Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
Plant Physiol Biochem. 2022 May 1;178:20-30. doi: 10.1016/j.plaphy.2022.02.025. Epub 2022 Mar 1.
Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.
干旱是农业生产的一大挑战。根系特性是培育应对不断变化气候条件的高产可持续小麦品种的重要目标性状。然而，有关小麦根系结构的转录组仍然不清楚。在这里，我们探索了基于 RNA-Seq 的转录组，以剖析在六种自然发生的小麦基因型（耐旱和敏感）中与根系系统变化相关的假定基因。基于全局 RNA-Seq 的根系转录组分析揭示了单核苷酸多态性（SNP）变异和差异表达基因。鉴定出与 15 个参与根系结构的基因相关的 56 个假定 SNP。使用 GO 术语对这些基因进行富集，表明差异表达基因（DEG）分为涉及分子功能、细胞成分和生物过程的亚类。在每个基因型比较中，KEGG 分析 DEG 包括代谢、次生代谢物的生物合成、不同环境中的微生物代谢和抗生素的生物合成。对 DEG 的更深入研究揭示了参与干旱响应和正向向重力性的各种途径。这些基因属于涉及根系发育和应激相关途径的各种转录因子家族，如 DOF、C3H、MYB 和 NAC。耐旱基因型 Local White 和 UZ-11-CWA-8 大量存在大多数 DEG 或转录因子。值得注意的是，参与正向向重力性的微管相关蛋白 MAPRE1 属于 RP/EB 家族，被富集。实时 PCR 分析显示 MAPRE1 和 PAL 基因的表达与 RNA-seq 数据一致。提供的数据和遗传资源似乎对研究耐旱和敏感基因型的根系系统结构相关基因具有重要价值。
