水稻孕穗期响应低温的MITEs类转座子大规模鉴定及其调控机制研究

Cold stress is one of the most important environmental conditions that adversely affect plant growth and development. Low temperature in booting stage causes pollen sterility, resulting in remarkable seed yield reduction. Rice has evolved in tropical and subtropical areas and is sensitive to cold stress. Therefore understanding cold responsive mechanism in rice is immense important to food security. Several pieces of evidence suggest that miniature inverted repeat transposable elements (MITEs) can respond to environmental conditions and regulate the expression of nearby genes. Our previous work showed that some MITEs insertions are associated with cold tolerance, implying that MITEs may play important roles in response to cold stress in rice at the booting stage. In order to investigate the regulatory function of MITEs in cold response, we will separate cold-tolerant and cold-sensitive strains based on our cold tolerance phenotype screening system and perform whole genome sequencing, RNA-seq, small RNA-seq and Bisulfite sequencing of each strain. Genome-wide bioinformatic analysis will be used to discover the differences between cold-tolerant and cold-sensitive strains at genome, transcriptome and epigenome levels and identify key regulatory MITEs and related genes in cold response. This grant proposal will contribute to explore the impact of TEs in low temperature adaptation and provide new clues for rice cold tolerance improvement.

低温冷害是影响植物生长发育的重要环境因素之一。孕穗期的低温直接影响作物结实率，导致产量严重下降。水稻是喜温作物，因此研究其孕穗期低温响应机制对提高水稻低温抗性、保障粮食安全具有重要意义。研究表明MITEs类转座子能够调控旁邻基因的表达并在植物胁迫应答中发挥重要作用，我们在前期研究中也发现某些MITEs插入与耐低温性状有相关性，故推测其可能参与了水稻孕穗期低温应答过程。为研究MITEs在低温应答中的作用，本项目拟利用已建立的水稻孕穗期耐低温表型鉴定体系筛选耐冷和冷敏材料，并利用高通量测序获得其基因组、转录组与表观组数据，使用生物信息手段分析二者之间的差异，从全基因组水平上深度挖掘低温应答中起关键作用的MITEs及其调控的基因，并结合分子生物学实验探寻其作用机理。本项目的研究成果可帮助揭示MITEs在低温响应过程中的调控作用，阐述转座子与植物低温适应性之间的关系，为耐低温品种改良奠定理论基础。

低温是威胁植物生长发育的重大环境灾害之一，孕穗期低温会对作物产量造成严重影响，因此研究水稻的低温响应机制对于粮食安全具有重要意义。转座子是基因组中的一类重要元件，水稻基因组中有35%的序列来源于转座子。MITEs是水稻中拷贝数最多的一类转座子，散在分布于基因富集的常染色质区。研究表明MITEs能够调控旁邻基因的表达并在植物胁迫应答中发挥重要作用，但其分子机制尚未可知。因此，本研究通过孕穗期低温处理，筛选极端耐低温与极端敏感水稻品种，并对其基因组、转录组与表观组进行了高通量测序。我们通过多种组学数据的分析与整合，结合分子生物学实验验证，鉴定到了1个与孕穗期低温响应相关的MITEs转座子。该转座子属于mPing家族，特异性插入到2个耐冷材料的羧肽酶基因中，位于5’UTR区，其插入导致了该基因低温下表达上调。进一步通过CRISPR敲除与表型鉴定，证实了该基因影响了水稻的耐冷性。本研究解析了转座子对植物低温适应性的调控作用，为耐低温作物品种改良提供了理论基础。