The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development

Abstract

Modern wheat production comes from two polyploid species, Triticum aestivum and Triticum turgidum (var durum), which putatively arose from diploid ancestors Triticum urartu, Aegilops speltoides, and Aegilops tauschii. How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid genomes through hybridization, polyploidization, and breeding selection is not well understood. This study describes the global landscape of gene activities during wheat embryogenesis and grain development. Using comprehensive transcriptomic analyses of two wheat cultivars and three diploid grasses, we investigated gene expression at seven stages of embryo development, two endosperm stages, and one pericarp stage. We identified transcriptional signatures and developmental similarities and differences among the five species, revealing the evolutionary divergence of gene expression programs and the contributions of A, B, and D subgenomes to grain development in polyploid wheats. The characterization of embryonic transcriptional programming in hexaploid wheat, tetraploid wheat, and diploid grass species provides insight into the landscape of gene expression in modern wheat and its ancestral species. This study presents a framework for understanding the evolution of domesticated wheat and the selective pressures placed on grain production, with important implications for future performance and yield improvements.

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

“…The final data set containing non-redundant B0 and Bplus transcripts (117,441 contigs in total) was screened using Transdecoder v5.3.0 to predict open reading frames and resulted in 61,817 protein-coding transcripts. Such a high number of transcripts is in line with previous findings [ 13 ], where a global gene expression atlas of developing embryos of wheat and their putative diploid ancestors including Ae. speltoides was provided.…”

Multi-Locus GWAS of Quality Traits in Bread Wheat: Mining More Candidate Genes and Possible Regulatory Network

“…TPM values of candidate genes in the six tissues (root, leaf, peduncle, awn, glume and grain) were downloaded from the wheat expression database ( ) ( Ramírez-González et al., 2018 ). Recently reported transcriptome data of embryo, endosperm and seed coat during wheat grain development were also used to analyze expression patterns of candidate genes to identify the possible regulatory network ( Xiang et al., 2019 ).The original read count number matrix was obtained from the supplemental data of Xiang’s paper, and the TPM value was calculated using TBtools. Also, previous reports on QTLs and identified genes associated with quality traits of wheat and rice were used to select the candidate genes.…”

“…Overall, genes involved in protein synthesis and metabolism, sugar synthesis and metabolism, protein/sugar transporter, histone modification, ribosome-related and transcription factor accounted for a large proportion, which may significantly affect the development of grain and the formation of quality traits ( Figure 5). To further speculate the possible roles of these candidate genes in the formation of wheat grain quality, a published RNA-seq dataset of wheat grain development was used to identify the expression characteristics of these genes in different parts of the grain ( Supplementary Table S7) (Xiang et al, 2019). More than 70% (223/318) of candidate genes were preferentially expressed in endosperm, and they were mainly concentrated in sugar/protein synthesis, storage substance protection, transcription factors, histone modifications, biotic/ abiotic stress response and ribosomal-related functional categories ( Figure 5).…”

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

“…Shoot apical meristem (SAM), root apical meristem (RAM), suspensor (Su), coleoptile (Cp), scutellum (Sc), epiblast (Ep), and coleorhiza (Cr), based on Souèges (1924) , Van Lammeren (1986) , Itoh et al. (2005) , and Xiang et al. (2019) .…”