Busconi Matteo, Wischnitzki Elisabeth, Del Corvo Marcello, Colli Licia, Soffritti Giovanna, Stagnati Lorenzo, Fluch Silvia, Sehr Eva Maria, de Los Mozos Pascual Marcelino, Fernández José Antonio
Faculty of Agriculture, Food and Environmental Sciences, Research Centre BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy.
Centre for Health and Bioresources, AIT Austrian Institute of Technology, Tulln, Austria.
Front Plant Sci. 2021 Mar 4;12:642631. doi: 10.3389/fpls.2021.642631. eCollection 2021.
This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analyzed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions' alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualize sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
这项工作是对藏红花进行的首次表观基因组研究。通过应用甲基化敏感限制酶测序（MRE-seq）方法，在表观遗传水平上分析了五个藏红花种质，这些种质在花被片色素沉着、藏红花产量和开花时间上存在差异。通过合并单个种质的序列数据，获得了五个种质特异性低甲基化组以及一个参考低甲基化组。将组装后的序列与现有的在线数据库进行注释比对。由于缺乏藏红花基因组，主要以水稻基因组作为参考，因为它是单子叶植物中注释最好的基因组。对低甲基化组的比较揭示了许多差异甲基化区域，证实了藏红花种质间存在高度的表观遗传变异性，包括一些编码蛋白质的序列，这些蛋白质可能是解释种质间不同表型的良好候选者。特别地，检测到了参与开花过程的转录因子（MADS-box和TFL）以及参与色素生成的转录因子（MYB）。最后，通过比较不同种质产生的序列，检测到大量可能由于长期无性繁殖而产生的单核苷酸多态性（SNP），这表明存在惊人的高遗传变异性。进行了基因本体论（GO）分析，以定位和可视化位于GO内的序列多态性，并比较它们在不同种质间的分布。这不仅表明可能存在具有遗传基础的不同表型，而且基于地理来源的种质间在多态性GO方面存在明显差异，这支持了印度种质相对于西班牙种质可能存在选择特征的观点。
