Evolutionary, structural and expression analysis of core genes involved in starch synthesis

Qu, Jianzhou; Xu, Shutu; Zhang, Zhengquan; Chen, Guangzhou; Zhong, Yuyue; Liu, Linsan; Zhang, Renhe; Xue, Jiquan; Guo, Dongwei

doi:10.1038/s41598-018-30411-y

Cited by 95 publications

(101 citation statements)

References 80 publications

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“…Invertases catalyze the irreversible breakdown of sucrose into glucose and fructose. For a comprehensive view of starch synthesis see [45][46][47][48].…”

Section: Following the Cycle Of Carbon In Plants: From Carbon Fixatiomentioning

confidence: 99%

Plant Cell Walls Tackling Climate Change: Biotechnological Strategies to Improve Crop Adaptations and Photosynthesis in Response to Global Warming

Ezquer

Salameh

Colombo

et al. 2020

Plants

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Plant cell wall (CW) is a complex and intricate structure that performs several functions throughout the plant life cycle. The CW of plants is critical to the maintenance of cells' structural integrity by resisting internal hydrostatic pressures, providing flexibility to support cell division and expansion during tissue differentiation, and acting as an environmental barrier that protects the cells in response to abiotic stress. Plant CW, comprised primarily of polysaccharides, represents the largest sink for photosynthetically fixed carbon, both in plants and in the biosphere. The CW structure is highly varied, not only between plant species but also among different organs, tissues, and cell types in the same organism. During the developmental processes, the main CW components, i.e., cellulose, pectins, hemicelluloses, and different types of CW-glycoproteins, interact constantly with each other and with the environment to maintain cell homeostasis. Differentiation processes are altered by positional effect and are also tightly linked to environmental changes, affecting CW both at the molecular and biochemical levels. The negative effect of climate change on the environment is multifaceted, from high temperatures, altered concentrations of greenhouse gases such as increasing CO 2 in the atmosphere, soil salinity, and drought, to increasing frequency of extreme weather events taking place concomitantly, therefore, climate change affects crop productivity in multiple ways. Rising CO 2 concentration in the atmosphere is expected to increase photosynthetic rates, especially at high temperatures and under water-limited conditions. This review aims to synthesize current knowledge regarding the effects of climate change on CW biogenesis and modification. We discuss specific cases in crops of interest carrying cell wall modifications that enhance tolerance to climate change-related stresses; from cereals such as rice, wheat, barley, or maize to dicots of interest such as brassica oilseed, cotton, soybean, tomato, or potato. This information could be used for the rational design of genetic engineering traits that aim to increase the stress tolerance in key crops. Future growing conditions expose plants to variable and extreme climate change factors, which negatively impact global agriculture, and therefore further research in this area is critical.

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“…Invertases catalyze the irreversible breakdown of sucrose into glucose and fructose. For a comprehensive view of starch synthesis see [45][46][47][48].…”

Section: Following the Cycle Of Carbon In Plants: From Carbon Fixatiomentioning

confidence: 99%

Plant Cell Walls Tackling Climate Change: Biotechnological Strategies to Improve Crop Adaptations and Photosynthesis in Response to Global Warming

Ezquer

Salameh

Colombo

et al. 2020

Plants

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“…The starch metabolism process is a metabolic process mainly based on energy reserves. In addition, starch biosynthesis is a complex and highly regulated process that requires coordinated activities among multiple enzymes, and different isozymes exert different effects (Jeon et al, 2010;Qu et al 2018). We analysed core genes of starch synthesis and found that the main differences in the expression patterns of 28 core genes between SD609 and HS68 were observed at 10 and 15 DAP, and the expression transition patterns of some core genes agree with the reported expression patterns (Fig.…”

Section: Discussionsupporting

confidence: 78%

“…5). We searched the core genes involved in starch synthesis in all the modules based on a previous study (Qu et al 2018). In total, 19 of the 28 core genes associated with starch synthesis were differentially expressed and were distributed among 10 modules, including Plum (AGPLS1), Plum_1 (SSIIa), Steel_blue (AGPLS4), Blue (SBEIIb and SSIV), Dark_magenta (su1), Dark_orange (SBEI, SBEIII and SSIIIb-b), Dark_violet (SSIIb), Grey_60 (AGPLS2, AGPSS3, PUL and SSI), Maroon (SSIIIb-a) and Orange-red_3 (AGPSS1, GBSSI, GBSSII and SSIIIa) ( Fig.…”

Section: Identification Of Weighted Gene Coexpression Network Analysimentioning

confidence: 99%

Untitled

Supplemental Information 13: GO Enrichment Analysis of the DEGs of SD609 and HS68

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The endosperm is a crucial organ for seeds that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ~70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15-and 20-day after pollination and found that 21,986 genes are involved in the programming of the highamylose maize and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated cellular and metabolic programs and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors (TFs) were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize.

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“…5). We searched the core genes involved in starch synthesis in all the modules based on a previous study (Qu et al 2018). In total, of the 28 core genes associated with starch synthesis were differentially expressed and were distributed among modules, namely, Plum (AGPLS1), Plum_1 (SSIIa), Steel_blue (AGPLS4), Blue (SBEIIb and SSIV), Dark_magenta (su1), Dark_orange (SBEI, SBEIII and SSIIIb-b), Dark_violet (SSIIb), Grey_60 (AGPLS2, AGPSS3, PUL and SSI), Maroon (SSIIIb-a) and Orange-red_3 (AGPSS1, GBSSI, GBSSII and SSIIIa) ( Fig.…”

Section: Identification Of Weighted Gene Coexpression Network Analysimentioning

confidence: 99%

“…The starch metabolism process is a metabolic process mainly based on energy reserves. In addition, starch biosynthesis is a complex and highly regulated process that requires coordinated activities among multiple enzymes, and different isozymes exert different effects (Jeon et al, 2010;Qu et al 2018). We analysed the core genes of starch synthesis and found that the main differences in the expression patterns of 28 core genes between SD609 and HS68 were observed at 10 and 15…”

Section: Manuscript To Be Reviewedmentioning

confidence: 99%

Peer Review #2 of "Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents (v0.1)"

2019

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In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ~70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15-and 20-day after pollination and found that 21,986 genes are involved in the programming of the highamylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.

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Evolutionary, structural and expression analysis of core genes involved in starch synthesis

Cited by 95 publications

References 80 publications

Plant Cell Walls Tackling Climate Change: Biotechnological Strategies to Improve Crop Adaptations and Photosynthesis in Response to Global Warming

Plant Cell Walls Tackling Climate Change: Biotechnological Strategies to Improve Crop Adaptations and Photosynthesis in Response to Global Warming

Untitled

Peer Review #2 of "Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents (v0.1)"

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