Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors

Abstract

Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage–specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.

Potential of Wild Relatives of Wheat: Ideal Genetic Resources for Future Breeding Programs

“…Progress in biotechnological tools, such as the GeneChip ® Wheat Genome array and RNA sequencing, have indicated that the transcripts associated with starch biosynthesis and defense proteins in hexaploid bread wheat are expressed 2-3 weeks after anthesis. The transcripts that are most numerous in growing plants, on the other hand, were associated with storage proteins that are expressed during the developmental phase [198][199][200][201]. While transcriptome analysis was done in hexaploid wheat during grain production [202,203], bread wheat and its wild progenitors have yet to be subjected to a thorough transcriptional characterization.…”

“…This will be useful to understand the changes in wheat grain consistency that occurred during the transition from ancient bread wheat to modern bread wheat. Kaushik et al [201] used RNAseq to study the development of bread wheat grains and their diploid progenitor cells to evaluate gene expression patterns and monitor differentially expressed genes. To analyze gene expression profiles and screen differentially expressed genes, they used transcriptomics methods to compare the expression of key genes in hexaploid bread wheat and its three diploid parents during the entire grain production process.…”

“…Grain production is critical for completing a crop's life cycle because it accumulates various nutrient stocks as well as embryo development and maturation. The nutritional and economic value of wheat grain is determined by the accumulation of these nutrient stocks [201].…”

“…Glutenins and gliadins are two types of gluten. Glutenins are often made up of proteins with high and low molecular weights [201,208]. Prior research has revealed that the glutenin and gliadin subunits of wild wheat relatives varied greatly.…”

“…speltoides (BB) shared the most transcripts of the three progenitors. When sub-genomic research was performed, it was discovered that the number of transcripts in hexaploid bread wheat's B genome was somewhat greater [201].…”