Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes

Fatima Rasool; Muhammad Ramzan Khan; Michael Schneider; Muhammad Uzair; Muhammad Aqeel; Wajya Ajmal; Jens Léon; Ali Ahmed Naz

doi:10.1016/j.plaphy.2022.02.025

Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes

Plant Physiol Biochem. 2022 May 1:178:20-30. doi: 10.1016/j.plaphy.2022.02.025. Epub 2022 Mar 1.

Authors

Fatima Rasool¹, Muhammad Ramzan Khan², Michael Schneider³, Muhammad Uzair⁴, Muhammad Aqeel⁴, Wajya Ajmal⁴, Jens Léon³, Ali Ahmed Naz⁵

Affiliations

¹ 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.
² 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. Electronic address: mrkhan@parc.gov.pk.
³ Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany.
⁴ National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
⁵ Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany. Electronic address: a.naz@uni-bonn.de.

PMID: 35247694
DOI: 10.1016/j.plaphy.2022.02.025

Abstract

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.

Keywords: Abiotic stress; Candidate genes; Climate change; Drought stress; Genetic variations; RNA-Seq.

MeSH terms

Droughts*
Gene Expression Profiling
Gene Expression Regulation, Plant
Genotype
Plant Breeding
Stress, Physiological / genetics
Transcriptome* / genetics
Triticum / genetics
Triticum / metabolism