Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil

Chandan Kumar Singh; Dharmendra Singh; Jyoti Taunk; Priya Chaudhary; Ram Sewak Singh Tomar; Shivani Chandra; Deepti Singh; Madan Pal; Noren Singh Konjengbam; M Premjit Singh; Rakesh Singh Sengar; Ashutosh Sarker

doi:10.3389/fpls.2021.693630

Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil

Front Plant Sci. 2021 Aug 31:12:693630. doi: 10.3389/fpls.2021.693630. eCollection 2021.

Authors

Affiliations

¹ Division of Genetics, Indian Agricultural Research Institute, New Delhi, India.
² Amity Institute of Biotechnology, Amity University, Noida, India.
³ Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India.
⁴ College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India.
⁵ Department of Botany, Meerut College, Meerut, India.
⁶ College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University-Imphal, Umiam, India.
⁷ College of Agriculture, Central Agricultural University-Imphal, Iroisemba, India.
⁸ College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut, India.
⁹ International Center for Agriculture Research in the Dry Areas, New Delhi, India.

Abstract

Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al³⁺ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al³⁺ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al³⁺ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al³⁺ stress.

Keywords: aluminium stress; interspecific; intraspecific; lentil; transcriptomics; wild.