ovation-Transcriptomic study of rice seed ageing

affy_rice_2012_01 - ovation - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate. 6 arrays - rice; treated vs untreated comparison

affy_rice_2012_01 - ovation - 未来农业的核心议题之一，便是如何保存具有农业应用价值的生物多样性。为此，筛选出可高效萌发（优良种子活力）且能长期维持活力（优良种子寿命）的优质作物品种至关重要。令人意外的是，尽管人类对谷类作物依赖度极高，目前却极少有研究鉴定出与谷类种子活力和寿命呈正相关的基因。为填补这一科学空白，本研究旨在鉴定与水稻种子活力和寿命正相关的基因。

我们采用受控劣变处理（controlled deterioration treatment, CDT；Tesnier等，2002）来模拟自然种子老化过程。具体流程为：首先将种子置于25℃、相对湿度85%的环境中平衡3天；随后将种子分为3组，在15天内分别接受以下处理：(i) 维持25℃、85%相对湿度（对照组种子）；(ii) 置于40℃、85%相对湿度环境（种子活力丧失组）；(iii) 置于45℃、85%相对湿度环境（萌发能力丧失组）。最后将所有种子置于25℃、32%相对湿度环境中平衡3天。通过该CDT处理，我们获得了种子活力或萌发能力存在显著差异的水稻种子样本。

我们从种子胚中提取总RNA，并利用Affymetrix水稻基因组芯片（Affymetrix Rice Genome Array）分析其转录组。

我们对参考水稻品种日本晴（Nipponbare）的种子施加了受控劣变处理。具体步骤为：先将所有种子在25℃、85%相对湿度下平衡，随后根据分组将种子置于25℃、40℃或45℃且85%相对湿度的环境中，最后再将其置于25℃、32%相对湿度下平衡。我们每隔8小时对3组种子的萌发情况进行一次检测，连续监测5天。

实验结果显示：全程置于25℃环境的种子组与冷藏保存的对照组种子表现一致，在48小时内萌发率接近100%；置于40℃环境15天的种子组萌发率为74%，但幼苗表型出现异常（种子活力丧失）；而置于45℃环境的种子组完全无法萌发。本数据集共包含6张水稻样本芯片，用于处理组与未处理组的表达差异比较。