Research

15 pages, 3302 KiB

Open AccessArticle

Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans

by Anmin Yu, Zekun Zhou, Yizhong Chen, Jing Sun, Ping Li, Xu Gu and Aizhong Liu

Int. J. Mol. Sci. 2024, 25(1), 92; https://doi.org/10.3390/ijms25010092 - 20 Dec 2023

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Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute [...] Read more.

Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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18 pages, 4634 KiB

Open AccessArticle

Efficient Accumulation of Amylopectin and Its Molecular Mechanism in the Submerged Duckweed Mutant

by Yu Liu, Ruiting Yan, Zonghao Li, Shusheng Fan, Chuantong Li, Ruikang Yu, Huaqing Liu, Yingzhen Kong, Haimei Li, Xianfeng Tang and Gongke Zhou

Int. J. Mol. Sci. 2023, 24(3), 2934; https://doi.org/10.3390/ijms24032934 - 02 Feb 2023

Cited by 1 | Viewed by 1681

Abstract

Large-scale use of fossil fuels has brought about increasingly serious problems of environmental pollution, development and utilization of renewable energy is one of the effective solutions. Duckweed has the advantages of fast growth, high starch content and no occupation of arable land, so [...] Read more.

Large-scale use of fossil fuels has brought about increasingly serious problems of environmental pollution, development and utilization of renewable energy is one of the effective solutions. Duckweed has the advantages of fast growth, high starch content and no occupation of arable land, so it is a promising starchy energy plant. A new submerged duckweed mutant (sub-1) with abundant starch accumulation was obtained, whose content of amylopectin accounts for 84.04% of the starch granules. Compared with the wild type (Lemna aequinoctialis), the branching degree of starch in sub-1 mutant was significantly increased by 19.6%. Chain length DP 6–12, DP 25–36 and DP > 36 of amylopectin significantly decreased, while chain length DP 13–24 significantly increased. Average chain length of wild-type and sub-1 mutant starches were greater than DP 22. Moreover, the crystal structure and physical properties of starch have changed markedly in sub-1 mutant. For example, the starch crystallinity of sub-1 mutant was only 8.94%, while that of wild-type was 22.3%. Compared with wild type, water solubility of starch was significantly reduced by 29.42%, whereas swelling power significantly increased by 97.07% in sub-1 mutant. In order to further analyze the molecular mechanism of efficient accumulation of amylopectin in sub-1 mutant, metabolome and transcriptome were performed. The results showed that glucose accumulated in sub-1 mutant, then degradation of starch to glucose mainly depends on α-amylase. At night, the down-regulated β-amylase gene resulted in the inhibition of starch degradation. The starch and sucrose metabolism pathways were significantly enriched. Up-regulated expression of SUS, AGPase2, AGPase3, PYG, GPI and GYS provide sufficient substrate for starch synthesis in sub-1 mutant. From the 0H to 16H light treatment, granule-bound starch synthase (GBSS1) gene was inhibited, on the contrary, the starch branching enzyme (SBE) gene was induced. Differential expression of GBSS1 and SBE may be an important reason for the decrease ratio of amylose/amylopectin in sub-1 mutant. Taken together, our results indicated that the sub-1 mutant can accumulate the amylopectin efficiently, potentially through altering the differential expression of AGPase, GBSS1, SBE, and BAM. This study also provides theoretical guidance for creating crop germplasm with high amylopectin by means of synthetic biology in the future. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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17 pages, 5519 KiB

Open AccessArticle

Genome-Wide Comparative Analysis of the Fasciclin-like Arabinogalactan Proteins (FLAs) in Salicacea and Identification of Secondary Tissue Development-Related Genes

by Yingying Zhang, Fangwei Zhou, Hui Wang, Yingnan Chen, Tongming Yin and Huaitong Wu

Int. J. Mol. Sci. 2023, 24(2), 1481; https://doi.org/10.3390/ijms24021481 - 12 Jan 2023

Cited by 3 | Viewed by 2128

Abstract

Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) containing both AGP-like glycated domains and fasciclin (FAS) domains, which are involved in plant growth and development and synthesis of the cell wall. However, these proteins have not been identified or analyzed [...] Read more.

Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) containing both AGP-like glycated domains and fasciclin (FAS) domains, which are involved in plant growth and development and synthesis of the cell wall. However, these proteins have not been identified or analyzed in willow, Salix, the sister genus of Populus. In this study, we performed a whole genome study of the FLA gene family of Salix suchowensis and compared it with the FLA gene family of Populus deltoides. The results showed the presence of 40 and 46 FLA genes in P. deltoides and S. suchowensis, distributed on 17 and 16 chromosomes, respectively. Four pairs of tandem repeat genes were found in willow, while poplar had no tandem repeat genes. Twelve and thirteen pairs of duplicated gene fragments were identified in poplar and willow, respectively. The multispecies phylogenetic tree showed that the FLA gene family could be divided into four groups (I–IV), with Group 1 showing significant expansion in woody plants. A gene expression analysis showed that PdeFLA19/27 in Group I of poplar was highly expressed, specifically during the secondary growth period of the stem and the rapid elongation of seed hairs. In the Group I genes of S. suchowensis, SsuFLA25/26/28 was also highly expressed during the secondary growth period, whereas increased expression of SsuFLA35 was associated with seed hair tissue. These results provide important clues about the differences in the FLA gene family during the evolution of herbs and woody plants, and suggest that the FLA gene family may play an essential role in regulating the secondary growth of woody plants. It also provides a reference for further studies on the regulation of secondary growth and seed hair development by FLA genes in poplar and willow. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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22 pages, 7053 KiB

Open AccessArticle

Genome-Wide Characterization and Expression Profiling of the GRAS Gene Family in Salt and Alkali Stresses in Miscanthus sinensis

by Xuhong Zhao, Yan Xu, Guo He, Kang He, Liang Xiao, Ruibo Hu and Shengjun Li

Int. J. Mol. Sci. 2022, 23(23), 14521; https://doi.org/10.3390/ijms232314521 - 22 Nov 2022

Cited by 3 | Viewed by 1283

Abstract

The GRAS family genes encode plant-specific transcription factors that play important roles in a diverse range of developmental processes and abiotic stress responses. However, the information of GRAS gene family in the bioenergy crop Miscanthus has not been available. Here, we report the [...] Read more.

The GRAS family genes encode plant-specific transcription factors that play important roles in a diverse range of developmental processes and abiotic stress responses. However, the information of GRAS gene family in the bioenergy crop Miscanthus has not been available. Here, we report the genome-wide identification of GRAS gene family in Micanthus sinensis. A total of 123 MsGRAS genes were identified, which were divided into ten subfamilies based on the phylogenetic analysis. The co-linearity analysis revealed that 59 MsGRAS genes experienced segmental duplication, forming 35 paralogous pairs. The expression of six MsGRAS genes in responding to salt, alkali, and mixed salt-alkali stresses was analyzed by transcriptome and real-time quantitative PCR (RT-qPCR) assays. Furthermore, the role of MsGRAS60 in salt and alkali stress response was characterized in transgenic Arabidopsis. The MsGRAS60 overexpression lines exhibited hyposensitivity to abscisic acid (ABA) treatment and resulted in compromised tolerance to salt and alkali stresses, suggesting that MsGRAS60 is a negative regulator of salt and alkali tolerance via an ABA-dependent signaling pathway. The salt and alkali stress-inducible MsGRAS genes identified serve as candidates for the improvement of abiotic stress tolerance in Miscanthus. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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21 pages, 5991 KiB

Open AccessArticle

Over-Expression of Phosphoserine Aminotransferase-Encoding Gene (AtPSAT1) Prompts Starch Accumulation in L. turionifera under Nitrogen Starvation

by Lei Wang, Shuiling Li, Ling Sun, Yana Tong, Lin Yang, Yerong Zhu and Yong Wang

Int. J. Mol. Sci. 2022, 23(19), 11563; https://doi.org/10.3390/ijms231911563 - 30 Sep 2022

Cited by 5 | Viewed by 1670

Abstract

It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the [...] Read more.

It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the energy plant duckweed (strain Lemna turionifera 5511) as the research object and used a stable genetic transformation system to heterologously over-expressing Arabidopsis AtPSAT1 (the gene encoding phosphoserine aminotransferase, the second enzyme of PPSB). Our results showed that, under nitrogen starvation, the transgenic plants grew faster, with higher values of Fv/Fm, rETR, and Y(II), as well as fresh and dry weight, than the wild-type. More promisingly, the accumulation of starch was also found to be significantly improved when over-expressing AtPSAT1 in the transgenic plants. qRT-PCR analysis results showed that the expression of genes related to nitrogen assimilation, carbon metabolism, and starch biosynthesis was up-regulated, while the expression of starch degradation-related genes was down-regulated by AtPSAT1 over-expression. We propose that the increased starch accumulation caused by AtPSAT1 over-expression may result from both elevated photosynthetic capacity and nitrogen utilization efficiency. This research sheds new light on the mechanism underlying the ability of PPSB to coordinate nitrogen and carbon metabolism, and provides a feasible way to improve starch production, that is, through engineering PPSB in crops. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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20 pages, 5843 KiB

Open AccessArticle

Transcriptome Analysis Reveals Critical Genes and Pathways in Carbon Metabolism and Ribosome Biogenesis in Poplar Fertilized with Glutamine

by Mei Han, Mingyue Xu, Tao Su, Shizhen Wang, Liangdan Wu, Junhu Feng and Changjun Ding

Int. J. Mol. Sci. 2022, 23(17), 9998; https://doi.org/10.3390/ijms23179998 - 02 Sep 2022

Cited by 6 | Viewed by 1465

Abstract

Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar ‘Nanlin895′ in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) [...] Read more.

Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar ‘Nanlin895′ in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) of poplar ‘Nanlin895’ fertilized with Gln (G) or the inorganic N (control, C) were performed. Compared with the control, 3109 differentially expressed genes (DEGs) and 5071 DEGs were detected in the GL and GR libraries, respectively. In the shoots, Gln treatment resulted in downregulation of a large number of ribosomal genes but significant induction of many starch and sucrose metabolism genes, demonstrating that poplars tend to distribute more energy to sugar metabolism rather than ribosome biosynthesis when fertilized with Gln-N. By contrast, in the roots, most of the DEGs were annotated to carbon metabolism, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis, suggesting that apart from N metabolism, exogenous Gln has an important role in regulating the redistribution of carbon resources and secondary metabolites. Therefore, it can be proposed that the promotion impact of Gln on poplar growth and photosynthesis may result from the improvement of both carbon and N allocation, accompanied by an efficient energy switch for growth and stress responses. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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12 pages, 4151 KiB

Open AccessArticle

Knockdown of p-Coumaroyl Shikimate/Quinate 3′-Hydroxylase Delays the Occurrence of Post-Harvest Physiological Deterioration in Cassava Storage Roots

by Qiuxiang Ma, Jia Xu, Yancai Feng, Xiaoyun Wu, Xinlu Lu and Peng Zhang

Int. J. Mol. Sci. 2022, 23(16), 9231; https://doi.org/10.3390/ijms23169231 - 17 Aug 2022

Cited by 5 | Viewed by 1436

Abstract

Cassava storage roots are an important source of food, feed, and material for starch-based industries in many countries. After harvest, rapid post-harvest physiological deterioration (PPD) reduces their palatability and marketability. During the PPD process, vascular streaking occurs through over-accumulation of coumarins, the biosynthesis [...] Read more.

Cassava storage roots are an important source of food, feed, and material for starch-based industries in many countries. After harvest, rapid post-harvest physiological deterioration (PPD) reduces their palatability and marketability. During the PPD process, vascular streaking occurs through over-accumulation of coumarins, the biosynthesis of which involves the key enzyme p-coumaroyl shikimate/quinate 3′-hydroxylase (C3′H). Repression of MeC3′H expression by RNA interference in transgenic cassava plants caused a significant delay in PPD by decreasing scopoletin and scopolin accumulation in field-harvested storage roots. This study demonstrates that MeC3′H is the key enzyme participating in coumarin biosynthesis during PPD and shows that MeC3′H is a useful target gene for editing to prolong the shelf life of cassava storage roots. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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20 pages, 3633 KiB

Open AccessArticle

Genome-Wide Identification of Switchgrass Laccases Involved in Lignin Biosynthesis and Heavy-Metal Responses

by Rui Li, Yan Zhao, Zhen Sun, Zhenying Wu, Honglun Wang, Chunxiang Fu, Hongbo Zhao and Feng He

Int. J. Mol. Sci. 2022, 23(12), 6530; https://doi.org/10.3390/ijms23126530 - 10 Jun 2022

Cited by 7 | Viewed by 1836

Abstract

Plant laccase genes belong to a multigene family, play key roles in lignin polymerization, and participate in the resistance of plants to biotic and abiotic stresses. Switchgrass is an important resource for forage and bioenergy production, yet information about the switchgrass laccase gene [...] Read more.

Plant laccase genes belong to a multigene family, play key roles in lignin polymerization, and participate in the resistance of plants to biotic and abiotic stresses. Switchgrass is an important resource for forage and bioenergy production, yet information about the switchgrass laccase gene family is scarce. Using bioinformatic approaches, a genome-wide analysis of the laccase multigene family in switchgrass was carried out in this study. In total, 49 laccase genes (PvLac1 to PvLac49) were identified; these can be divided into five subclades, and 20 of them were identified as targets of miR397. The tandem and segmental duplication of laccase genes on Chr05 and Chr08 contributed to the expansion of the laccase family. The laccase proteins shared conserved signature sequences but displayed relatively low sequence similarity, indicating the potential functional diversity of switchgrass laccases. Switchgrass laccases exhibited distinct tissue/organ expression patterns, revealing that some laccases might be involved in the lignification process during stem development. All five of the laccase isoforms selected from different subclades responded to heavy metal. The immediate response of lignin-related laccases, as well as the delayed response of low-abundance laccases, to heavy-metal treatment shed light on the multiple roles of laccase isoforms in response to heavy-metal stress. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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Review

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16 pages, 746 KiB

Open AccessReview

Advances in Genetic Engineering in Improving Photosynthesis and Microalgal Productivity

by Jinlu Hu, Dan Wang, Hui Chen and Qiang Wang

Int. J. Mol. Sci. 2023, 24(3), 1898; https://doi.org/10.3390/ijms24031898 - 18 Jan 2023

Cited by 11 | Viewed by 4194

Abstract

Even though sunlight energy far outweighs the energy required by human activities, its utilization is a key goal in the field of renewable energies. Microalgae have emerged as a promising new and sustainable feedstock for meeting rising food and feed demand. Because traditional [...] Read more.

Even though sunlight energy far outweighs the energy required by human activities, its utilization is a key goal in the field of renewable energies. Microalgae have emerged as a promising new and sustainable feedstock for meeting rising food and feed demand. Because traditional methods of microalgal improvement are likely to have reached their limits, genetic engineering is expected to allow for further increases in the photosynthesis and productivity of microalgae. Understanding the mechanisms that control photosynthesis will enable researchers to identify targets for genetic engineering and, in the end, increase biomass yield, offsetting the costs of cultivation systems and downstream biomass processing. This review describes the molecular events that happen during photosynthesis and microalgal productivity through genetic engineering and discusses future strategies and the limitations of genetic engineering in microalgal productivity. We highlight the major achievements in manipulating the fundamental mechanisms of microalgal photosynthesis and biomass production, as well as promising approaches for making significant contributions to upcoming microalgal-based biotechnology. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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17 pages, 1388 KiB

Open AccessReview

Recent Advances in Molecular Improvement for Potato Tuber Traits

by Daraz Ahmad, Zhongwei Zhang, Haroon Rasheed, Xiaoyong Xu and Jinsong Bao

Int. J. Mol. Sci. 2022, 23(17), 9982; https://doi.org/10.3390/ijms23179982 - 01 Sep 2022

Cited by 7 | Viewed by 4744

Abstract

Potato is an important crop due to its nutritional value and high yield potential. Improving the quality and quantity of tubers remains one of the most important breeding objectives. Genetic mapping helps to identify suitable markers for use in the molecular breeding, and [...] Read more.

Potato is an important crop due to its nutritional value and high yield potential. Improving the quality and quantity of tubers remains one of the most important breeding objectives. Genetic mapping helps to identify suitable markers for use in the molecular breeding, and combined with transgenic approaches provides an efficient way for gaining desirable traits. The advanced plant breeding tools and molecular techniques, e.g., TALENS, CRISPR-Cas9, RNAi, and cisgenesis, have been successfully used to improve the yield and nutritional value of potatoes in an increasing world population scenario. The emerging methods like genome editing tools can avoid incorporating transgene to keep the food more secure. Multiple success cases have been documented in genome editing literature. Recent advances in potato breeding and transgenic approaches to improve tuber quality and quantity have been summarized in this review. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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17 pages, 2021 KiB

Open AccessPerspective

Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications

by Lin Yang, Qin Zhou, Xuan Sheng, Xiangqian Chen, Yuqing Hua, Shuang Lin, Qiyun Luo, Boju Yu, Ti Shao, Yixiao Wu, Junli Chang, Yin Li and Min Tu

Int. J. Mol. Sci. 2023, 24(19), 14549; https://doi.org/10.3390/ijms241914549 - 26 Sep 2023

Viewed by 1119

Abstract

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce [...] Read more.

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications. Full article

(This article belongs to the Special Issue Functional Genomics of Energy Crops)

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