Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana

First author: Alejandra Martínez-Berdeja; Affiliations:  University of California, Davis (加州大学戴维斯分校): CA, USA

Corresponding author: Johanna Schmitt

The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.

种子发芽的季节性时机决定了植物的环境生态位，同时对于植物的气候适应能力也非常重要。种子发芽的季节时间依赖于种子休眠解除的模式或是低温诱导，与开花时间变异相互作用，共同构建了不同季节的生活史。为了解析种子低温响应以及相关的生活史特征自然变异的潜在遗传基础以及气候相关性，作者选择了来自全球各个地区的559个已测序的一年生模式植物拟南芥材料，记录了13种冷分层处理下各个材料的种子发芽、开花时间和衰老时间。这些材料的发芽策略主要沿着两个主轴呈连续性变化，一是总的发芽率，另一个是由低温引起的休眠诱导与解除。种子对于低温响应的自然变异与开花时间和衰老相关，从而形成了一个季节性生活史特征范围。全基因关联分析鉴定了一些与种子低温响应自然变异相关的位点，包括一个已知的在候选基因DOG1的自结合结构域上的功能性多态位点。DOG1单倍型的系统发育树显示这些功能性变异的古老分化与更新世的气候变化有关，另外梯度森林分析显示候选SNP的等位基因更替显著与气候梯度相关。本文的研究表明拟南芥的发芽生态位以及相关的生活史特征是由以往的气候周期与当代的区域气候适应共同塑造的。

通讯：Johanna Schmitt  (https://biology.ucdavis.edu/people/johanna-schmitt)

个人简介：1974年，斯沃斯摩尔学院，学士；1981年，斯坦福大学，博士。

研究方向：植物生态基因组学和演化生态学；表型可塑性、地域适应和对环境变化的响应机制。

doi: https://doi.org/10.1073/pnas.1912451117

Journal: PNAS

First Published: January 21, 2020