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Gou N, Chen C, Huang M, Zhang Y, Bai H, Li H, Wang L, Wuyun T. Transcriptome and Metabolome Analyses Reveal Sugar and Acid Accumulation during Apricot Fruit Development. Int J Mol Sci 2023; 24:16992. [PMID: 38069317 PMCID: PMC10707722 DOI: 10.3390/ijms242316992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The apricot (Prunus armeniaca L.) is a fruit that belongs to the Rosaceae family; it has a unique flavor and is of important economic and nutritional value. The composition and content of soluble sugars and organic acids in fruit are key factors in determining the flavor quality. However, the molecular mechanism of sugar and acid accumulation in apricots remains unclear. We measured sucrose, fructose, glucose, sorbitol, starch, malate, citric acid, titratable acid, and pH, and investigated the transcriptome profiles of three apricots (the high-sugar cultivar 'Shushanggan', common-sugar cultivar 'Sungold', and low-sugar cultivar 'F43') at three distinct developmental phases. The findings indicated that 'Shushanggan' accumulates a greater amount of sucrose, glucose, fructose, and sorbitol, and less citric acid and titratable acid, resulting in a better flavor; 'Sungold' mainly accumulates more sucrose and less citric acid and starch for the second flavor; and 'F43' mainly accumulates more titratable acid, citric acid, and starch for a lesser degree of sweetness. We investigated the DEGs associated with the starch and sucrose metabolism pathways, citrate cycle pathway, glycolysis pathway, and a handful of sugar transporter proteins, which were considered to be important regulators of sugar and acid accumulation. Additionally, an analysis of the co-expression network of weighted genes unveiled a robust correlation between the brown module and sucrose, glucose, and fructose, with VIP being identified as a hub gene that interacted with four sugar transporter proteins (SLC35B3, SLC32A, SLC2A8, and SLC2A13), as well as three structural genes for sugar and acid metabolism (MUR3, E3.2.1.67, and CSLD). Furthermore, we found some lncRNAs and miRNAs that regulate these genes. Our findings provide clues to the functional genes related to sugar metabolism, and lay the foundation for the selection and cultivation of high-sugar apricots in the future.
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Affiliation(s)
- Ningning Gou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chen Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Mengzhen Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yujing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Haikun Bai
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Tana Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (N.G.); (C.C.); (M.H.); (Y.Z.); (H.B.); (H.L.); (L.W.)
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou 450003, China
- Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
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Yadav VK, Jalmi SK, Tiwari S, Kerkar S. Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach. Sci Rep 2023; 13:15101. [PMID: 37699996 PMCID: PMC10497521 DOI: 10.1038/s41598-023-42420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/10/2023] [Indexed: 09/14/2023] Open
Abstract
Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of the genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana, 11,565 in Oryza sativa, and 32,397 in Zea mays for their characteristic features and explored the associated genomic and epigenomic features. We found lncRNAs were distributed throughout the chromosomes and the Helitron family of transposable elements (TEs) enriched, while the terminal inverted repeat depleted in lncRNA transcribing regions. Our analyses determined that lncRNA transcribing regions show rare or weak signals for most epigenetic marks except for H3K9me2 and cytosine methylation in all three plant species. LncRNAs showed preferential localization in the nucleus and cytoplasm; however, the distribution ratio in the cytoplasm and nucleus varies among the studied plant species. We identified several conserved endogenous target mimic sites in the lncRNAs among the studied plants. We found 233, 301, and 273 unique miRNAs, potentially targeting the lncRNAs of A. thaliana, O. sativa, and Z. mays, respectively. Our study has revealed that miRNAs, which interact with lncRNAs, target genes that are involved in a diverse array of biological and molecular processes. The miRNA-targeted lncRNAs displayed a strong affinity for several transcription factors, including ERF and BBR-BPC, mutually present in all three plants, advocating their conserved functions. Overall, the present study showed that plant lncRNAs exhibit conserved genomic and epigenomic characteristics and potentially govern the growth and development of plants.
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Affiliation(s)
- Vikash Kumar Yadav
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India.
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Siddhi Kashinath Jalmi
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Shalini Tiwari
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, 74078, OK, USA
| | - Savita Kerkar
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
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Soorni A, Karimi M, Al Sharif B, Habibi K. Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC PLANT BIOLOGY 2023; 23:3. [PMID: 36588159 PMCID: PMC9806901 DOI: 10.1186/s12870-022-04031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. RESULTS For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. CONCLUSION Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | | | - Batoul Al Sharif
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Khashayar Habibi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Xing M, Peng Z, Guan C, Guan M. Comparative study on abortion characteristics of Nsa CMS and Pol CMS and analysis of long non-coding RNAs related to pollen abortion in Brassica napus. PLoS One 2023; 18:e0284287. [PMID: 37053132 PMCID: PMC10101420 DOI: 10.1371/journal.pone.0284287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Cytoplasmic male sterile system (CMS) is one of the important methods for the utilization of heterosisin Brassica napus. The involvement of long non-coding RNAs (lncRNAs) in anther and pollen development in B.napus has been recognized, but there is little data on the involvement of lncRNAs in pollen abortion in different types of rapeseed CMS. The present study compared the cytological, physiological and biochemical characteristics of Nsa CMS (1258A) and Pol CMS (P5A) during pollen abortion, and high-throughput sequencing of flower buds of different sizes before and after pollen abortion. The results showed that insufficient energy supply was an important physiological basis for 1258A and P5A pollen abortion, and 1258A had excessive ROS (reactive oxygen species) accumulation in the stage of pollen abortion. Functional analysis showed that Starch and sucrose metabolism and Sulfur metabolism were significantly enriched before and after pollen abortion in 1258A and P5A, and a large number of genes were down-regulated. In 1258A, 227 lncRNAs had cis-targeting regulation, and 240 cis-target genes of the lncRNAs were identified. In P5A, 116 lncRNAs had cis-targeting regulation, and 101 cis-target genes of the lncRNAs were identified. There were five lncRNAs cis-target genes in 1258A and P5A during pollen abortion, and LOC106445716 encodes β-D-glucopyranosyl abscisate β-glucosidase and could regulate pollen abortion. Taken together, this study, provides a new perspective for lncRNAs to participate in the regulation of Nsa CMS and Pol CMS pollen abortion.
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Affiliation(s)
- Man Xing
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Zechuan Peng
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Chunyun Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Mei Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
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Dong Y, Feng ZQ, Ye F, Li T, Li GL, Li ZS, Hao YC, Zhang XH, Liu WX, Xue JQ, Xu ST. Genome-wide association analysis for grain moisture content and dehydration rate on maize hybrids. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:5. [PMID: 37312866 PMCID: PMC10248682 DOI: 10.1007/s11032-022-01349-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/13/2022] [Indexed: 06/15/2023]
Abstract
For mechanized maize production, a low grain water content (GWC) at harvest is necessary. However, as a complex quantitative trait, understand the genetic mechanism of GWC remains a large gap, especially in hybrids. In this study, a hybrid population through two environments including 442 F1 was used for genome-wide association analysis of GWC and the grain dehydration rate (GDR), using the area under the dry down curve (AUDDC) as the index. Then, we identified 19 and 17 associated SNPs for GWC and AUDDC, including 10 co-localized SNPs, along with 64 and 77 pairs of epistatic SNPs for GWC and AUDDC, respectively. These loci could explain 11.39-68.2% of the total phenotypic variation for GWC and 41.07-67.02% for AUDDC at different stages, whose major effect was the additive and epistatic effect. By exploring the candidate genes around the significant sites, a total of 398 and 457 possible protein-coding genes were screened, including autophagy pathway and auxin regulation-related genes, and five inbred lines with the potential to reduce GWC in the combined F1 hybrid were identified. Our research not only provides a certain reference for the genetic mechanism analysis of GWC in hybrids but also provides an added reference for breeding low-GWC materials. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01349-x.
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Affiliation(s)
- Yuan Dong
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Zhi-qian Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Guo-liang Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193 China
| | - Zhou-Shuai Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Yin-chuan Hao
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Xing-hua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Wen-xin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193 China
| | - Ji-quan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Shu-tu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
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Liu G, Liu F, Wang Y, Liu X. A novel long noncoding RNA CIL1 enhances cold stress tolerance in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111370. [PMID: 35788028 DOI: 10.1016/j.plantsci.2022.111370] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
With the intensification of global warming, extreme weather events have occurred more frequently, among which cold stress has become one of the major environmental factors that restrict global crop yield and production. Multiple long noncoding RNAs (lncRNAs) have been predicted or recognized in the plant response to cold stress, however, the molecular biological functions of most of these RNAs are still poorly understood. Here, we identified a novel lncRNA, COLD INDUCED lncRNA 1 (CIL1), as a positive regulator of the plant response to cold stress in Arabidopsis. CIL1 was significantly induced when the plant was exposed to cold stress. Moreover, knockdown mutants showed more sensitivity to cold stress than the wild type did, accompanied by an increased content of endogenous ROS (reactive oxygen species) and reduced osmoregulatory substances. Genome-wide transcriptome analysis indicated that 256 genes were downregulated and 34 genes were upregulated in cil1 mutants under cold stress, which were mainly involved in hormone signal transduction, ROS homeostasis and glucose metabolism. Our study implies that CIL1 has a positive effect on the plant response to cold stress by regulating the expression of multiple stress-related genes during the seedling stage.
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Affiliation(s)
- Guangchao Liu
- Key Lab of Plant Biotechnology in University of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Fuxia Liu
- Key Lab of Plant Biotechnology in University of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Yue Wang
- Key Lab of Plant Biotechnology in University of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xin Liu
- Key Lab of Plant Biotechnology in University of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China.
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