Genetic Dissection of Boll Size Regulation and Genome Wide M
发布时间：2024-03-19 01:12
随着世界人口的增长,人们对棉花的需求也越来越大,导致棉花育种工作的主要目标是保障棉花纤维产量的稳定。由于单铃籽棉重是由多重产量性状决定,因此提高棉花的产量是一个巨大的挑战。产量和纤维品质共同调控棉铃发育。解析调控棉铃大小农艺性状的遗传和生物学机制,对棉花研究者来说仍是一个巨大的挑战。为了解析其遗传机制,一个通过种间杂交获得的小棉铃突变体BS41,在调控单铃籽棉重,皮棉重,百粒重等性状表现出杂种衰败。通过多重标记的检测,在12染色体上鉴定到了一个稳定的调控位点,qSCW-c12。在后代BC2F4群体中,这个位点qSCW-c12在AD-A1207和AD-FM44标记之间,大小为0.89 cM。一个主效的杂交衰败多效性位点(qSCW-c12),其在多个连续的群体中被证实调控棉铃的大小和产量性状。通过连续的精细定位,在12号染色体上将其缩小到0.89 cM遗传区间,与之相对应是包含11个基因的180 Kb的物理区段。同源比对也测到了一个40个碱基插入缺失位点在AD-FM44克隆序列,在与SCW紧密连锁的GhBRH1A<...
【文章页数】：150 页
【学位级别】：博士
【文章目录】：
Abstract
摘要
List of abbreviations
Chapter 01 Introduction
1.1 Cotton taxonomy and economic importance
1.2 Era of cotton genomics
1.3 Genetic linkage mapping
1.4 Bulk segregation analysis(BSA)
1.5 Mapping populations
1.6 Molecular markers and QTL mapping
1.7 Mapping QTLs for complex yield traits
1.8 Fine mapping strategies
1.9 Fine mapping complex trait in crops
1.10 Fine mapping and map-based cloning in cotton
1.11 Boll development phases in cotton
1.12 Microsatellites motif imperfection
1.13 Mechanism of motif imperfection in SSRs
1.14 Intrinsic DNA features relate imperfection in microsatellites
1.15 Motif imperfection and evolution of polyploidy in crops
1.16 Study objectives and significance
Chapter 02 Map-based cloning qSCW-cl2
2.1 Introduction
2.2 Materials and methods
2.2.1 Plant materials and mapping populations
2.2.2 Phenotype evaluation and analysis
2.2.3 Designing markers from genomic sequences
2.2.4 PCR, PAGE and SSR genotyping
2.2.5 Genetic map construction and QTL mapping
2.2.6 Regional association mapping
2.2.7 Scanning electron microscopy (SEM)
2.2.8 Ovule culture assay
2.2.9 Measurement of total fiber units (TFU)
2.2.10 Gene annotations prediction
2.2.11 Digital expression analysis in Li1 transcriptome
2.2.12 RNA extraction and real-time PCR
2.2.13 Cloning for structural variations in GhBRH1A12
2.2.14 Shoot elongation and BL sensitivity assay
2.2.15 Histological analysis
2.3 Results
2.3.1 Boll size variations between Emian22 and BS41
2.3.2 Phenotypic analysis of boll weight traits
2.3.3 Detecting yield trait QTLs on chr12
2.3.4 qSCW-c12 identification, validation in different populations
2.3.7 Fine mapping qSCW-c12
2.3.8 Refine mapping qSCW-c12
2.3.9 Homology mapping and candidate gene prediction
2.3.10 Map-based cloning qSCW-c12
2.3.11 Candidate gene prediction based on their expression
2.3.12 GhBRH1A12 was differentially expressed in ODPA ovules
2.3.13 GhBRH1A12 involved in modulating BR homeostasis
2.3.14 BS41 exhibited BR-deficient mutant like phenotype
2.3.15 BS41, a novel BR-insensitive mutant
2.3.16 BR insensitivity attenuated cell expansion in BS41
2.3.17 BS41 features quality fiber production
2.4 Discussion
2.4.1 BILs are valuable resource for fine mapping QTLs
2.4.2 Boll size regulating QTLs on chr12
2.4.3 qSCW-c12 interval consistent with previously mapped QTLs
2.4.4 GhBRHA12, a new player in regulating Fiber initiation
2.4.5 QTL qSCW-c12 is a pleiotropic locus
2.4.6 GhBRH1A12 involved in modulating BR homeostasis
2.4.7 BS41, a novel boll size mutant producing quality fiber
2.5 Conclusion
Chapter 03 Functional analysis of BRH1 gene family in cotton
3.1 Introduction
3.2 Material and methods
3.2.1 Sequence retrieval, gene structure, and phylogenetic analysis
3.2.2 Protein domain, motif, annotation, and GO analysis
3.2.3 Prediction of transmembrane topology
3.2.4 Expression profiling
3.2.5 Digital expression analysis in Li1 transcriptome
3.2.6 Cloning for structural variations in GhBRH1A12
3.2.7 Constructing overexpression vectors
3.2.8 RNAi vector construction
3.2.9 Genetic transformation and cotton tissue culture
3.2.10 RNA extraction and qRT-PCR
3.2.11 Phenotype evaluation and analysis
3.3 Results
3.3.1 Structure of BRH1 peptide
3.3.2 Identification of putative BRH1 genes in four cotton genomes
3.3.3 Phylogenetic analysis of cotton BRH1 genes
3.3.4 Genetic diversity and evolution of GhBRH1 gene family
3.3.5 Characteristics of GhBRH1 gene family
3.3.6 Expression profiling of GhBRH1 genes in cultivated cotton
3.3.7 GhBRH1 differentially expressed during fiber development
3.3.8 Gene regulatory elements of GhBRH1A12 in BS41
3.3.9 Genetic transformation of a GhBRH1A12 in cotton
3.3.10 GhBRH1A12 expression in transgenic (T0) plants
3.4 Discussion
Chapter 04 Evolutionary dynamics of motif imperfection in cotton
4.1 Introduction
4.2 Material and methods
4.2.1 Genome assemblies of 13 plant species
4.2.2 Imperfect microsatellites identification
4.2.3 Motif Imperfection and repeat length analyses
4.2.4 Transposable elements (TEs)distribution
4.2.5 Motif imperfection in coding region of Gossypium species
4.2.6 Microsatellites conservation analysis
4.2.7 Microsatellite loss during paleopolyploidization event
4.3 Results
4.3.1 Frequency and distribution of microsatellites
4.3.2 Motif imperfection and repeat length relationship
4.3.3 Motif imperfection in Gossypium genomes
4.3.4 Motif interruptions in coding sequence
4.3.5 Large motif repeats well conserved in Gossypium species
4.3.6 Microsatellite decay estimation
4.3.7 Biased distribution of 2nt repeats in Gossypium species
4.4 Discussion
4.5 Conclusion
References
Supplementary information
Publications
Acknowledgement
附件
本文编号：3932095
【文章页数】：150 页
【学位级别】：博士
【文章目录】：
Abstract
摘要
List of abbreviations
Chapter 01 Introduction
1.1 Cotton taxonomy and economic importance
1.2 Era of cotton genomics
1.3 Genetic linkage mapping
1.4 Bulk segregation analysis(BSA)
1.5 Mapping populations
1.6 Molecular markers and QTL mapping
1.7 Mapping QTLs for complex yield traits
1.8 Fine mapping strategies
1.9 Fine mapping complex trait in crops
1.10 Fine mapping and map-based cloning in cotton
1.11 Boll development phases in cotton
1.12 Microsatellites motif imperfection
1.13 Mechanism of motif imperfection in SSRs
1.14 Intrinsic DNA features relate imperfection in microsatellites
1.15 Motif imperfection and evolution of polyploidy in crops
1.16 Study objectives and significance
Chapter 02 Map-based cloning qSCW-cl2
2.1 Introduction
2.2 Materials and methods
2.2.1 Plant materials and mapping populations
2.2.2 Phenotype evaluation and analysis
2.2.3 Designing markers from genomic sequences
2.2.4 PCR, PAGE and SSR genotyping
2.2.5 Genetic map construction and QTL mapping
2.2.6 Regional association mapping
2.2.7 Scanning electron microscopy (SEM)
2.2.8 Ovule culture assay
2.2.9 Measurement of total fiber units (TFU)
2.2.10 Gene annotations prediction
2.2.11 Digital expression analysis in Li1 transcriptome
2.2.12 RNA extraction and real-time PCR
2.2.13 Cloning for structural variations in GhBRH1A12
2.2.14 Shoot elongation and BL sensitivity assay
2.2.15 Histological analysis
2.3 Results
2.3.1 Boll size variations between Emian22 and BS41
2.3.2 Phenotypic analysis of boll weight traits
2.3.3 Detecting yield trait QTLs on chr12
2.3.4 qSCW-c12 identification, validation in different populations
2.3.7 Fine mapping qSCW-c12
2.3.8 Refine mapping qSCW-c12
2.3.9 Homology mapping and candidate gene prediction
2.3.10 Map-based cloning qSCW-c12
2.3.11 Candidate gene prediction based on their expression
2.3.12 GhBRH1A12 was differentially expressed in ODPA ovules
2.3.13 GhBRH1A12 involved in modulating BR homeostasis
2.3.14 BS41 exhibited BR-deficient mutant like phenotype
2.3.15 BS41, a novel BR-insensitive mutant
2.3.16 BR insensitivity attenuated cell expansion in BS41
2.3.17 BS41 features quality fiber production
2.4 Discussion
2.4.1 BILs are valuable resource for fine mapping QTLs
2.4.2 Boll size regulating QTLs on chr12
2.4.3 qSCW-c12 interval consistent with previously mapped QTLs
2.4.4 GhBRHA12, a new player in regulating Fiber initiation
2.4.5 QTL qSCW-c12 is a pleiotropic locus
2.4.6 GhBRH1A12 involved in modulating BR homeostasis
2.4.7 BS41, a novel boll size mutant producing quality fiber
2.5 Conclusion
Chapter 03 Functional analysis of BRH1 gene family in cotton
3.1 Introduction
3.2 Material and methods
3.2.1 Sequence retrieval, gene structure, and phylogenetic analysis
3.2.2 Protein domain, motif, annotation, and GO analysis
3.2.3 Prediction of transmembrane topology
3.2.4 Expression profiling
3.2.5 Digital expression analysis in Li1 transcriptome
3.2.6 Cloning for structural variations in GhBRH1A12
3.2.7 Constructing overexpression vectors
3.2.8 RNAi vector construction
3.2.9 Genetic transformation and cotton tissue culture
3.2.10 RNA extraction and qRT-PCR
3.2.11 Phenotype evaluation and analysis
3.3 Results
3.3.1 Structure of BRH1 peptide
3.3.2 Identification of putative BRH1 genes in four cotton genomes
3.3.3 Phylogenetic analysis of cotton BRH1 genes
3.3.4 Genetic diversity and evolution of GhBRH1 gene family
3.3.5 Characteristics of GhBRH1 gene family
3.3.6 Expression profiling of GhBRH1 genes in cultivated cotton
3.3.7 GhBRH1 differentially expressed during fiber development
3.3.8 Gene regulatory elements of GhBRH1A12 in BS41
3.3.9 Genetic transformation of a GhBRH1A12 in cotton
3.3.10 GhBRH1A12 expression in transgenic (T0) plants
3.4 Discussion
Chapter 04 Evolutionary dynamics of motif imperfection in cotton
4.1 Introduction
4.2 Material and methods
4.2.1 Genome assemblies of 13 plant species
4.2.2 Imperfect microsatellites identification
4.2.3 Motif Imperfection and repeat length analyses
4.2.4 Transposable elements (TEs)distribution
4.2.5 Motif imperfection in coding region of Gossypium species
4.2.6 Microsatellites conservation analysis
4.2.7 Microsatellite loss during paleopolyploidization event
4.3 Results
4.3.1 Frequency and distribution of microsatellites
4.3.2 Motif imperfection and repeat length relationship
4.3.3 Motif imperfection in Gossypium genomes
4.3.4 Motif interruptions in coding sequence
4.3.5 Large motif repeats well conserved in Gossypium species
4.3.6 Microsatellite decay estimation
4.3.7 Biased distribution of 2nt repeats in Gossypium species
4.4 Discussion
4.5 Conclusion
References
Supplementary information
Publications
Acknowledgement
附件
本文编号：3932095
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