Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity.

Mayank Kaashyap,Kadambot H M Siddique,Nitin Mantri,Rajeev K Varshney,Anita Mann,Rebecca Ford

doi:10.3390/plants11030434

Abstract

Salinity is increasingly becoming a significant problem for the most important yet intrinsically salt-sensitive grain legume chickpea. Chickpea is extremely sensitive to salinity during the reproductive phase. Therefore, it is essential to understand the molecular mechanisms by comparing the transcriptomic dynamics between the two contrasting genotypes in response to salt stress. Chickpea exhibits considerable genetic variation amongst improved cultivars, which show better yields in saline conditions but still need to be enhanced for sustainable crop production. Based on previous extensive multi-location physiological screening, two identified genotypes, JG11 (salt-tolerant) and ICCV2 (salt-sensitive), were subjected to salt stress to evaluate their phenological and transcriptional responses. RNA-Sequencing is a revolutionary tool that allows for comprehensive transcriptome profiling to identify genes and alleles associated with stress tolerance and sensitivity. After the first flowering, the whole flower from stress-tolerant and sensitive genotypes was collected. A total of ~300 million RNA-Seq reads were sequenced, resulting in 2022 differentially expressed genes (DEGs) in response to salt stress. Genes involved in flowering time such as FLOWERING LOCUS T (FT) and pollen development such as ABORTED MICROSPORES (AMS), rho-GTPase, and pollen-receptor kinase were significantly differentially regulated, suggesting their role in salt tolerance. In addition to this, we identify a suite of essential genes such as MYB proteins, MADS-box, and chloride ion channel genes, which are crucial regulators of transcriptional responses to salinity tolerance. The gene set enrichment analysis and functional annotation of these genes in flower development suggest that they can be potential candidates for chickpea crop improvement for salt tolerance.

Highlights

Chickpea is the most important cool-season food legume and provides nutritional food to the growing population [1,2]
Stage 3 fully opened flowers from both control and stress conditions were collected for transcriptomic analysis
The essential salt tolerance candidate genes are highly induced in the tolerant genotype but are repressed in the sensitive genotype, suggesting their potential role in regulating the tolerance to salinity

Summary

Introduction

Chickpea is the most important cool-season food legume and provides nutritional food to the growing population [1,2]. Chickpea will become an increasingly important crop [3,4,5]. Salinity is a significant constraint that reduces chickpea production by 8-10 per cent at a global scale— a static which is increasingly alarming in the context of growing population and climate challenged food security [7,8,9,10]. Considerable breeding efforts have been made to underpin the salt tolerance traits; confounding effects of abiotic stress during the field trials and the polygenic nature of salt stress have rendered these approaches inadequate to uncover the intricate nature of complex gene networks. Due to continued climatic shifts, these QTLs ought to be unstable and far could not be deployed in crop breeding programs to improve salt tolerance and develop new crop varieties

Methods

Results

Conclusion