RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response

Abstract

Heat stress is one of the significant constraints affecting wheat production worldwide. To ensure food security for ever-increasing world population, improving wheat for heat stress tolerance is needed in the presently drifting climatic conditions. At the molecular level, heat stress tolerance in wheat is governed by a complex interplay of various heat stress-associated genes. We used a comparative transcriptome sequencing approach to study the effect of heat stress (5°C above ambient threshold temperature of 20°C) during grain filling stages in wheat genotype K7903 (Halna). At 7 DPA (days post-anthesis), heat stress treatment was given at four stages: 0, 24, 48, and 120 h. In total, 115,656 wheat genes were identified, including 309 differentially expressed genes (DEGs) involved in many critical processes, such as signal transduction, starch synthetic pathway, antioxidant pathway, and heat stress-responsive conserved and uncharacterized putative genes that play an essential role in maintaining the grain filling rate at the high temperature. A total of 98,412 Simple Sequences Repeats (SSR) were identified from de novo transcriptome assembly of wheat and validated. The miRNA target prediction from differential expressed genes was performed by psRNATarget server against 119 mature miRNA. Further, 107,107 variants including 80,936 Single nucleotide polymorphism (SNPs) and 26,171 insertion/deletion (Indels) were also identified in de novo transcriptome assembly of wheat and wheat genome Ensembl version 31. The present study enriches our understanding of known heat response mechanisms during the grain filling stage supported by discovery of novel transcripts, microsatellite markers, putative miRNA targets, and genetic variant. This enhances gene functions and regulators, paving the way for improved heat tolerance in wheat varieties, making them more suitable for production in the current climate change scenario.

RNA-Seq Transcriptome Profiling of Immature Grain Wheat: A Comparative Modeling of Baking Quality

“…Our results indicated that TraesCS2A01G483600 (encodes Elongation factor 1-alpha) expressed only in "O-64.1.10" genotypes (Paul et al, 2022). suggested that Elongation factor 1-alpha gene play an important role in cell expansion in early developmental wheat grain.…”

RNA-Seq transcriptome profiling of immature grain wheat is a technique for understanding comparative modeling of baking quality

“…5 ), were up-regulated compared to the wild-type (Table 4 ). Elongation factor 1-alpha (EF1α) play a crucial role in the protein synthesis machinery of cells, and its function extends to various physiological processes in plants, including wheat 48 . Our results indicated that this gene were highly expressed in “O-64.1.10” genotype.…”

“…Identifying genes expressed during the grain filling stage can be useful for improving yield and grain quality 17 , 18 . Several studies have applied transcriptomics approaches to investigate the gene expression during grain development stages in wheat 2 , 15 – 17 , 19 – 21 . The grain development process of wheat can be categorized into three stages, including cell division and expansion (0 ~ 14 DPA (days post-anthesis)), effective grain filling (14 ~ 28 DPA), and maturation and desiccation (28 DPA to maturity) 22 .…”

P53 expression, Genome-wide transcriptome profiling and LGS test (a blood test to detect cancer): comparison of UVA exposed lymphocytes from malignant melanoma patients and healthy controls.

“…Sequence data can be aligned to a reference genome to build full-length transcripts. Transcriptome sequencing data can be used to de ne novel transcripts, leading to the discovery of neoantigens (Triulzi et al, 2015, Paul et al, 2022 In this assay, the transcriptional changes are assessed only in a limited number of genes during tissue culture (ex-vivo). Changes are mainly seen in genes involved in biological processes, whose molecular function can affect the stabilisation or regulation of cellular compartments.…”