6 QTL mapping/linkage analysis
1.2.7 Association mapping/marker-trait association analysis
1.2.8 Genome-wide association mapping
1.2.9 Candidate gene association mapping
1.3 MAJOR GRAIN SIZE REGULATORS AND QTL
1.3.1 GS3 and DEP
1.3.2 MAPK signaling pathway functions in grain size
1.3.3 Ubiquitin-proteasome pathways(UPP)
1.3.4 Phytohormones control grain size
1.3.5 Auxin
1.3.6 Cytokinin
1.3.7 Grain size control by transcriptional regulatory factors
1.4 LIMITATIONS,CHALLENGES AND PROSPECT OF QTL MAPPING OF GRAIN SIZE
CHAPTER 2 Rapid Identification Of Major Quantitative Trait Loci Associated With Grain Size Using Advance Backcross Generation In Rice
2.1 INTRODUCTION
2.2 MATERIALS AND METHODS
2.2.1 Plant materials
2.2.2 Field trial and phenotypic evaluation
2.2.3 Statistical analysis
2.2.4 Marker development and bulk sergeant analysis method
2.2.5 Identification of QTL and linkage map construction
2.2.6 DNA extraction and genotyping
2.3 RESULTS
2.3.1 Phenotypic performance of two parents and introgression line
2.3.2 Genetic map and QTL analysis
2.3.3 QTL environmental interaction analysis and stability of QTL for grain size
2.4 Discussion
CHAPTER 3 Association mapping of quantitative trait loci affecting grain size in advance backcross-generation derived by Oryza rufipogon griff
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 Plant materials construction
3.2.2 Field trial and phenotypic evaluation
3.2.3 Statistical analysis
3.2.4 DNA extraction and SNP genotyping
3.2.5 Genome-wide association mapping and allele mining
3.2.6 DNA sequence analysis
3.2.7 Gene expression analysis
3.3 RESULTS
3.3.1 Phenotypic evaluation of parents and introgression line
3.3.2 Basic statistics of SNP markers
3.3.3 Genome-wide association analysis
3.3.4 Pleiotropy or gene linkage
3.3.5 DNA sequence and haplotype analysis
3.3.6 Gene expression analysis
3.4 DISCUSSION
CHAPTER 4 Rna-Seq/Next-Generation Sequencing Of Young Panicles Of Rice
4.1 INTRODUCTION
4.2 MATERIALS AND METHODS
4.2.1 Plant material
4.2.2 RNA extraction and quality control
4.2.3 Library preparation
4.2.4 Mapping of reads
4.2.5 Gene expression analysis
4.2.6 Gene expression statistics
4.2.7 Repeat sample correlation analysis
4.2.8 Differential gene expression analysis and expression level
4.2.9 Significant differentially expressed gene DEG screening
4.2.10 Differentially expressed gene analysis
4.2.11 Gene ontology(GO)function and enrichment analysis and classification
4.2.12 DEG GO function,classification and GO enrichment
4.2.13 Functional analysis of DEG,KEGG pathway and enrichment analysis
4.2.14 Cluster analysis of differential gene expression
4.2.15 Variable splicing analysis
4.2.16 New transcription predictive analysis,
4.2.17 Point mutation(SNP)analysis
4.3 RESULTS AND DISCUSSION
4.3.1 Sequencing data statistics
4.3.2 Gene expression analysis of DEGs
4.3.3 Significant differentially expressed gene DGE screening
4.3.4 Grouping of DEGs
4.3.5 Gene ontology(GO)annotation and enrichment analysis
4.3.6 Cluster analysis
4.3.7 Variable splicing analysis
4.3.8 Point mutation(SNP)analysis
4.3.9 New transcript prediction analysis
CHAPTER 5 SUMMARY AND RECOMMENDATIONS
5.1 SUMMARY
5.2 MAJOR FINDINGS
5.3 FUTURE DESIGN
REFERENCE
APPENDICES
LIST OF PUBLICATIONS DURING PH.D.STUDY
ACKNOWLEDGEMENT
AUTHOR RESUME
【参考文献】：
期刊论文
[1]水稻粒形性状的遗传及相关基因定位与克隆研究进展[J]. 高志强,占小登,梁永书,程式华,曹立勇. 遗传. 2011(04)
[2]水稻粒长基因GS3在聚合育种中的效应[J]. 杨梯丰,曾瑞珍,朱海涛,陈岚,张泽民,丁效华,李文涛,张桂权. 分子植物育种. 2010(01)
[3]Genetic Analysis and Fine Mapping of Two Genes for Grain Shape and Weight in Rice[J]. Longbiao Guo1,Lilian Ma1,2,Hua Jiang1,Dali Zeng1,Jiang Hu1,Liwen Wu1,2,Zhenyu Gao1,Guangheng Zhang1 and Qian Qian1(1State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China;2Graduate School of the Chinese Academy of Agricultural Sciences,Beijing 100081,China). Journal of Integrative Plant Biology. 2009(01)
[4]栽培稻旱胁迫叶片相关性状的遗传解析(英文)[J]. 郭龙彪,钱前,曾大力,董国军,滕胜,朱立煌. 遗传学报. 2004(03)
[5]水稻粒型和粒重的QTL定位分析[J]. 林荔辉,吴为人. 分子植物育种. 2003(03)
[6]水稻粒形类型及其遗传的研究进展[J]. 杨联松,白一松,许传万,胡兴明,王伍梅,佘德红,陈桂芝. 安徽农业科学. 2001(02)
[7]水稻子粒形态性状遗传研究[J]. 周清元,安华,张毅,沈福成. 西南农业大学学报. 2000(02)
[8]籼稻粒形及产量性状的加性相关和显性相关分析[J]. 石春海,申宗坦. 作物学报. 1996(01)
[9]早籼粒形的遗传和改良[J]. 石春海,申宗坦. 中国水稻科学. 1995(01)
[10]早籼稻谷粒性状遗传效应的分析[J]. 石春海,申宗坦. 浙江农业大学学报. 1994(04)
本文编号：3252658
【文章来源】：中国农业科学院北京市
【文章页数】：132 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
LIST OF ABBREVIATIONS
CHAPTER 1 INTRODUCTION
1.1 GENERAL INTRODUCTION
1.2 LITERATURE REVIEW
1.2.1 What is grain size
1.2.2 Genetic analysis of grain size and weight
1.2.3 What are quantitative trait loci(QTL)
1.2.4 Genetic mapping of quantitative trait loci in rice
1.2.5 Identification of QTL
1.2.6 QTL mapping/linkage analysis
1.2.7 Association mapping/marker-trait association analysis
1.2.8 Genome-wide association mapping
1.2.9 Candidate gene association mapping
1.3 MAJOR GRAIN SIZE REGULATORS AND QTL
1.3.1 GS3 and DEP
1.3.2 MAPK signaling pathway functions in grain size
1.3.3 Ubiquitin-proteasome pathways(UPP)
1.3.4 Phytohormones control grain size
1.3.5 Auxin
1.3.6 Cytokinin
1.3.7 Grain size control by transcriptional regulatory factors
1.4 LIMITATIONS,CHALLENGES AND PROSPECT OF QTL MAPPING OF GRAIN SIZE
CHAPTER 2 Rapid Identification Of Major Quantitative Trait Loci Associated With Grain Size Using Advance Backcross Generation In Rice
2.1 INTRODUCTION
2.2 MATERIALS AND METHODS
2.2.1 Plant materials
2.2.2 Field trial and phenotypic evaluation
2.2.3 Statistical analysis
2.2.4 Marker development and bulk sergeant analysis method
2.2.5 Identification of QTL and linkage map construction
2.2.6 DNA extraction and genotyping
2.3 RESULTS
2.3.1 Phenotypic performance of two parents and introgression line
2.3.2 Genetic map and QTL analysis
2.3.3 QTL environmental interaction analysis and stability of QTL for grain size
2.4 Discussion
CHAPTER 3 Association mapping of quantitative trait loci affecting grain size in advance backcross-generation derived by Oryza rufipogon griff
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 Plant materials construction
3.2.2 Field trial and phenotypic evaluation
3.2.3 Statistical analysis
3.2.4 DNA extraction and SNP genotyping
3.2.5 Genome-wide association mapping and allele mining
3.2.6 DNA sequence analysis
3.2.7 Gene expression analysis
3.3 RESULTS
3.3.1 Phenotypic evaluation of parents and introgression line
3.3.2 Basic statistics of SNP markers
3.3.3 Genome-wide association analysis
3.3.4 Pleiotropy or gene linkage
3.3.5 DNA sequence and haplotype analysis
3.3.6 Gene expression analysis
3.4 DISCUSSION
CHAPTER 4 Rna-Seq/Next-Generation Sequencing Of Young Panicles Of Rice
4.1 INTRODUCTION
4.2 MATERIALS AND METHODS
4.2.1 Plant material
4.2.2 RNA extraction and quality control
4.2.3 Library preparation
4.2.4 Mapping of reads
4.2.5 Gene expression analysis
4.2.6 Gene expression statistics
4.2.7 Repeat sample correlation analysis
4.2.8 Differential gene expression analysis and expression level
4.2.9 Significant differentially expressed gene DEG screening
4.2.10 Differentially expressed gene analysis
4.2.11 Gene ontology(GO)function and enrichment analysis and classification
4.2.12 DEG GO function,classification and GO enrichment
4.2.13 Functional analysis of DEG,KEGG pathway and enrichment analysis
4.2.14 Cluster analysis of differential gene expression
4.2.15 Variable splicing analysis
4.2.16 New transcription predictive analysis,
4.2.17 Point mutation(SNP)analysis
4.3 RESULTS AND DISCUSSION
4.3.1 Sequencing data statistics
4.3.2 Gene expression analysis of DEGs
4.3.3 Significant differentially expressed gene DGE screening
4.3.4 Grouping of DEGs
4.3.5 Gene ontology(GO)annotation and enrichment analysis
4.3.6 Cluster analysis
4.3.7 Variable splicing analysis
4.3.8 Point mutation(SNP)analysis
4.3.9 New transcript prediction analysis
CHAPTER 5 SUMMARY AND RECOMMENDATIONS
5.1 SUMMARY
5.2 MAJOR FINDINGS
5.3 FUTURE DESIGN
REFERENCE
APPENDICES
LIST OF PUBLICATIONS DURING PH.D.STUDY
ACKNOWLEDGEMENT
AUTHOR RESUME
【参考文献】：
期刊论文
[1]水稻粒形性状的遗传及相关基因定位与克隆研究进展[J]. 高志强,占小登,梁永书,程式华,曹立勇. 遗传. 2011(04)
[2]水稻粒长基因GS3在聚合育种中的效应[J]. 杨梯丰,曾瑞珍,朱海涛,陈岚,张泽民,丁效华,李文涛,张桂权. 分子植物育种. 2010(01)
[3]Genetic Analysis and Fine Mapping of Two Genes for Grain Shape and Weight in Rice[J]. Longbiao Guo1,Lilian Ma1,2,Hua Jiang1,Dali Zeng1,Jiang Hu1,Liwen Wu1,2,Zhenyu Gao1,Guangheng Zhang1 and Qian Qian1(1State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China;2Graduate School of the Chinese Academy of Agricultural Sciences,Beijing 100081,China). Journal of Integrative Plant Biology. 2009(01)
[4]栽培稻旱胁迫叶片相关性状的遗传解析(英文)[J]. 郭龙彪,钱前,曾大力,董国军,滕胜,朱立煌. 遗传学报. 2004(03)
[5]水稻粒型和粒重的QTL定位分析[J]. 林荔辉,吴为人. 分子植物育种. 2003(03)
[6]水稻粒形类型及其遗传的研究进展[J]. 杨联松,白一松,许传万,胡兴明,王伍梅,佘德红,陈桂芝. 安徽农业科学. 2001(02)
[7]水稻子粒形态性状遗传研究[J]. 周清元,安华,张毅,沈福成. 西南农业大学学报. 2000(02)
[8]籼稻粒形及产量性状的加性相关和显性相关分析[J]. 石春海,申宗坦. 作物学报. 1996(01)
[9]早籼粒形的遗传和改良[J]. 石春海,申宗坦. 中国水稻科学. 1995(01)
[10]早籼稻谷粒性状遗传效应的分析[J]. 石春海,申宗坦. 浙江农业大学学报. 1994(04)
本文编号：3252658
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