Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics.
Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics.
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DOI：
10.1186/s12864-016-2775-2
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发表时间：
2016-07-16
期刊：
影响因子：
4.4
通讯作者：
Bancroft I
中科院分区：
文献类型：
--
作者：
Miller CN;Harper AL;Trick M;Werner P;Waldron K;Bancroft I
目前减少高肥条件下生长的小麦因籽粒重量而塌陷（倒伏）的趋势的方法是通过引入 Rht 基因来降低茎高。然而，这些都降低了秸秆（本身就是一种重要商品）的产量，并引入了其他不良特性。因此，识别替代高度控制基因座至关重要。此外，茎机械强度的提高提供了减少倒伏的进一步途径。为了研究 Rht 遗传替代品的前景，我们在由 100 个针对 Rht 固定的小麦材料组成的训练遗传多样性小组中评估了株高和茎强度特性的变化。使用从叶子中纯化的 RNA 衍生的 mRNAseq 数据，为包含 42,066 个单核苷酸多态性 (SNP) 标记和 94,060 个基因表达标记 (GEM) 的组开发了功能基因型。在最近开发的关联转录组学方法在小麦中的首次应用中，我们确定了性状变异与 SNP 和 GEM 之间的关联。标记-性状关联分析揭示了性状变异背后致病基因的候选基因，表明木聚糖乙酰化和 COP9 信号体有助于茎强度和生长素控制观察到的株高变异。使用 30 个其他小麦品种的测试遗传多样性组验证了茎强度关键标记的预测能力。这项工作说明了关联转录组学在探索小麦中具有高度农艺重要性的复杂性状方面的力量。分析中包含的基因型的仔细选择允许对这种主要作物中新的性状控制基因座进行高分辨率定位。基因表达标记与更传统的基于序列的标记的结合使用，提供了理解所观察到的标记-性状关联的生物学背景所需的能力。这不仅增加了我们努力积累的有关基因功能和植物适应的知识财富，而且还为育种者提供了所需的信息，以便就将特定标记的使用纳入未来育种计划的潜在后果做出更明智的决策。本文的在线版本 (doi:10.1186/s12864-016-2775-2) 包含补充材料，可供授权用户使用。
The current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse (lodge) under the weight of its grain is based on reducing stem height via the introduction of Rht genes. However, these reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Identification of alternative height-control loci is therefore of key interest. In addition, the improvement of stem mechanical strength provides a further way through which lodging can be reduced. To investigate the prospects for genetic alternatives to Rht, we assessed variation for plant height and stem strength properties in a training genetic diversity panel of 100 wheat accessions fixed for Rht. Using mRNAseq data derived from RNA purified from leaves, functional genotypes were developed for the panel comprising 42,066 Single Nucleotide Polymorphism (SNP) markers and 94,060 Gene Expression Markers (GEMs). In the first application in wheat of the recently-developed method of Associative Transcriptomics, we identified associations between trait variation and both SNPs and GEMs. Analysis of marker-trait associations revealed candidates for the causative genes underlying the trait variation, implicating xylan acetylation and the COP9 signalosome as contributing to stem strength and auxin in the control of the observed variation for plant height. Predictive capabilities of key markers for stem strength were validated using a test genetic diversity panel of 30 further wheat accessions. This work illustrates the power of Associative Transcriptomics for the exploration of complex traits of high agronomic importance in wheat. The careful selection of genotypes included in the analysis, allowed for high resolution mapping of novel trait-controlling loci in this staple crop. The use of Gene Expression markers coupled with the more traditional sequence-based markers, provides the power required to understand the biological context of the marker-trait associations observed. This not only adds to the wealth of knowledge that we strive to accumulate regarding gene function and plant adaptation, but also provides breeders with the information required to make more informed decisions regarding the potential consequences of incorporating the use of particular markers into future breeding programmes. The online version of this article (doi:10.1186/s12864-016-2775-2) contains supplementary material, which is available to authorized users.