High resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana

A primary component of seedling establishment is the photomorphogenic
response as seedlings emerge from the soil. This process is characterized
by a reduced growth rate in the hypocotyl, increased root growth, opening
of the apical hook, and expansion of the cotyledons as photosynthetic
organs. While fundamental to plant success, the photomorphogenic response
can be highly variable. Additionally, studies of Arabidopsis thaliana are
made difficult by subtle differences in growth rate between individuals.
High-resolution imaging and computational processing have emerged as
useful tools for quantification of such phenotypes. This study sought to:
1) develop an imaging methodology which could capture changes in growth
rate as seedlings transition from darkness to blue light in real time, and
2) apply this methodology to single-QTL analysis using the Cvi x Ler RIL
mapping population. Significant differences in the photomorphogenic
response were observed between the parent lines and analysis of 158 RILs
revealed a wide range of growth rate phenotypes. QTL analysis detected
significant loci associated with dark growth rate on chromosome 5 and
significant loci associated with light growth rate on chromosome 2.
Candidate genes associated with these loci, such as the previously
characterized ER locus, highlight the application of this approach for QTL
analysis. Genetic analysis of Landsberg lines without the erecta mutation
also supports a role for ER in modulating the photomorphogenic response,
consistent with previous QTL analyses of this population. Strengths and
limitations of this methodology are presented, as well as means of
improvement.

幼苗建成的核心环节之一是幼苗破土而出时的光形态建成响应（photomorphogenic response）。该过程以下胚轴（hypocotyl）生长速率降低、根系生长加快、顶钩（apical hook）展开以及作为光合器官的子叶（cotyledons）扩张为典型特征。尽管光形态建成响应对植物生存至关重要，但其表现存在显著的个体差异。此外，拟南芥（Arabidopsis thaliana）个体间生长速率的细微差异，也为相关研究带来了不小的挑战。高分辨率成像与计算处理技术已成为量化此类表型的有效工具。本研究旨在达成两个目标：其一，开发一种可实时捕捉幼苗从黑暗过渡到蓝光时生长速率变化的成像方法；其二，将该方法应用于以Cvi × Ler重组自交系（Recombinant Inbred Line, RIL）作图群体为材料的单数量性状位点（Quantitative Trait Locus, QTL）分析。研究观察到亲本株系间的光形态建成响应存在显著差异，对158个RIL的分析则显示其生长速率表型分布范围广泛。QTL分析检测到与5号染色体上黑暗条件下生长速率相关的显著位点，以及2号染色体上光照条件下生长速率相关的显著位点。与这些位点相关的候选基因（如已被深入表征的ER位点（ER locus）），印证了该方法在QTL分析中的应用价值。对不含erecta突变（erecta mutation）的Landsberg株系的遗传分析同样支持ER在调控光形态建成响应中的作用，这与该群体此前的QTL分析结果一致。本研究同时阐述了该方法的优势与局限，并探讨了其改进路径。