Gene Expression analysis associated with salt stress in a reciprocally crossed rice population

Samsad Razzaque,Sudip Biswas,Abdelbagi M Ismail,Harkamal Walia,Sazzadur Rahman,Zeba I Seraj,Taslima Haque,Xiaoyu Weng,Thomas E Juenger,Sabrina M Elias,G M Nurnabi Azad Jewel

doi:10.1038/s41598-019-44757-4

Abstract

The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed Horkuch with high yielding but salt sensitive IR29 to detect the complement of genes that were responsible for conferring salt tolerance versus sensitivity at the seedling developmental stage. We looked at tolerant and sensitive F3 families from individual F2 segregating plants and analyzed them for differential gene expressions using RNAseq. In general, we observed higher numbers of genes differentially expressed in leaves compared to root tissues. This included both upregulation and downregulation of gene expression across our experimental factors. Gene expression decreased in sensitive leaf after stress exposure where tolerant plants showed the opposite trend. In root, tolerant plants expression decreased at higher time points of stress exposure. We also observed a strong maternal cytoplasmic effect on gene expression and this was most evident in roots where there was upregulation in functional enrichments related to phosphorylation, electron carriers, transporter and cation transmembrane activities. Stress groups (tolerant and sensitive) response in F3 families were distinctive in both cytoplasmic backgrounds and involved uniquely upregulated genes in tolerant progenies including membrane sensor proteins, enzymes involved with signaling pathways, such as those producing trehalose and G-protein coupled receptor proteins, photosynthesis-related enzymes and golgi body recycling as well as prolamin precursor proteins involved in refolding of proteins. On the other hand, sensitivity was found to be associated with differential upregulation of only a few redox proteins and higher number of apoptosis related genes compared to the tolerant response. Overall, our highly replicated experimental design was powerful and allowed the detection of relatively subtle differential expression. Our future goal is to correlate these expression differences with QTLs in this population, which would help identify the relative importance of specific genetic loci and provide a direct avenue for combining higher levels of salt tolerance with better agronomic traits in rice.

Highlights

1 million ha of coastal soil in Bangladesh or nearly a ninth of the total cultivable area is affected by soil salinity, mostly due to sea-water intrusion[1]
In addition to its toxicity, sodium itself has been proposed to function as a signaling molecule of salt stress after perception by non-selective cation channels (NSCC) of the depolarization type, which acts in a few seconds in the membrane[23,24]
The rice landrace, Horkuch was grouped with aromatic rice and is divergent from the common indica salt tolerance donors such as Pokkali and Nona Bokra used in breeding lines developed at IRRI and in Bangladesh[16]

Summary

Introduction

1 million ha of coastal soil in Bangladesh or nearly a ninth of the total cultivable area is affected by soil salinity, mostly due to sea-water intrusion[1]. During the dry season water levels are usually low due to upper riparian withdrawal as well as its overexploitation, causing a build-up of salts These coastal areas are home to many salt tolerant rice landraces, including both indica and aromatic subgroups, which have allelic diversity at several genetic loci associated with tolerance from donor landraces like Pokkali and Nona Bokra[3,4]. A common mechanism for salt tolerance in rice is maintenance of lower shoot Na+ content[15,16], which can be due to sodium exclusion[17], effective sequestration of toxic salts into older leaves[18,19] and roots[20] and compartmentalization and extrusion of Na+ into vacuoles and out of cells[21] Despite these common physiological trends in response to salt stress in tolerant rice cultivars, there is wide variability in injury scores and the amount of Na+ in the seedling, the 3rd leaf referred to as 3leafNa22. An ideal strategy for accomplishing these goals would be to recombine genetic loci controlling this variation in genetic mapping populations

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