Programmed Cell Death in Developing Brachypodium distachyon Grain

Abstract

The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species such as barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of the wild model species Brachypodium distachyon. We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified in Brachypodium the orthologs of protease genes known to contribute to grain PCD and surveyed their expression. We found that, similar to cereals, PCD in the Brachypodium nucellus occurs in a centrifugal pattern following anthesis. However, compared to cereals, the rate of post-mortem clearance in the Brachypodium nucellus is slower. However, compared to wheat and barley, mesocarp PCD in Brachypodium proceeds more rapidly in lateral cells. Remarkably, Brachypodium mesocarp PCD is not coordinated with endosperm development. Phylogenetic analysis suggests that barley and wheat possess more vacuolar processing enzymes that drive nucellar PCD compared to Brachypodium and rice. Our expression analysis highlighted putative grain-specific PCD proteases in Brachypodium. Combined with existing knowledge on grain PCD, our study suggests that the rate of nucellar PCD moderates grain size and that the pattern of mesocarp PCD influences grain shape.

Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon

“…We downloaded the RNA-seq data of E-MTAB-4400 on https://www.ebi.ac.uk/gxa/experiments/E-MTAB-4400/Results (accessed on 1 November 2023), E-MTAB-4401 https://www.ebi.ac.uk/gxa/experiments/E-MTAB-4401 /Results (accessed on 1 November 2023), and E-MTAB-2039 https://www.ebi.ac.uk/gxa/ experiments/E-MTAB-2039/Results (accessed on 1 November 2023) for Sorghum bicolor BTx623, B. distachyon Bd21, and Oryza sativa japonica (Nipponbare), respectively [34]. We also used RNA-seq data from E-MTAB-7607 https://www.ebi.ac.uk/gxa/experiments/ E-MTAB-7607/Results (accessed on 1 November 2023) to assay the B. distachyon Bd21 expression of TLP genes at grain development and germination [36]. Expression profiles were generated using the heatmap function from the ggplot2 package [52] with default parameters.…”

“…Based on the cis-acting elements analysis, BdTLPs may be involved in light, hormone, and development responses. To investigate the expression patterns of the B. distachyon TLPs across development, we analyzed three publicly available RNA-Seq datasets [34,36]. The three poaceae species' (B. distachyon B21, O. sativa japonica var.…”

“…The expression data BdTLPs have diverse functional roles. To further explore the putative expression of BdTLPs, we retrieved and analyzed the public expression RNA-seq data, as described in Materials and Methods, from young grains to germinating grains and young seedlings (Figure 4a) [36]. Most BdTLP genes are upregulated in germinating grains and young seedlings.…”

“…Several studies focused on TLPs in many monocot plant species, but none included the model B. distachyon [9,17,20,21,23]. Here, we studied the B. distachyon TLP (BdTLP) gene family to obtain an insight into how BdTLPs evolved to other monocots and infer their function from high-throughput experiments [34][35][36]. In addition, we explored BdTLPs' natural variation of 11 inbred lines to deduce diversity in rice and sorghum and to identify the amino acids affecting the protein structure.…”

Killing me softly - Programmed cell death in plant reproduction from sporogenesis to fertilization

“…In contrast to domesticated cereals, nucellar projection PCD in Brachypodium (Brachypodium distachyon) occurs slower, suggesting that domestication selected for a rapid nucellar projection cell death to allow more extensive endosperm expansion. Interestingly, Brachypodium lacks direct VPE2 orthologs, which might explain slower nucellar projection breakdown rates in this wild relative of barley and wheat [48].…”