海岛棉和陆地棉纤维发育的遗传基因组学研究

英文题名：Genetical Genomics Research for Fiber Development between Gossypium Barbadense and Gossypium Hirsutum
作者：陈向东
论文级别：博士
学科专业名称：作物遗传育种学
中文关键词：棉花 ; 微阵列 ; 纤维发育 ; 基因表达 ; 表达QTL
英文关键词：Gossypium ; microarray ; fiber development ; gene expression ; expression
英文关键词：quantitative trait loci (eQTL)
学位年度：2011
导师：张天真
学科代码：090102
学位授予单位：南京农业大学

摘要

棉花是我国最重要的经济作物之一,也是主要的自然纤维作物。中国是世界上最大的纺织品生产国和消费国,常年种植面积在8,000万亩左右,棉花种植业与纺织业在我国国民经济中起着重要的作用。但是,目前国产原棉在质量上已经不能满足市场需要,适纺高档棉纱的优质原棉,主要依赖进口。长期以来,我国棉花纤维品质偏差,平均跨长和比强度均较低,成为制约棉花产业可持续发展的主要障碍。纤维品质包括纤维长度、强度、细度等性状的综合指标受纤维的伸长和次生壁合成过程影响。因此,研究棉花纤维发育转录组以阐明纤维细胞基因表达模式,整合遗传和遗传基因组学以发掘影响纤维品质基因及了解棉纤维品质调控的分子机制,对改善纤维品质具有极为显著的意义。
     本研究开发了海陆群体的AFLP, SAMPL, SABPL和EST等分子标记,为本实验室构建的海陆遗传图谱增加了244个非SSR类型的多态位点,尤其是EST相关的功能标记。这些标记增加了遗传标记的类型,填充了染色体上某些空白区域。结合本实验加密的比较饱和海陆回交遗传图谱,我们整合四年纤检的纤维品质数据,利用多QTL联合分析方法检测了纤维长度、强度、细度、伸长率及整齐度等纤维品质性状基因型及环境互作效应,得到22个纤维品质QTL(LOD≥3),包括6个主效QTL,16个与环境互作的QTL；纤维长度和强度QTL主要定位在A亚组(A1、A3、A5和A11),而纤维整齐度和马克隆值QTL主要定位在D亚组(D1、D4、D7和D12)。一致或稳定的QTL将为研究影响纤维品质的候选基因提供基础。
     本研究利用高通量的微阵列平台,筛选了涉及陆地棉标准系TM-1纤维起始、伸长及次生壁加厚时期的差异表达基因。我们利用SAM (Significant Analysis of Microarray)软件的multiclass方法对28k棉花芯片上10,902个基因不同时期的信号强度分析,得到了6,186个时期差异表达基因(q-value≤5%)。 KEGG分析发现细胞骨架蛋白、类黄酮合成、氧化磷酸化和糖酵解代谢途径处于显著差异水平。我们对6,186个时期差异表达基因的11个时期平均最高信号强度值和次之信号值利用t-test方法(P<0.05)和1.5倍差异标准筛选,最终得到了192个时期特异表达的基因。这些时期特异表达基因决定了纤维细胞在特异时期的独特的分子事件。另外纤维的发育阶段也能够利用差异表达基因的聚类清晰的分开,在分子水平上分开了3个重要的纤维发育阶段。这项研究为四倍体栽培棉种的纤维发育机制提供了新的视点,也为纤维发育的研究提供了大量的特异表达基因资源,更为进一步通过遗传改良方法提高棉纤维的品质提供了一定基础。
     利用高通量的微阵列技术对陆地棉和海岛棉纤维基因表达进行了比较研究。我们测量了海岛棉Hai7124和陆地棉TM-1纤维整个伸长发育期不同时间点的长度(5-38days post anthesis, DPA),发现陆地棉和海岛棉纤维长度分别在15-20和23-28DPA之前线性增长,最终达到一个相对平稳的时期,较大的差异发生在20-33DPA。我们利用12k棉花纤维cDNA芯片与在5个时间点(5、10、15、20和25DPA)的Hai7124和TM-1纤维发育细胞的RNA杂交,利用R语言LIMMA软件包的经验贝叶斯(eBayes)方法在错误发现率FDR<0.05及2倍差异的标准下比较了发育纤维细胞在种内相邻时间点和种间差异表达基因的数目,在Hai7124相邻时期比较分别有276(5vs.10DPA),2402(10vs.15DPA),94(15vs.20DPA)和44(20vs.25DPA)个差异基因,而在TM-1分别得到473、2224、148和396个差异基因,在Hai7124和TM-1纤维细胞间5个时间点分别发现151、233、195、100和232个差异基因。10和25DPA有更多的差异表达基因,是两个非常关键的时期,对这两个时期的深入研究有利于弄清控制纤维快速伸长基因及决定海岛棉持续伸长或陆地棉停止伸长的基因。
     为了深入解析海陆棉花差异原因,发掘与纤维品质相关的基因,我们选择了10和25DPA的纤维进行了遗传基因组学研究。我们利用28k棉花cDNA芯片从10和25DPA的纤维细胞中分别检测到13,760和13,411个有效基因,利用R语言LIMMA软件包的经验贝叶斯(eBayes)方法,错误发现率控制在5%的水平上,发现在亲本TM-1和Hai7124间分别有142和302个差异表达基因。在这两个时期的66个棉花BC1S1株系分别用相同的芯片平台检测了表达谱,进一步用于连锁分析。在P<0.05水平上总共定位了916个表达QTL(eQTL),包括纤维伸长时期的293个和次生壁合成时期的623个；通过比较转录本的表达连锁位置和遗传标记定位预测了一些潜在的顺式或反式eQTL。另外,我们得到了46个eQTL热点,其中A亚组30个,D亚组16个,同时筛选了这些热点内包含的转录因子。比较eQTL与纤维QTL的位置,我们得到了一批纤维QTL在eQTL共定位的基因,尤其是在25DPA发现大量与纤维长度、强度和细度相关的基因,纤维品质可能由纤维品质QTL区域的基因表达调控因子影响,研究这些基因能够帮助我们进一步揭示海岛棉和陆地棉纤维长度差异的分子机制。结合这些研究结果,我们推测在纤维发育过渡阶段,ABA和乙烯信号途径基因的下调,生长素调控因子和细胞壁疏松酶等纤维伸长正向调控基因的长时间及高水平表达是海岛棉保持持续伸长的主要分子基础,这可能也是海岛棉具有优异的纤维品质的一个原因。棉花遗传和表达QTL的整合为纤维品质功能基因的发掘提供了新视点,有助于进一步通过分子手段改良棉花的纤维品质。
Cotton (Gossypium spp.) is one of the most important economic crops due to its excellent natural fiber properties. China is the world's largest producer and consumer of textiles, around the growing area of80million acres every year, the cotton textile industry in national economy plays an important part in our country. But, at present domestic raw cotton quality have not already met the demands of the market, and the superior quality raw cotton with a higher spinning performance almost all rely on imports. The domestic cotton fiber quality is poor because of low average span length and strength, which restrict sustainable development in cotton industry. Cotton fiber qualities including length, strength and fineness are controlled by genes that affect cell elongation and secondary cell wall (SCW) biosynthesis. Therefore, the research on cotton fiber development transcriptomics can be used to clarify gene expression patterns for crucial genes, and integratation of genetics and genetical genomics can help us understand the molecular mechanisms controlling the cotton fiber qualities, which will be remarkable significance for genetic improvement of fiber qualities.
     We developed AFLP, SAMPL, SABPL and EST molecular markers in BC1population of G. hirsutum acc. TM-1and G. barbadense cv. Hai7124, increasing244loci in our backbone BC1population, particular for EST functional markers, enriched types of molecular markers and dense area of chromosomes. The combination of four-year fiber trait data that were obtained from the same genetic materials revealed22QTL for fiber length (FL), strength (FS), micronaire reading (FM), elongation (FE), and uniformity (FU) involving genotype and interaction of genotype and environment [logarithm of odds (LOD)≥3.0] by multi-QTL joint analysis, including6main effect QTL,16QTL-by-environment interaction. QTL for FL and FS were mapped on A-subgenome (At) chromosomes (A1, A3, A5and All), whereas QTL for FU and FM were mainly mapped on D-subgenome (Dt) chromosomes (D1, D4, D7and D12). Stable or consistent QTL will provide foundation for identification of genes affecting fiber qualities.
     Cotton fiber is a highly elongated trichome from epidermal cell of cotton ovule that is one of the most important natural raw materials for the textile industry. Upland cotton (G hirsutum L.) accounts for about95%of the annual cotton production in the world. To reveal developmental features of upland cotton fiber cells, we combined11developmental stages (-3-25days post-anthesis, DPA) of microarray data in G. hirsutum acc.TM-1, and identified10,902effective genes during fiber cell initiation, elongation and secondary cell wall (SCW) synthesis. Of these genes, we determined6,186differentially expressed genes (DEGs) among11development times by SAM (significant analysis of microarray) multiclass. Several significant metabolic pathways from6,186DEGs were identified by Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis in fiber development, primarily including cytoskeleton proteins, flavonoid biosynthesis, oxidative phosphorylation, and glycolysis/gluconeogenesis. Comparative analyses of transcriptomes showed192specific-times expressed genes across a developmental time-course involving in4gene clusters, and many key genes were confirmed by real-time quantitative reverse transcription PCR (QRT-PCR) analysis. These specific-times expressed genes may determine that cotton fiber cell at a certain stage has its own unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript profiles. This study also gains new insights to understand the molecular mechanism of cultivated tetraploid cotton fiber development.
     Comparative analysis of gene expression in G. hirsutum and G. barbadense was conducted using the high-throughput microarray platform. To reveal the differential feature of fiber development that may account for fiber qualities, we measured dynamic change of fiber length of TM-1and Hai7124at different time points (5-38DPA), and observed that fiber length increased approximately linearly over the first15-20DPA in TM-1and23-28DPA in Hai7124, and plateaued as the fibers reached their final dimensions, great difference occurred between20-33DPA during elongation. To investigate differentially regulated genes in fiber developmental process, we hybridized a cotton fiber cDNA microarray (GPL2610) with RNA samples of TM-1and Hai7124fiber from five different developmental time-points,5,10,15,20and25DPA. We compare mRNA expression levels in developing fiber-cells using the empirical eBayes method in LIMMA, and revealed the numbers of DEGs between adjacent time-points during fiber development within and between species based on the criterion of false discovery rate (FDR)<0.05and fold change (FC)≥2. Within each species, the number of DEGs was unequally distributed between adjacent time points. In Hai7124,276(5vs.10DPA),2,402(10vs.15DPA),94(15vs.20DPA) and44(20vs.25DPA) genes were differentially expressed, whereas in TM-1,473,2,224,148and396genes were differentially expressed. Between Hai7124and TM-1, there were151,233,195,100and232genes differentially expressed at five time points (5-25DPA). Thus, the two periods10and25DPA with higher numbers of DEGs will be crucial for identification of fiber genes regulating elongation at fast elongation stage and determination G. barbadense fiber continuative elongation or the termination of G. hirsutum fiber elongation at the transition stage.
     To deeply identify fiber quality genes, we selected these two respective periods for further linkage analysis of expression profiles. We extensively investigated gene expression in fiber cells of66randomly selected BC1S1lines as well as the two parents TM-1and Hai7124using another cDNA microarray platform (GPL8569) with abundant probes. A total of13,760and13,411active transcripts at10and25DPA, respectively, were detected and142and302DEGs between TM-1and Hai7124were further identified. Furthermore,444expression traits in66cotton BC1S1lines were used to expression quantitative trait loci (eQTL) analysis. A total of916eQTL were statistically significant with a logarithm of odds (LOD) score exceeding permutation based thresholds (P<0.05), including293and623eQTL at10and25DPA, respectively. Many positional cis-/trans-acting eQTL could be estimated by comparing chromosomal location of each transcript and position of its eQTL A total of46eQTL hotspots were identified, of them,30on At and16on Dt, and some transcriptional factors were existed in the hotspot regions. By comparative analysis of eQTL and consistent or stable fiber QTL in the present study, especially for eQTL hotspots were observed within the intervals regions of fiber QTL, we identified functional fiber quality genes differentially espressed between G. hirsutum and G. barbadense. Most noteworthy, the fiber transcript abundance variation at25DPA predominantly affected fiber qualities. The temporal regulation of gene expression and QRT-PCR identified the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism of fiber difference between G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulation expression of ABA and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities.

引文

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