RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress.
RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress.
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RNA-seq 用于盐度胁迫下狗牙根根生长相关的基因鉴定和转录谱分析
DOI：
10.1186/s12864-015-1799-3
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发表时间：
2015-08-04
期刊：
影响因子：
4.4
通讯作者：
Fu J
中科院分区：
文献类型：
--
作者：
Hu L;Li H;Chen L;Lou Y;Amombo E;Fu J
背景土壤盐分是影响植物地上部和根系生长的最重要的非生物胁迫之一。根构型对盐分时空异质性的调节对植物的生长和存活尤为重要。狗牙根（Cynodon dactylon）是一种耐盐性很强的多年生草坪草和饲用禾草。盐度似乎刺激根的生长，并降低其死亡率耐受狗牙根。为了估计一个广谱的基因根伸长受盐胁迫和控制的分子机制，积极响应的根结构对盐度的影响，我们分析了转录组的狗牙根根尖响应salinity. ResultsRNA测序进行在根尖的两个狗牙根基因型对比耐盐性。共生成237，850，130个高质量干净读段，并组装了250，359个转录物，平均长度为1115 bp。共获得103，324个unigenes，其中53，765个unigenes（52%）在数据库中成功注释。生物信息学分析表明，与胁迫响应和生长调控相关的主要转录因子家族（MYB、bHLH、WRKY）在盐胁迫下狗牙根根尖中差异表达。此外，相关的基因细胞壁松动和僵硬（木葡聚糖内切转葡糖基酶/水解酶，过氧化物酶）被identified.ConclusionsRNA-seq分析确定候选基因编码TF参与调节木质素的合成，活性氧（ROS）由过氧化物酶控制的体内平衡，并调节植物激素信号，促进细胞壁松动，因此根在盐度下的生长。
BackgroundSoil salinity is one of the most significant abiotic stresses affecting plant shoots and roots growth. The adjustment of root architecture to spatio-temporal heterogeneity in salinity is particularly critical for plant growth and survival. Bermudagrass (Cynodon dactylon) is a widely used turf and forage perennial grass with a high degree of salinity tolerance. Salinity appears to stimulate the growth of roots and decrease their mortality in tolerant bermudagrass. To estimate a broad spectrum of genes related to root elongation affected by salt stress and the molecular mechanisms that control the positive response of root architecture to salinity, we analyzed the transcriptome of bermudagrass root tips in response to salinity.ResultsRNA-sequencing was performed in root tips of two bermudagrass genotypes contrasting in salt tolerance. A total of 237,850,130 high quality clean reads were generated and 250,359 transcripts were assembled with an average length of 1115 bp. Totally, 103,324 unigenes obtained with 53,765 unigenes (52 %) successfully annotated in databases. Bioinformatics analysis indicated that major transcription factor (TF) families linked to stress responses and growth regulation (MYB, bHLH, WRKY) were differentially expressed in root tips of bermudagrass under salinity. In addition, genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were identified.ConclusionsRNA-seq analysis identified candidate genes encoding TFs involved in the regulation of lignin synthesis, reactive oxygen species (ROS) homeostasis controlled by peroxidases, and the regulation of phytohormone signaling that promote cell wall loosening and therefore root growth under salinity.