Comparative transcriptome analysis reveals molecular regulation of salt tolerance in two contrasting chickpea genotypes

Hammad Aziz Khan; Niharika Sharma; Kadambot H M Siddique; Timothy David Colmer; Tim Sutton; Ute Baumann

doi:10.3389/fpls.2023.1191457

Comparative transcriptome analysis reveals molecular regulation of salt tolerance in two contrasting chickpea genotypes

Front Plant Sci. 2023 May 30:14:1191457. doi: 10.3389/fpls.2023.1191457. eCollection 2023.

Authors

Hammad Aziz Khan^{1

2}, Niharika Sharma³, Kadambot H M Siddique^{1

2}, Timothy David Colmer^{1

2}, Tim Sutton^{4

5}, Ute Baumann⁴

Affiliations

¹ UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
² The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
³ NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia.
⁴ School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia.
⁵ Department of Primary Industries and Regions, South Australian Research and Development Institute (SARDI), Adelaide, SA, Australia.

Abstract

Salinity is a major abiotic stress that causes substantial agricultural losses worldwide. Chickpea (Cicer arietinum L.) is an important legume crop but is salt-sensitive. Previous physiological and genetic studies revealed the contrasting response of two desi chickpea varieties, salt-sensitive Rupali and salt-tolerant Genesis836, to salt stress. To understand the complex molecular regulation of salt tolerance mechanisms in these two chickpea genotypes, we examined the leaf transcriptome repertoire of Rupali and Genesis836 in control and salt-stressed conditions. Using linear models, we identified categories of differentially expressed genes (DEGs) describing the genotypic differences: salt-responsive DEGs in Rupali (1,604) and Genesis836 (1,751) with 907 and 1,054 DEGs unique to Rupali and Genesis836, respectively, salt responsive DEGs (3,376), genotype-dependent DEGs (4,170), and genotype-dependent salt-responsive DEGs (122). Functional DEG annotation revealed that the salt treatment affected genes involved in ion transport, osmotic adjustment, photosynthesis, energy generation, stress and hormone signalling, and regulatory pathways. Our results showed that while Genesis836 and Rupali have similar primary salt response mechanisms (common salt-responsive DEGs), their contrasting salt response is attributed to the differential expression of genes primarily involved in ion transport and photosynthesis. Interestingly, variant calling between the two genotypes identified SNPs/InDels in 768 Genesis836 and 701 Rupali salt-responsive DEGs with 1,741 variants identified in Genesis836 and 1,449 variants identified in Rupali. In addition, the presence of premature stop codons was detected in 35 genes in Rupali. This study provides valuable insights into the molecular regulation underpinning the physiological basis of salt tolerance in two chickpea genotypes and offers potential candidate genes for the improvement of salt tolerance in chickpeas.

Keywords: RNA-sequencing; chickpea (Cicer arietinum L.); gene sequence variation.; salt stress; salt tolerance; transcriptome analysis.

Grants and funding

The study was supported by funds from the Australia-India Strategic Research Fund (Project GCF010013) of the Australian Government Department of Industry.