Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

Abstract

BackgroundThere is an urgent need to increase global crop production. Identifying and combining specific genes controlling distinct biological processes holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially regulated genes and pathways that potentially influence pericarp cell size and grain weight in wheat.ResultsWe sampled grains at 4 and 8 days post anthesis and found that genes associated with metabolism, biosynthesis, proteolysis and the defence response are upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts differentially expressed (DE) between 5A NILs at either time point, including eight potential candidates for the causal 5A gene and its downstream targets. The 112 DE transcripts had functional annotations including non-coding RNA, transposon-associated, cell-cycle control, ubiquitin-related, heat-shock, transcription and histone-related. Many of the genes identified belong to families that have been previously associated with seed/grain development in other species. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT-HOOK and Trihelix transcription factor families.ConclusionsIn this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Few of these are the direct orthologues of grain size genes in other species and none have been previously characterised in wheat. Further functional characterisation of these candidates and how they interact will provide novel insights into the control of grain size in cereals.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1241-5) contains supplementary material, which is available to authorized users.

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

“…This is possibly due in part to the study being carried out before the advent of a complete wheat genome annotation, relying instead on mapping of transcriptome assemblies to incomplete chromosome contigs. We have shown previously that earlier gene annotations could be incomplete or mis-annotated ( Brinton et al 2018 ). However, this discrepancy in numbers of differentially expressed genes is most likely a result of the more liberal significance cut-off used in the current study, as compared to the stringent combination of four statistical tests which were used to reduce false positive discoveries in the original study ( Pearce et al 2014 ).…”

TaDA1, a conserved negative regulator of kernel size, has an additive effect with TaGW2 in common wheat (Triticum aestivum L.)

“…Expansin A7 was also found to be up-regulated in GW2-Ri-3 ( Figure 7d). The expansin proteins are highly related to cell expansion, and expansin-like A1 was the first verified substrate of GW2 in rice (Choi et al, 2018). Furthermore, several crucial proteins involved in starch synthesis are also up-regulated in GW2-Ri-3, including ADP-glucose brittle-1 transporter precursor and sucrose synthase 1 (Figure 7d).…”

“…The ubiquitin-proteasome pathway plays a key role in controlling organ size in dicot and monocot plants (Brinton et al, 2018;Li and Li, 2016;Shi et al, 2019). Recently, increasing evidence has indicated that the ubiquitin receptor DA1, a conserved component of the ubiquitin-proteasome pathway, has important functions in regulating seed size.…”

“…The RING finger-type E3 ubiquitin ligases BIG BROTHER (BB) and DA2 restrict organ growth (Disch et al, 2006;Xia et al, 2013) and function synergistically with DA1 in organ size determination (Li et al, 2008;Xia et al, 2013). A recent study showed that BB and DA2 ubiquitylate DA1 and activate its peptidase activity, and then activated DA1 cleaves and destabilizes BB and DA2 in a feedback mechanism (Dong et al, 2017).…”

First the seed: Genomic advances in seed science for improved crop productivity and food security

“…For instance, comparative transcriptomic research between wheat lines with contrasting seed size and weight in both early and maturation phases identified candidate regulators of seed size and weight a number of markers such as ubiquitin‐related proteins, transposon‐associated and cell cycle control genes, and genes involved in carbohydrate and starch biosynthetic processes (Brinton et al. 2018; Yamasaki et al. 2017; Yan et al.…”