Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response
Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response
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DOI：
10.1101/2020.11.27.400986
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发表时间：
2020-11
期刊：
影响因子：
4.4
通讯作者：
S. Woodhouse;Zhesi He;Hugh C. Woolfenden;B. Steuernagel;W. Haerty;I. Bancroft;J. Irwin;R. Morris;R. Wells
中科院分区：
文献类型：
--
作者：
S. Woodhouse;Zhesi He;Hugh C. Woolfenden;B. Steuernagel;W. Haerty;I. Bancroft;J. Irwin;R. Morris;R. Wells
结合转录组学在甘蓝型油菜中得到了广泛的应用，可以快速识别与感兴趣性状相关的标记。然而，在重要的蔬菜作物物种甘蓝中，由于缺乏固定的遗传资源和由于自交不亲和而产生材料的困难，结合转录组学的使用受到限制。在芸苔属蔬菜中，可收获的产品可以是营养组织或花组织，因此花过渡的同步是种植者和育种者的重要目标。众所周知，春化是花过渡的关键决定因素，但不同的春化处理如何影响甘蓝开花尚不清楚。结果在不同的环境条件下，对69份甘蓝品种的抽穗和开花性状进行了表型分析。我们开发了一种新的关联转录组学管道，并推断和验证了表型接入的群体结构。一项全基因组关联研究确定miR172D是春化反应的候选基因。基因表达标记关联鉴定了BoFLC的表达变异。C2作为春化反应的进一步候选。结论本研究为甘蓝相关转录组学研究开辟了一条新的途径。以开花时间为例，通过结合转录组学研究了甘蓝春化反应的遗传基础，并证实了其作为一个复杂的gxe性状的特征。候选导联在miR172D和BoFLC中被确定。C2。这些结果可以促进基于标记的育种工作，以生产抽穗期更同步的甘蓝系，从而有可能提高产量。
Background Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea , the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood. Results Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC. C2 as a further candidate for vernalisation response. Conclusions This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea . Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2 . These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.