Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

Yu, Yonglong; Zhu, Dong; Ma, Chao; Cao, Hui; Wang, Yaping; Xu, Yonghong; Zhang, Wenying; Yan, Yueming

doi:10.1016/j.cj.2016.01.006

Cited by 66 publications

(49 citation statements)

References 54 publications

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“…As grain development progresses, genes associated with transport, proteolysis, carbohydrate metabolism and starch synthesis are upregulated, in addition to genes encoding storage proteins (Laudencia‐Chingcuanco et al ; Pellny et al ; Ma et al ; Pfeifer et al ; Yu et al ). Interestingly, many studies have shown that genes with stress and defense‐related ontologies are also upregulated during grain development (Laudencia‐Chingcuanco et al ; Nadaud et al ; Capron et al ; Ma et al ; Brinton et al ).…”

Section: Genetic Control Of Grain Weightmentioning

confidence: 99%

A reductionist approach to dissecting grain weight and yield in wheat

Brinton

Uauy

2019

JIPB

137

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Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub‐components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on‐farm yield.

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Section: Genetic Control Of Grain Weightmentioning

confidence: 99%

A reductionist approach to dissecting grain weight and yield in wheat

Brinton

Uauy

2019

JIPB

137

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“…During this stage, increases in grain size are largely driven by cell expansion in the pericarp [54, 55], consistent with our previous finding that increased pericarp cell size underlies the difference in final grain length. These time points are also relatively early compared to other grain related RNA-seq studies which have focused on later grain filling processes [36, 56, 35]. The ‘across time’ comparisons ( and ) identified > 2,700 DE transcripts in each NIL, and there was a large overlap in the biological processes being differentially regulated.…”

Section: Discussionmentioning

confidence: 84%

“…However, these studies have mostly focused on the later stages of grain development, often focusing on starch accumulation in the endosperm. Additionally, many of these studies were performed using microarrays [33, 36, 37], which represent a fraction of the transcriptome and are unable to distinguish between homoeologous gene copies. More recent studies have used RNA-seq [35, 34], which is an open-ended platform that provides homoeolog specific resolution.…”

Section: Introductionmentioning

confidence: 99%

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

Brinton

Simmonds

Uauy

2017

Preprint

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BackgroundThere is an urgent need to increase global crop production. Identifying and combining genes controlling indidviual yield components, such as grain weight, 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 expressed (DE) genes and pathways that potentially influence pericarp cell size and grain weight in wheat.ResultsWe sampled grains at four and eight days post anthesis and found genes associated with metabolism, biosynthesis, proteoloysis and defence response to be upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts DE between 5A NILs at either time point, including seven potential candidates for the causal gene underlying the 5A QTL. The 112 DE transcripts had functional annotations including non-coding RNA, transpon-associated, cell-cycle control, and ubiquitin-related processes. Many of the wheat genes identified belong to families that have been previously associated with seed/grain development in other species. However, few of these wheat genes are the direct orthologs and none have been previously characterised in wheat. 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. Further functional characterisation of these candidates and how they interact could provide new insights into the control of grain size in cereals, ultimately improving crop yield.

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“…This suggests that high-N fertilization can increase the accumulation of photosynthetic products under water-deficit conditions by enhancing the photosynthetic capacity of wheat flag leaves, particularly at the early grain-filling stages. Significantly, previous genome-wide transcriptional profiling analysis showed that the period from 11-15 DPA was more critical than the 15-20 DPA stage for the synthesis and accumulation of nutritive reserves [70]. In addition, two DAPs involved in energy and carbohydrate metabolism (FBA and GAPDH) upregulated in the combined treatment were also upregulated in the high-N treatment (Table 1).…”

Section: Daps Responsive To Combining Water-deficit and High-n Treatmmentioning

confidence: 85%

Effects of Independent and Combined Water-Deficit and High-Nitrogen Treatments on Flag Leaf Proteomes during Wheat Grain Development

Zhu

Zhang

et al. 2020

IJMS

Self Cite

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We present the first comprehensive proteome analysis of wheat flag leaves under water-deficit, high-nitrogen (N) fertilization, and combined treatments during grain development in the field. Physiological and agronomic trait analyses showed that leaf relative water content, total chlorophyll content, photosynthetic efficiency, and grain weight and yield were significantly reduced under water-deficit conditions, but dramatically enhanced under high-N fertilization and moderately promoted under the combined treatment. Two-dimensional electrophoresis detected 72 differentially accumulated protein (DAP) spots representing 65 unique proteins, primarily involved in photosynthesis, signal transduction, carbohydrate metabolism, redox homeostasis, stress defense, and energy metabolism. DAPs associated with photosynthesis and protein folding showed significant downregulation and upregulation in response to water-deficit and high-N treatments, respectively. The combined treatment caused a moderate upregulation of DAPs related to photosynthesis and energy and carbohydrate metabolism, suggesting that high-N fertilization can alleviate losses in yield caused by water-deficit conditions by enhancing leaf photosynthesis and grain storage compound synthesis.

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Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

Cited by 66 publications

References 54 publications

A reductionist approach to dissecting grain weight and yield in wheat

A reductionist approach to dissecting grain weight and yield in wheat

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

Effects of Independent and Combined Water-Deficit and High-Nitrogen Treatments on Flag Leaf Proteomes during Wheat Grain Development

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