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| 调控陆稻陆生适应性功能基因的挖掘与解析 | |
| Alternative Title | Mining and Deciphering Functional Genes for Regulating Aerobic Adaptation in Upland Rice |
杨君
| |
| Thesis Advisor | 余迪求 |
| 2020 | |
| Degree Grantor | 中国科学院大学 |
| Place of Conferral | 中国科学院西双版纳热带植物园 |
| Degree Name | 理学博士 |
| Degree Discipline | 植物学 |
| Keyword | 株高 陆生适应性 候选基因 分子机制 多组学定位 |
| Abstract | 由水生变为无明显水分压力的且通气的陆生环境是水稻向旱稻发展的驱动力，也是水稻和陆稻具有明显水、陆生环境适应性差异遗传基础的成因。陆生适应强调的是在植物生长和发育过程中与土壤水分供应特征保持一致，为了避旱，其生长水分需求期与当地雨季期吻合，因此，耐旱并非是陆稻适应旱地的第一驱动力，陆生适应性则是水、陆稻遗传分化的关键。但在诸多的表型差异及基因组上相应的遗传变异中，与亚洲栽培稻适应陆生环境相关联的关键遗传变异并不明确，亟待于从这些众多的差异中进一步寻找强烈分化的基因位点，从而鉴定出亚洲栽培稻适应陆生环境的关键基因。为了解析陆稻陆生适应性的关键候选基因，本研究避免了干旱的干扰，在旱地以产量为指标、以水稻明恢63 为母本和受体亲本、陆稻陆引46 为父本和供体亲本，连续筛选得到其高世代回交自交重组渗入系IL-U135，并详细考察了两个亲本及渗入系在水、陆生环境下的非产量性状和产量性状，证实了水稻在陆生环境下株高变矮、生育期延迟是不适应陆生环境的直观表型，说明来自陆稻的QTL 在陆生环境下起到增加株高和抽穗期不延迟的作用以适应陆生环境，最终提高其在陆生环境下的产量。渗入系的陆生适应性是由陆引 46 渗入片段引起，利用基因组重测序技术，解析了IL-U135 的染色体结构，发现有12 个来自陆引46 的染色体片段渗入到渗入系中，涉及到有效SNP 变异基因2088 个、有效InDel 基因689 个；水、陆生环境下的苗期和开花期转录组分析表明，水生条件下，IL-U135 与明恢63 相比有20 个差异表达基因（log2fold-change≥1；false discovery rate ≤0.01），陆引46 与明恢63 相比有306 个差异表达基因（log2fold-change≥1；false discovery rate≤0.01）；在陆生环境下，IL-U135 与明恢63 相比有8 个差异表达基因，陆引46与明恢63 相比有188 个差异表达基因。对这些差异表达基因进行基因本体（GeneOntology）分析，结果表明，陆生适应与CLAVATA3/EMBRYO-SURROUNDING REGION（CLV3/ESR）信号途径、CLAVATA1 激酶活性、水杨酸相关生物合成途径及赤霉素生物合成途径有关。利用传统 QTL 定位，在渗入系中得到一个与株高相关的QTL qAER1,该区域包含17 个候选基因，通过结合基因组重测序和转录组测序结果综合分析，在IL-U135 的渗入区段中具有有效SNP 和InDel 基因，又在IL-U135 和MH63 中具有表达差异，且定位在qAER1 区域的候选基因，一共有三个，即SD1（ LOC_Os01g66100 ）、反转录转座子两个（ LOC_Os01g66080 ， 080 和LOC_Os01g66090，090）。随后的基因组SNP 差异分析、qRT-PCR 分析验证了这三个基因为陆生适应性差异候选基因。通过基因互补和敲除验证了SD1 是陆生适应性直观表型株高调控的主效基因，080 和090 是重要的调控因子。我们在 SD1-080-090 调控陆稻陆生适应性的机制方面做了初步探索，初步提出如下假设：陆生环境下，地上部分株高受SD1-080-090 的调控，SD1 启动子能结合TCP 和锌指转录因子ZOS 基因家族，这些转录因子家族可能介导SD1 的表达来调控株高，或是080/090 通过介导small RNA 而调控SD1 的表达，进而参与GA 合成途径而调控株高；地下部分，080/090 可能通过与某些蛋白互作而调控根部的在土壤中的深度从而适应陆生。这些结果为我们进一步解析陆稻的陆生适应性分子机制打下了重要的基础。 |
| Other Abstract | Transition from aquatic environments to aerobic environments without obvious water pressure and ventilation is the driving force for the development of irrigated rice to upland rice, and it is also the cause of the genetic basis of obvious differences in adaptability of aquqtic and aerobic environments between irrigated rice and upland rice.Aerobic adaptation emphasizes that it is consistent with the characteristics of soil water supply during plant growth and development. To avoid drought stress, the water demending period for growth must be consistent with the local rainy season.Therefore, drought tolerance is not the first driving force of upland rice adaptation to aerobic environments. However, the aerobic adaptation is the key to genetic differentiation of irrigated and upland rice. Among many phenotypic variations and the corresponding genetic variations in the genome, the key genetic variations associated with the Asian cultivated rice adaptation to aerobic environments are not clear, and it is urgent to find the strongly differentiated genetic loci from these many differencs, so as to identify the key genes of Asian cultivated rice adaptation to aerobic environments. To decifer the candidate genes for aerobic adaptation of upland rice, our study have avoided the interference of drought stress, and the yield was used as an indicator on the dry land, irrigated rice Minghui 63 was used as the female and recipient parent and upland rice Luyin 46 as male and donor parent. A high generation backcross inbred line IL-U135 was screened in the succession selected. Then, the non-yield and yield traits of two parents and infiltrated lines under irragted and aerobic conditions were observed. The reduced plant height and delayed growth period of irrigated rice under aerobic conditions were the intuitive phenotype that did not adapt to aerobic environment, which indicates that the QTLs from upland rice could increase or maintain the plant height and not delay the heading date under aerobic conditions so as to adapt to aerobic conditions, ultimately increased yields. Because of the introgression fragments from Luyin 46 to Minghui 63, the introgression line IL-U135 exibited the aerobic adaptability. With genomic resequencing technology, the chromosome structure of IL-U135 was analyzed, 12 chromosome fragments from Luyin 46 were infiltrated into Minghui 63, which involved 2088 genes with effective single nucleotide polymorphisms (SNPs) and 689 genes with effective insertion and deletions (InDels); In addition, the transcriptome analyzes of Minghui 63, Luyin 46 and IL-U135 at seedling and heading stages under irrigated and aerobic conditions revealed that IL-U135 had 20 differntially expressed genes [log2(fold-change)≥1）；false discovery rate ≤0.01] compared with Minghui 63, Luyin 46 had 306 differntially expressed genes [log2(fold-change)≥1 ）； false discovery rate ≤0.01] compared with Minghui 63 under irrigated conditions; IL-U135 had 8 differntially expressed genes [log2(fold-change)≥1）；false discovery rate ≤0.01] compared with Minghui 63, Luyin 46 had 188 differntially expressed genes [log2(fold-change)≥1）；false discovery rate ≤0.01] compared with Minghui 63 under aerobic conditions. Gene Ontology analysis was performed on these differentially expressed genes. The results showed that the aerobic adaptation of upland rice was related with CLAVATA3/EMBRYO-SURROUNDING REGION(CLV3/ESR) signaling pathway, CLAVATA1 kinase activity, salicylic acid-related biosynthetic pathways and Gibberellin biosynthetic pathway. With the traditional QTL mapping, a plant height-related QTL qAER1 was detected in IL-U135, which contains 17 candidate genes. By comprehensive analysis of genomic resequencing and transcriptome sequencing results, there were three candidate genes which were with effective SNPs and InDels and differential expressed located in the qAER1 region, they were SD1 (LOC_Os01g66100) and two retrotransposons [(LOC_Os01g66080, 080) and LOC_Os01g66090, 090)]. Subsequent genomic SNP and qRT-PCR analyzes confirmed that these three genes responsible genes for upland rice aerobic adaptation.Gene complementation and knockout experiments verified that SD1 was the main effect gene of the plant height regulation for aerobic adaptation, 080 and 090 were important regulatory factors. At last, we have made a preliminary exploration on the mechanism of SD1-080-090 regulating aerobic adaptation of upland rice, and initially put forward the following hypothesis: in the aerobic environment, for the above-ground plant part, the plant height was regulated by the gene module SD1-080-090, further the SD1 promoter could be binded by transcription factors (TFs) such as TCP and zinc finger TF ZOS gene family, which may mediate SD1 expression to regulate plant height, or 080/090 could mediate small RNAs to regulate SD1 expression, and then participated in the GA synthesis pathway to regulate plant height; for the below-ground plant part, 080/090 could interact with some certain proteins to regulate the root depth in the aerobic soil. These results could lay an important foundation for further deciphering the molecular mechanisms of aerobic adaptaion. Key words: plant height; aerobic adaptation; candidate genes; molecular mechanism; multiomics mapping |
| Pages | 170 |
| Language | 中文 |
| Document Type | 学位论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/11703 |
| Collection | 西双版纳热带植物园毕业生学位论文 |
| Affiliation | 1.中国科学院大学; 2.中国科学院西双版纳热带植物园 |
| Recommended Citation GB/T 7714 | 杨君. 调控陆稻陆生适应性功能基因的挖掘与解析[D]. 中国科学院西双版纳热带植物园. 中国科学院大学,2020. |
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| 杨君.pdf（7118KB） | 学位论文 | 开放获取 | CC BY-NC-SA | Application Full Text | ||
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