Gene Expression in the Developing Seed of Wild and Domesticated Rice

Abstract

The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

“…(b) The transcriptional expression of Blp1 and Blp2 homologous genes in the husk/pericarp tissues of BNIL and YNIL at green (early milk stage, S1) and black grain stages (late milk, S3). (c) The transcriptional profiles of Blp1 and Blp2 homologous genes in the panicles of black‐coloured rice genotypes Oryza meridionalis and Oryza rufipogon , and non‐black genotype Nipponbare at several stages after days post anthesis (Hasan et al ., 2022 ). (d) The expression levels of Blp1 and Blp2 homologous genes in the husk/pericarp samples of black‐coloured durum wheat at green (early milk stage, S1) and black grain stages (late milk, S3).…”

“…Of these, the content of L‐tyrosine was significantly correlated with the expression level of HvBlp , implying that HvBlp functions as an L‐tyrosine transporter, which is similar to the observation of OsBh4 (Zhu et al ., 2011 ). Among the identified 42 DETs, 3 candidate genes encoding polyphenol oxidase (PPO) ( novel2290.t1 ), cytochrome P450 ( Horvu_13821_1H01G537900.1 ) and peroxidase (POD) ( Horvu_13821_3H01G432900 ), respectively (Figure 6 ), were identified for their oxidative functions, highly consistent with previous suggestions that PPO is critical for melanin production (Glagoleva et al ., 2020 ; Hasan et al ., 2022 ). In addition, three heat shock protein 20 (HSP20) ( Horvu_13821_3H01G128600 , Horvu_13821_3H01G128700 and Horvu_13821_4H01G094500 ) and four glutathione S‐transferases (GSTs) ( Horvu_13821_1H01G293500 , Horvu_13821_3H01G577000 , Horvu_13821_4H01G304400 and Horvu_13821_5H01G571200 ), involving in ‘protein processing in endoplasmic reticulum’ and ‘glutathione metabolism’ pathways, respectively, were identified, which may be involved in metabolite translocation.…”