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Associative expression and systems analysis of complex traits in oilseed rape / canola - ASSYST (PRR-CROPP)

油菜/油菜复杂性状的关联表达和系统分析 - ASSYST (PRR-CROPP)

基本信息

批准号：
BB/G024952/1
负责人：
Judith Irwin
金额：
$ 45.64万
依托单位：
John Innes Centre
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2009
资助国家：
英国
起止时间：
2009 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FG024952%2F1
关键词：
Associative expression systems analysis complex

项目摘要

A pilot experiment will evaluate the capabilities of the PBI/NRC 454-NGS platform for SNP discovery. The resulting markers, along with the public genome-wide SNPs from UGI and the public EST-SNPs from the AAFC/DLM project, will become available for the development of a public high throughput SNP genotyping platform during 2008/09. The platform we develop will subsequently be used to screen two DH mapping populations and 450 members of a genotype diversity panel, providing the data for two new high-density SNP maps and for whole-genome association analysis. Global transcriptome data will be obtained from germinated seedlings of 93 DH lines from the mapping population 'Express' x 'V8' plus the two parental genotypes and the F1. Whole-seedling transcript libraries will be sequenced using the next-generation Illumina (Solexa) Genome Analyzer. The quantitative global transcript data will be used to identify polymorphic gene expression markers (GEMs) in the mapping population, and for eQTL analysis. Developing seed will be collected from a population of 250 DH spring type B. napus lines 18 days after flowering and immediately frozen. In addition, mature seed will be collected for analysing seed quality traits. The seedlings and developing seeds will be utilised for hormone profiling and global transcriptome analysis. Alignment of metabolite QTL (mQTL), eQTL and QTLs controlling seed quality traits will identify target regions of the B. napus genome for further characterisation. Quantitative plant hormone metabolite data from all plant populations being analysed in the project will be used for comparison of mQTL with developing seed and seedling trait QTL. Detailed, quantitative hormone profiles from the developing seed and seedling tissue samples will be obtained for 36 compounds. We will adapt and apply computational biology techniques to identify relationships between the transcriptome and a range of developmental, metabolic and performance traits. This will exploit transcriptome datasets developed both prior to this project and during this project, and trait datasets which could include: Seedling biomass traits, quantitative developing seed and seedling hormone measurements, oil content and fatty acid composition, protein and fibre content, seed glucosinolate content, seed weight and seed yield along with mid-parent heterosis for all of the abovementioned traits. We will use appropriate computational platforms for the more detailed analysis of a small number of specific pathways. A B. napus association mapping population of 450 genetically diverse genotypes will be compiled by combining genetic diversity sets from previous studies. These include inbred lines from a core set of 150 rapeseed (B. napus ssp. napus) and 100 swede (B. napus ssp. pabularia) genebank accessions generated in a previous project (RESGEN) by UGI and other European partners, 54 older winter rapeseed varieties and breeding lines from a previous project in Germany (GABI-BRIDGE), 90 genetically diverse modern winter oilseed rape varieties and 180 fixed diversity founder lines. For analysis of the population structure a set of 100 genome-wide SSR markers distributed evenly over all chromosomes will be used. Seedling development of the entire association mapping population will be examined in a greenhouse experiment. The data generated in the greenhouse and field trials will be used for in depth analyses of the correlations between seedling vigour parameters, agronomic traits and seed quality characters, and for detection of marker-phenotype associations with all analysed traits. The B. napus SNP array will be used for high-throughput screening of the association mapping population. This data will be used to identify genome regions contributing to variation in the regulation of genes involved in seedling development.

试点实验将评估PBI/NRC 454-NGS平台用于SNP发现的能力。由此产生的标记，沿着公共全基因组SNP从UGI和公共EST-SNP从AAFC/DLM项目，将成为一个公共的高通量SNP基因分型平台的开发在2008/09年。我们开发的平台随后将用于筛选两个DH作图群体和450个基因型多样性小组成员，为两个新的高密度SNP图谱和全基因组关联分析提供数据。将从来自作图群体“Express”X“V8”加上两个亲本基因型和F1的93个DH系的发芽幼苗获得全局转录组数据。将使用下一代Illumina（Solexa）基因组分析仪对全苗转录文库进行测序。定量的全局转录本数据将用于鉴定作图群体中的多态性基因表达标记（GEM），并用于eQTL分析。将从250 DH春季B型群体中收集发育中的种子。油菜品系开花后18天，立即冷冻。此外，将收集成熟种子用于分析种子质量性状。幼苗和发育中的种子将用于激素谱分析和全局转录组分析。代谢物QTL（mQTL）、eQTL和控制种子品质性状的QTL的比对将确定B的目标区域。napus基因组进行进一步表征。来自该项目中分析的所有植物群体的定量植物激素代谢物数据将用于比较mQTL与发育中的种子和幼苗性状QTL。将获得36种化合物的发育种子和幼苗组织样品的详细定量激素谱。我们将适应和应用计算生物学技术来确定转录组和一系列发育，代谢和性能性状之间的关系。这将利用在本项目之前和本项目期间开发的转录组数据集，以及性状数据集，其可以包括：幼苗生物量性状、定量发育种子和幼苗激素测量、油含量和脂肪酸组成、蛋白质和纤维含量、种子硫代葡萄糖苷含量、种子重量和种子产量沿着以及所有上述性状的中亲杂种优势。我们将使用适当的计算平台对少数特定途径进行更详细的分析。A B。将通过结合先前研究的遗传多样性集合来编制450个遗传多样性基因型的油菜关联作图群体。这些包括来自150个油菜籽核心组的近交系（B.油菜napus）和100瑞典（B.油菜在UGI和其他欧洲合作伙伴的先前项目（RESGEN）中产生的54个老的冬油菜品种和育种系、来自德国的先前项目（GABI-BRIDGE）的90个遗传多样性现代冬油菜品种和180个固定多样性创始系。为了分析群体结构，将使用均匀分布在所有染色体上的一组100个全基因组SSR标记。整个关联作图群体的幼苗发育将在温室实验中进行检查。温室和田间试验中产生的数据将用于深入分析幼苗活力参数、农艺性状和种子质量性状之间的相关性，并用于检测标记-表型与所有分析性状的关联。B。将利用油菜SNP阵列进行关联作图群体的高通量筛选。这些数据将被用来确定基因组区域的变化，参与幼苗发育的基因调控。