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

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.

Physiological and proteomic characterization revealed the response mechanisms underlying aluminium tolerance in lentil (Lens culinaris Medikus)

“…The major metabolic pathways, namely antioxidative mechanism, plant hormone signal transduction, pathways involved in maintaining calcium homeostasis and energy conservation, were found to play a crucial role in conferring Al tolerance. These results, which are complementary to the transcriptomic analysis (Singh et al, 2021c), could be used…”

“…The major metabolic pathways, namely antioxidative mechanism, plant hormone signal transduction, pathways involved in maintaining calcium homeostasis and energy conservation, were found to play a crucial role in conferring Al tolerance. These results, which are complementary to the transcriptomic analysis (Singh et al, 2021c), could be used as guidance to develop better Al‐adaptable lentil genotypes for future crop improvement programmes together with a fine understanding of Al tolerance mechanisms and pathways.…”

“…Integration of proteomic and transcriptomic data can provide a comprehensive understanding of cellular processes enhancing the depth and accuracy of biological insights. In our previous study, whole genome transcriptomic analysis was performed to elucidate the candidate genes for Al tolerance in the same set of Al‐tolerant and Al‐sensitive genotypes, namely L‐4602 and BM‐4 (Singh et al, 2021c). Comparison of transcriptomic and proteomic data showed a similar set of gene(s) and proteins regulated in Al‐tolerant and Al‐sensitive genotypes.…”

Establishment of an efficient regeneration protocol of six different varieties of wheat (Triticum aestivum L.)

“…Simultaneously, wheat genome size is ~17000 Mb, which is challenging to improve genetically. As compared to traditional breeding, robust techniques of biotechnology such as CRISPR/ Cas9 and other most advanced technology to modify DNA with addition or deletion of nucleotides are more precise and encompass all challenges (El-Sappah et al, 2021), additionally, inter-and intra-species transmission of stress associated traits is also possible with a shortest duration (Singh et al, 2021). To employ aforementioned techniques, a robust and highly efficient regeneration protocol is mandatory (Yu et al, 2008).…”

Multi-Species Transcriptome Assemblies of Cultivated and Wild Lentils (Lens sp.) Provide a First Glimpse at the Lentil Pangenome

“…Not surprisingly, most of the studies at the transcriptome level have been conducted on L. culinaris, and very few on the other species of Lens. In one of the few exceptions [20], researchers assembled the transcriptomes of L. culinaris and L. nigricans to study differential expressed genes and pathways under Al 3+ stress. They completed the study with trait-associated SNPs and SSR markers that could be used in breeding programs to improve resistance to Al 3+ in lentils and other crops.…”