Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Abstract

Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. Conclusion The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

Early responses to salt stress in quinoa genotypes with opposite behavior

“…The osmotic component of the salt stress is believed to dominate at initial stages (several days at least; Munns, 2005), and our findings are in agreement with the fact that the early signaling events in the osmotic phase occur within seconds to hours after salt stress exposure (Duarte-Delgado et al, 2020).Our analysis highlights the co-up-regulation (with a FC of more than 3) of a gene coding for a NAC domain-containing protein (AUR62015630) and three NCED genes (AUR62002735, AUR62037951, AUR62043087) in the shoots of the sensitive Q30. It has been already reported that drought and salt stress caused the induction of NAC domain-containing transcription factors (Iovieno et al, 2016;Shi & Gu, 2020).…”

“…Here, genes typically involved in the drought response (Balestrini et al, 2019; Iovieno et al, 2016) were found to be regulated. The osmotic component of the salt stress is believed to dominate at initial stages (several days at least; Munns, 2005), and our findings are in agreement with the fact that the early signaling events in the osmotic phase occur within seconds to hours after salt stress exposure (Duarte‐Delgado et al, 2020). Our analysis highlights the co‐up‐regulation (with a FC of more than 3) of a gene coding for a NAC domain‐containing protein (AUR62015630) and three NCED genes (AUR62002735, AUR62037951, AUR62043087) in the shoots of the sensitive Q30.…”

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

“…The STEM clustering method was applied to analyze the expression patterns of DEGs in the bovine mammary gland during the period of lactation decline [ 14 , 32 ]. Each gene was assigned to the closest profile using a Pearson correlation-based distance metric.…”

Genetic Insight Into the Insect Resistance in Bread Wheat Exploiting the Untapped Natural Diversity

“…We, therefore, conclude that these resistance loci can be a potential starting point to impart environment friendly and climate smart WBM resistance in wheat. In addition, arrival of many new technologies such as MACE (Massive Analysis of cDNA 3′ ends) and RNA -sequencing (Duarte-Delgado et al, 2020) may help to understand the mechanisms behind the resistance loci being reported.…”