Functional characterization of the IGT gene family in wheat reveals conservation and variation in root architecture under drought condition
Fatima Rasool,
Muhammad Uzair,
Kotb A. Attia,
Asmaa M. Abushady,
Obaid ur Rehman,
Muhammad Shahbaz Farooq,
Sajid Fiaz,
Umer Farooq,
Bilal Saleem,
Zoqia Tariq,
Safeena Inam,
Nazia Rehman,
Itoh Kimiko,
Muhammad Ramzan Khan
Affiliations
Fatima Rasool
Institute of Biochemistry, Biotechnology & Bioinformatics, The Islamia University of Bahawalpur, Pakistan; Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Muhammad Uzair
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan; Corresponding authors.
Kotb A. Attia
Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
Asmaa M. Abushady
Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City, Giza 12588, Egypt; Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt
Obaid ur Rehman
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan; Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
Muhammad Shahbaz Farooq
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan; Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
Sajid Fiaz
Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620 Pakistan
Umer Farooq
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Bilal Saleem
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Zoqia Tariq
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Safeena Inam
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Nazia Rehman
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
Itoh Kimiko
Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata 950-2181, Japan
Muhammad Ramzan Khan
Functional Genomics and Bioinformatics Labs, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan; Corresponding authors.
Plant architecture traits are a pivotal component in crop improvement and one of the key aspects of breeding programs for centuries. Among architecture traits, leaves and roots angle are most important whereas roots angle is considered to play a vital role in plant response to drought avoidance. Several genes regulating drought response reported in plants, such as LAZY1, Deeper Rooting 1 (DRO1), and Tiller angle control 1 (TAC1), belong to the IGT family. The wheat (Triticum aestivum L.) genome is complex because it consists of three subgenomes A, B, and D. A genome-wide (A, B, and D) identification and characterization of IGT family genes in wheat was reported in this study. A total of 12 IGT genes were identified and categorized based on phylogenetic reconstruction and gene structure analysis. These genes were distributed on chromosomes 2, 5, and 6 corresponding to the A, B, and D genomes of wheat. Most of the genes showed similar structures. Cis-regulatory elements in the promoter regions interpreted the presence of light, stress, development, and hormone-related elements. Five miRNAs (tae-miR9773, tae-miR531, tae-miR9678–3p, tae-miR9781, and tae-miR5049–3p) were predicted which target these TaIGT. Both the RNA-seq-based transcriptomic and real-time gene expression analysis suggested that all the genes are strongly expressed in roots, thus showing function conservation. 3D models and molecular docking of TaIGT were also carried out systematically, and binding patterns and the orientation of ligands in the active site of proteins were predicted. This study delves further into TaIGT genes and their expression patterns. The findings of this work are important for understanding the molecular control of root development and for future functional characterization of wheat root architecture genes. Key message: IGT gene family has not been identified and characterized and we identified 12 genes strongly expressing in roots. Furthermore, five miRNAs were predicted and could have a role in root conservation.
