Data_Sheet_2_Functional analysis of PHYB polymorphisms in Arabidopsis thaliana collected in Patagonia.zip

Arabidopsis thaliana shows a wide range of natural genetic variation in light responses. Shade avoidance syndrome is a strategy of major adaptive significance that includes seed germination, elongation of vegetative structures, leaf hyponasty, and acceleration of flowering. Previously, we found that the southernmost Arabidopsis accession, collected in the south of Patagonia (Pat), is hyposensitive to light and displays a reduced response to shade light. This work aimed to explore the genetic basis of the shade avoidance response (SAR) for hypocotyl growth by QTL mapping in a recently developed 162 RIL population between Col-0 and Pat. We mapped four QTL for seedling hypocotyl growth: WL1 and WL2 QTL in white light, SHADE1 QTL in shade light, and SAR1 QTL for the SAR. PHYB is the strongest candidate gene for SAR1 QTL. Here we studied the function of two polymorphic indels in the promoter region, a GGGR deletion, and three non-synonymous polymorphisms on the PHYB coding region compared with the Col-0 reference genome. To decipher the contribution and relevance of each PHYB-Pat polymorphism, we constructed transgenic lines with single or double polymorphisms by using Col-0 as a reference genome. We found that single polymorphisms in the coding region of PHYB have discrete functions in seed germination, seedling development, and shade avoidance response. These results suggest distinct functions for each PHYB polymorphism to the adjustment of plant development to variable light conditions.拟南芥（Arabidopsis thaliana）在光响应过程中存在广泛的自然遗传变异。避荫综合征（shade avoidance syndrome）是一类具有重要自适应意义的策略，涵盖种子萌发、营养结构伸长、叶片偏上性（leaf hyponasty）以及开花加速等生理过程。此前本团队发现，采集自巴塔哥尼亚南部的最南端拟南芥种质系（Pat）对光不敏感，且遮荫光响应显著减弱。本研究旨在通过Col-0与Pat杂交构建的162个重组自交系（Recombinant Inbred Line, RIL）群体的数量性状位点（Quantitative Trait Locus, QTL）定位，解析调控下胚轴生长的避荫响应（shade avoidance response, SAR）的遗传基础。我们共定位到4个与幼苗下胚轴生长相关的QTL：白光条件下的WL1和WL2数量性状位点、遮荫光条件下的SHADE1数量性状位点，以及介导避荫响应的SAR1数量性状位点。光敏素B（Phytochrome B, PHYB）是SAR1 QTL的最强候选功能基因。相较于Col-0参考基因组，Pat来源的PHYB基因存在以下三类多态性：启动子区域的2个插入缺失多态性（insertion-deletion, indel）、一处GGGR序列缺失，以及编码区的3处非同义多态性。为解析每一处Pat来源的PHYB多态性的调控贡献与生物学意义，我们以Col-0为遗传背景，构建了携带单处或双处多态性的转基因株系。研究发现，PHYB编码区的单处多态性在种子萌发、幼苗发育以及避荫响应中均发挥独立的调控功能。上述结果表明，不同PHYB多态性可通过各自独特的功能，协助植物发育适应多变的光环境。