Transcriptomic Analysis Reveals Differential Gene Expressions for Cell Growth and Functional Secondary Metabolites in Induced Autotetraploid of Chinese Woad (Isatis indigotica Fort.)

The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.同源多倍体诱导产生的巨型器官与次生代谢物浓度提升，在药用与农用植物育种及遗传机制研究中极具应用价值。传统药用植物菘蓝（Chinese woad，Isatis indigotica Fort.，2n=2x=14）目前在国内仍被广泛用于治疗细菌性与病毒性疾病。本研究通过高通量RNA测序技术，对该植物的同源多倍体株系（3x、4x）及其二倍体（2x）亲本的表型与转录组变化进行了鉴定与分析。随着基因组剂量的增加，细胞与器官的巨型化表型愈发显著，光合速率也随之提升。四倍体株系主要呈现正常的减数分裂染色体配对（二价体与四价体）及均等分离，由此可产生绝大多数四倍体后代。本研究从头组装得到70136条All-unigenes，并基于公共数据库的BLASTx比对，为其中56482条（占比80.53%）unigenes完成了功能注释。通过对二倍体、三倍体、四倍体株系的转录组数据进行两两比对，本研究共检测到1856条（占比2.65%，二倍体vs四倍体）、693条（占比0.98%，二倍体vs三倍体）及1045条（占比1.48%，三倍体vs四倍体）unigenes为差异表达基因（differentially expressed genes, DEGs），涵盖上调与下调表达两类。上述差异表达基因主要参与细胞生长（伸展蛋白与果胶合成）、细胞壁构建、次生代谢物生物合成、胁迫响应及光合通路。诱导产生的同源四倍体中，部分参与功能化合物代谢通路的差异表达基因呈现上调表达，这证实了该药用植物可通过多倍体化获得生物量与目标代谢物含量均提升的优良新种质。