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Wu Q, Li A, Zhao P, Xia H, Zhang Y, Que Y. Theory to practice: a success in breeding sugarcane variety YZ08-1609 known as the King of Sugar. FRONTIERS IN PLANT SCIENCE 2024; 15:1413108. [PMID: 38807781 PMCID: PMC11130468 DOI: 10.3389/fpls.2024.1413108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 05/30/2024]
Abstract
Sugarcane, a significant cash crop in tropical and subtropical regions, contributes to 80% of sugar production and 40% of bioethanol production in the world. It is a key sugar crop, accounting for 85% of sugar production in China. Developing new varieties with high yield, high sugar, and better stress resistance is crucial for the sustainable growth of sugar industry. Hybrid breeding is the most widely used and effective method, with over 98% of Chinese sugarcane varieties resulting from this approach. Over the past two decades, Chinese breeders have developed the theory of high-heterogeneous composite high-sugar breeding, leading to the successful breeding of the fifth-generation sugarcane varieties. Among them, YZ08-1609, a complex hybrid of Saccharum spp., was developed by Sugarcane Research Institute (YSRI) of Yunnan Academy of Agricultural Sciences. The average cane yield of YZ08-1609 was 14.4% higher than ROC22. It is highly resistant to mosaic disease, and highly tolerant to drought stress, but moderately susceptible to smut disease. Notably, YZ08-1609 stands out with a sucrose content of 20.3%, setting an international record, earning the reputation as "King of Sugar". To summarize experience and inspire breeding, we provided here the detailed insights into the selection of parents, breeding process, and characteristics of YZ08-1609. Besides, the biological mechanisms underlying its high yield and high sugar was excavated at both transcriptional and metabolic levels. The challenges and prospects in breeding sugarcane varieties especially with high sugar were also discussed, offering a foundation for the future development of high-sugar varieties.
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Affiliation(s)
- Qibin Wu
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aomei Li
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Peifang Zhao
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Hongming Xia
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Yuebin Zhang
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Youxiong Que
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Sanya, China
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences/Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhao J, Li S, Xu Y, Ahmad N, Kuang B, Feng M, Wei N, Yang X. The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis. J Adv Res 2023; 54:1-13. [PMID: 36781019 DOI: 10.1016/j.jare.2023.02.001] [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: 11/07/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
INTRODUCTION Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear. OBJECTIVE To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation. METHODS PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation. RESULTS A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids. CONCLUSION Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.
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Affiliation(s)
- Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Nazir Ahmad
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
| | - Bowen Kuang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mengfan Feng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ni Wei
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China.
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Chang G, Xue H, Ji J, Wang L, Zhu X, Zhang K, Li D, Gao X, Niu L, Gao M, Luo J, Cui J. Risk assessment of predatory lady beetle Propylea japonica's multi-generational exposure to three non-insecticidal agrochemicals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 886:163931. [PMID: 37156379 DOI: 10.1016/j.scitotenv.2023.163931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
The effects of non-insecticidal agrochemicals on pest natural predators remain largely unexplored except bees and silkworm. The herbicide quizalofop-p-ethyl (QpE), fungicide thiophanate-methyl (TM), and plant growth regulator mepiquat chloride (MC) have been extensively applied as non-insecticidal agrochemicals. Here, we systematically evaluated multiple effects of these 3 non-insecticidal agrochemicals on three generations of Propylea japonica, an important agroforestry predatory beetle, including the effects on its development, reproduction, enterobacteria, and transcriptomic response. The results showed that QpE exhibited a hormetic effect on P. japonica, thus significantly increasing the survival rate of generation 2 (F2) females, generation 3 (F3) females, and F3 males and body weight of F3 males. However, three successive generations exposed to TM and MC had no significant effect on longevity, body weight, survival rate, pre-oviposition period, and fecundity of P. japonica. Additionally, we investigated the effects of MC, TM, and QpE exposure on gene expression and gut bacterial community of F3 P. japonica. Under MC, TM, and QpE exposure, the overwhelming genes of P. japonica (99.90 %, 99.45 %, and 99.7 %) remained unaffected, respectively. Under TM and MC exposure, differentially expressed genes (DEGs) were not significantly enriched in any KEGG pathway, indicating TM and MC did not significantly affect functions of P. japonica, but under QpE exposure, the expression levels of drug metabolism-related genes were down-regulated. Although QpE treatment did not affect gut dominant bacterial community composition, it significantly increased relative abundances of detoxification metabolism-related bacteria such as Wolbachia, Pseudomonas and Burkholderia in P. japonica. However, TM and MC had no significant effect on the gut bacterial community composition and relative abundance in P. japonica. This study revealed for the first time the mechanism by which P. japonica might compensate for gene downregulation-induced detoxification metabolism decline through altering symbiotic bacteria under QpE exposure. Our findings provide reference for the rational application of non-insecticidal agrochemicals.
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Affiliation(s)
- Guofeng Chang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hui Xue
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jichao Ji
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xiangzhen Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Kaixin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Dongyang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xueke Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Lin Niu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Mengxue Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Junyu Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jinjie Cui
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
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Wang X, Zhou Q, Wang X, Song S, Liu J, Dong S. Mepiquat chloride inhibits soybean growth but improves drought resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:982415. [PMID: 36147232 PMCID: PMC9486081 DOI: 10.3389/fpls.2022.982415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 06/01/2023]
Abstract
Soybeans are an important economic crop. As the most widely used growth regulator globally, the molecular mechanism of mepiquat chloride (DPC) in soybean remains unknown. In this study, RNA sequencing technology combined with ultra-performance liquid chromatography and tandem mass spectrometry were used to analyze the changes in the leaf transcriptome and metabolomics of soybean leaves at the seedling stage under DPC stress. The results showed that differentially expressed genes related to photosynthesis and cell wall synthesis were significantly downregulated at the transcriptional level. In addition, the syntheses of gibberellin, zeatin, brassinolide, and other plant hormones were inhibited in the signal transduction pathway of plant hormones, thereby inhibiting plant growth. In contrast, at the metabolic level, the expression levels of flavonoid differential metabolites were significantly increased, and the proportions of flavonoids in the two varieties were 61.5 and 66%, respectively. The combined analysis of transcriptome and metabolomics showed that the differential expressed genes and metabolites were mainly enriched in the isoflavonoid biosynthesis and flavonoid biosynthesis pathways. Principally, DPC inhibited plant growth but improved drought resistance. Our study is the first to report the molecular mechanism of DPC regulation in soybean, providing useful insights into the rational application of DPC in soybean.
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Affiliation(s)
- Xiyue Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Qi Zhou
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xin Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shuang Song
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jun Liu
- Lab of Functional Genomics and Bioinformatics, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shoukun Dong
- College of Agriculture, Northeast Agricultural University, Harbin, China
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Transcriptome Analysis of Sugarcane Young Leaves and Protoplasts after Enzymatic Digestion. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081210. [PMID: 36013389 PMCID: PMC9410293 DOI: 10.3390/life12081210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
Sugarcane somatic cell hybridization can break through the barrier of genetic incompatibility between distantly related species in traditional breeding. However, the molecular mechanisms of sugarcane protoplast regeneration and the conditions for protoplast preparation remain largely unknown. In this study, young sugarcane (ROC22) leaves were enzymatically digested, and the viability of protoplasts reached more than 90% after enzymatic digestion (Enzymatic combination: 2% cellulase + 0.5% pectinase + 0.1% dissociative enzyme + 0.3% hemicellulase, pH = 5.8). Transcriptome sequencing was performed on young sugarcane leaves and protoplasts after enzymatic digestion to analyze the differences in gene expression in somatic cells before and after enzymatic digestion. A total of 117,411 unigenes and 43,460 differentially expressed genes were obtained, of which 21,123 were up-regulated and 22,337 down-regulated. The GO terms for the 43,460 differentially expressed genes (DEGs) were classified into three main categories: biological process, cellular component and molecular function, which related to developmental process, growth, cell proliferation, transcription regulator activity, signal transducer activity, antioxidant activity, oxidative stress, kinase activity, cell cycle, cell differentiation, plant hormone signal transduction, and so on. After enzymatic digestion of young sugarcane leaves, the expressions of GAUT, CESA, PSK, CyclinB, CyclinA, CyclinD3 and cdc2 genes associated with plant regeneration were significantly down-regulated to 65%, 47%, 2%, 18.60%, 21.32%, 52% and 45% of young leaves, respectively. After enzymatic digestion, Aux/IAA expression was up-regulated compared with young leaves, and Aux/IAA expression was 3.53 times higher than that of young leaves. Compared with young leaves, these key genes were significantly changed after enzymatic digestion. These results indicate that the process of somatic enzymatic digestion process may affect the regeneration of heterozygous cells to a certain extent.
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MicroSugar: A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.). Genomics 2022; 114:110420. [PMID: 35760231 DOI: 10.1016/j.ygeno.2022.110420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022]
Abstract
microRNA (miRNA) is a group of small non-coding RNA that plays important role in post-transcription of gene expression. With the studies about miRNA increase in sugarcane, the researchers lack an exhaustive resource to achieve the data. To fill this gap, we developed MicroSugar, a database that supported mRNA and miRNA annotation for sugarcane (http://suc.gene-db.com). MicroSugar is an integrated resource developed for 194,528 genes including 80,746 unigenes from long reads of Pacbio platform and 468 miRNAs from 72 samples. Internode elongation (jointing) is the key biological characteristic for the growth of sugarcane tillers into sugarcane stems. The present study combined the sequencing data from the different stages in internode elongation of stem and tiller. In total, the 14,300 3' untranslated region (UTR) sequences were extracted from the gene sequences and 3019 mRNAs as target of 327 miRNA were identified by miRanda algorithm and Spearman's Rho of expression levels. To determine the gene functions regulated by these miRNAs, the gene ontology enrichment analysis was performed and it confirmed that the over-represented Gene Ontology (GO) terms were associated with organism formation indicating the growth controlling function by miRNAs in sugarcane. Moreover, MicroSugar is a comprehensive and integrated database with a user-friendly responsive template. By browsing, searching and downloading of the nucleotide sequences, expression and miRNA targets, the user can retrieve information promptly. The database provides a valuable resource to facilitate the understanding of miRNA in sugarcane development and growth which will contribute to the study of sugarcane and other plants.
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Transcriptome Profiling Provides New Insights into the Molecular Mechanism Underlying the Sensitivity of Cotton Varieties to Mepiquat Chloride. Int J Mol Sci 2022; 23:ijms23095043. [PMID: 35563437 PMCID: PMC9105546 DOI: 10.3390/ijms23095043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Mepiquat chloride (MC) is a plant growth regulator widely used in cotton production to control vegetative overgrowth of cotton plants to achieve ideal plant architecture required for high yielding. Cotton varieties respond differently to MC application, but there is little information about the molecular mechanisms underlying the varietal difference. In this study, comparative transcriptome analysis was conducted by using two Upland cotton varieties with different sensitivity (XLZ74, insensitive; SD1068, sensitive) to MC treatment, aiming to understand the molecular mechanisms responsible for varietal difference of MC sensitivity. RNA-seq data were generated from the two varieties treated with MC or water at three time points, 1, 3 and 6 days post-spray (dps). Genes differentially expressed between the MC and mock treatments of XLZ74 (6252) and SD1068 (6163) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two varieties. Signal transduction of phytohormones, biosynthesis of gibberellins (GAs) and brassinosteroids (BRs) and profiles of transcription factors (TFs) seemed to be differentially affected by MC in the two varieties. The transcriptomic results were further consolidated with the content changes of phytohormones in young stem. Several GA catabolic genes, GA2ox, were highly induced by MC in both varieties especially in SD1068, consistent with a more significant decrease in GA4 in SD1068. Several AUX/IAA and SAUR genes and CKX genes were induced by MC in both varieties, but with a more profound effect observed in SD1068 that showed a significant reduction in indole-3-acetic acid (IAA) and a significant increase in cytokinin (CTK) at 6 days post-spray (dps). BR biosynthesis-related genes were downregulated in SD1068, but not in XLZ74. Additionally, more downregulated TFs were observed in MC-treated SD1068 than in MC-treated XLZ74, and the two varieties had very different profiles of genes involved in starch and sucrose metabolism, with those of SD1068 and XLZ74 being downregulated and upregulated by MC treatment, respectively. Together, these results indicate that although the same or similar biological pathways are affected by MC treatment in cotton varieties showing different MC sensitivity, the extent of effect is variable, leading to their different phenotypic outcomes. How the quantitative effect of MC on the biological processes associated with growth retardation is regulated is still an open question.
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Gao M, Jiang W, Lin Z, Lin Q, Ye Q, Wang W, Xie Q, He X, Luo C, Chen Q. SMRT and Illumina RNA-Seq Identifies Potential Candidate Genes Related to the Double Flower Phenotype and Unveils SsAP2 as a Key Regulator of the Double-Flower Trait in Sagittaria sagittifolia. Int J Mol Sci 2022; 23:ijms23042240. [PMID: 35216356 PMCID: PMC8875719 DOI: 10.3390/ijms23042240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/01/2022] Open
Abstract
Double flowers are one of the important objectives of ornamental plant breeding. Sagittaria sagittifolia is an aquatic herb in the Alismataceae family that is widely used as an ornamental plant in gardens. However, the reference genome has not been published, and the molecular regulatory mechanism of flower formation remains unclear. In this study, single molecule real-time (SMRT) sequencing technology combined with Illumina RNA-Seq was used to perform a more comprehensive analysis of S. sagittifolia for the first time. We obtained high-quality full-length transcripts, including 53,422 complete open reading frames, and identified 5980 transcription factors that belonged to 67 families, with many MADS-box genes involved in flower formation being obtained. The transcription factors regulated by plant hormone signals played an important role in the development of double flowers. We also identified an AP2 orthologous gene, SsAP2, with a deletion of the binding site for miR172, that overexpressed SsAP2 in S. sagittifolia and exhibited a delayed flowering time and an increased number of petals. This study is the first report of a full-length transcriptome of S. sagittifolia. These reference transcripts will be valuable resources for the analysis of gene structures and sequences, which provide a theoretical basis for the molecular regulatory mechanism governing the formation of double flowers.
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Affiliation(s)
- Meiping Gao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (Q.Y.); (W.W.); (Q.X.)
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (W.J.); (Z.L.); (Q.L.)
| | - Wen Jiang
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (W.J.); (Z.L.); (Q.L.)
| | - Zhicheng Lin
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (W.J.); (Z.L.); (Q.L.)
| | - Qian Lin
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (W.J.); (Z.L.); (Q.L.)
| | - Qinghua Ye
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (Q.Y.); (W.W.); (Q.X.)
| | - Wei Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (Q.Y.); (W.W.); (Q.X.)
| | - Qian Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (Q.Y.); (W.W.); (Q.X.)
| | - Xinhua He
- College of Agriculture, Guangxi University, 100 Daxue Road, Nanning 530004, China; (X.H.); (C.L.)
| | - Cong Luo
- College of Agriculture, Guangxi University, 100 Daxue Road, Nanning 530004, China; (X.H.); (C.L.)
| | - Qingxi Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (Q.Y.); (W.W.); (Q.X.)
- Correspondence: ; Tel.: +86-0771-324-3484
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