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Yan G, Li S, Ma M, Quan C, Tian X, Tu J, Shen J, Yi B, Fu T, Ma C, Guo L, Dai C. The transcription factor BnaWRKY10 regulates cytokinin dehydrogenase BnaCKX2 to control cytokinin distribution and seed size in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4994-5013. [PMID: 37246599 DOI: 10.1093/jxb/erad201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Cytokinins (CKs) are phytohormones that promote cell division and differentiation. However, the regulation of CK distribution and homeostasis in Brassica napus is poorly understood. Here, the endogenous CKs were first quantified by LC-ESI-MS/MS in rapeseed tissues and visualized by TCSn::GUS reporter lines. Interestingly, the cytokinin oxidase/dehydrogenase BnaCKX2 homologs were mainly expressed in reproductive organs. Subsequently, the quadruple mutants of the four BnaCKX2 homologs were generated. Endogenous CKs were increased in the seeds of the BnaCKX2 quadruple mutants, resulting in a significantly reduced seed size. In contrast, overexpression of BnaA9.CKX2 resulted in larger seeds, probably by delaying endosperm cellularization. Furthermore, the transcription factor BnaC6.WRKY10b, but not BnaC6.WRKY10a, positively regulated BnaA9.CKX2 expression by binding directly to its promoter region. Overexpression of BnaC6.WRKY10b rather than BnaC6.WRKY10a resulted in lower concentration of CKs and larger seeds by activating BnaA9.CKX2 expression, indicating that the functional differentiation of BnaWRKY10 homologs might have occurred during B. napus evolution or domestication. Notably, the haploid types of BnaA9.CKX2 were associated with 1000-seed weight in the natural B. napus population. Overall, the study reveals the distribution of CKs in B. napus tissues, and shows that BnaWRKY10-mediated BnaCKX2 expression is essential for seed size regulation, providing promising targets for oil crop improvement.
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Affiliation(s)
- Guanbo Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengya Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xia Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Tan M, Niu J, Peng DZ, Cheng Q, Luan MB, Zhang ZQ. Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis. BMC PLANT BIOLOGY 2022; 22:192. [PMID: 35410118 PMCID: PMC9003975 DOI: 10.1186/s12870-022-03549-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/16/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Fatty acid composition and content affect rapeseed oil quality. Fatty acid synthesis-related genes in rapeseed have been studied globally by researchers. Nevertheless, rapeseed oil is mainly composed of seven different fatty acids (FA), and each fatty acid was regulated by different genes. Furthermore, different FA affect each other, which needs continuous and in-depth research to obtain more clear results in Brassica napus. RESULTS In this paper, broad-scale miRNA expression profiles were constructed and 21 differentially expressed miRNAs were detected. GO enrichment analysis showed that most up-regulated proteins were involved in transcription factor activity and catalytic activity. KEGG pathway enrichment analysis indicated that 20 pathways involving 36 target genes were enriched, of which the bna00592 pathway may be involved in fatty acid metabolism. The results were verified using a quantitative real-time PCR (RT-qPCR) analysis, we found that the target gene of bna-miR156b > c > g was the OPR (12-oxo-phytodienoic acid reductase). Four copies of OPR gene were found, and the over-expression vectors (pCAMBIA1300-35 s-OPR and pCAMBIA1300-RNAi-OPR) were constructed to verify their functions. In T1 and T2 generation, the content of linoleic acid (LA) increased significantly in OE but deceased in OPRi. CONCLUSIONS This is the first study to provide four copies of the OPR gene that regulates LA metabolism, can be used for the molecular mechanism of LA and optimizing fatty acid profiles in oilseed for breeding programs.
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Affiliation(s)
- Min Tan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Juan Niu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Duo Zi Peng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Qian Cheng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Ming Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
| | - Zhen Qian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Song J, Xie X, Chen C, Shu J, Thapa RK, Nguyen V, Bian S, Kohalmi SE, Marsolais F, Zou J, Cui Y. LEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis. Nat Commun 2021; 12:3963. [PMID: 34172749 PMCID: PMC8233312 DOI: 10.1038/s41467-021-24234-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
The endosperm provides nutrients and growth regulators to the embryo during seed development. LEAFY COTYLEDON1 (LEC1) has long been known to be essential for embryo maturation. LEC1 is expressed in both the embryo and the endosperm; however, the functional relevance of the endosperm-expressed LEC1 for seed development is unclear. Here, we provide genetic and transgenic evidence demonstrating that endosperm-expressed LEC1 is necessary and sufficient for embryo maturation. We show that endosperm-synthesized LEC1 is capable of orchestrating full seed maturation in the absence of embryo-expressed LEC1. Inversely, without LEC1 expression in the endosperm, embryo development arrests even in the presence of functional LEC1 alleles in the embryo. We further reveal that LEC1 expression in the endosperm begins at the zygote stage and the LEC1 protein is then trafficked to the embryo to activate processes of seed maturation. Our findings thus establish a key role for endosperm in regulating embryo development.
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Affiliation(s)
- Jingpu Song
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada. .,Department of Biology, Western University, London, ON, Canada.
| | - Xin Xie
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Shu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Raj K Thapa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Vi Nguyen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Shaomin Bian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,College of Plant Science, Jilin University, Changchun, China
| | | | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada.
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Department of Biology, Western University, London, ON, Canada.
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Jo L, Pelletier JM, Harada JJ. Central role of the LEAFY COTYLEDON1 transcription factor in seed development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:564-580. [PMID: 30916433 DOI: 10.1111/jipb.12806] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/16/2019] [Indexed: 05/04/2023]
Abstract
Seed development is a complex period of the flowering plant life cycle. After fertilization, the three main regions of the seed, embryo, endosperm and seed coat, undergo a series of developmental processes that result in the production of a mature seed that is developmentally arrested, desiccated, and metabolically quiescent. These processes are highly coordinated, both temporally and spatially, to ensure the proper growth and development of the seed. The transcription factor, LEAFY COTYLEDON1 (LEC1), is a central regulator that controls several aspects of embryo and endosperm development, including embryo morphogenesis, photosynthesis, and storage reserve accumulation. Thus, LEC1 regulates distinct sets of genes at different stages of seed development. Despite its critical importance for seed development, an understanding of the mechanisms underlying LEC1's multifunctionality is only beginning to be obtained. Recent studies describe the roles of specific transcription factors and the hormones, gibberellic acid and abscisic acid, in controlling the activity and transcriptional specificity of LEC1 across seed development. Moreover, studies indicate that LEC1 acts as a pioneer transcription factor to promote epigenetic reprogramming during embryogenesis. In this review, we discuss the mechanisms that enable LEC1 to serve as a central regulator of seed development.
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Affiliation(s)
- Leonardo Jo
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
| | - Julie M Pelletier
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
| | - John J Harada
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
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Hua S, Chen ZH, Zhang Y, Yu H, Lin B, Zhang D. Chlorophyll and carbohydrate metabolism in developing silique and seed are prerequisite to seed oil content of Brassica napus L. BOTANICAL STUDIES 2014; 55:34. [PMID: 28510961 PMCID: PMC5432831 DOI: 10.1186/1999-3110-55-34] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 12/03/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Although the seed oil content in canola is a crucial quality determining trait, the regulatory mechanisms of its formation are not fully discovered. This study compared the silique and seed physiological characteristics including fresh and dry weight, seed oil content, chlorophyll content, and carbohydrate content in a high oil content line (HOCL) and a low oil content line (LOCL) of canola derived from a recombinant inbred line in 2010, 2011, and 2012. The aim of the investigation is to uncover the physiological regulation of silique and seed developmental events on seed oil content in canola. RESULTS On average, 83% and 86% of silique matter while 69% and 63% of seed matter was produced before 30 days after anthesis (DAA) in HOCL and LOCL, respectively, over three years. Furthermore, HOCL exhibited significantly higher fresh and dry matter at most developmental stages of siliques and seeds. From 20 DAA, lipids were deposited in the seed of HOCL significantly faster than that of LOCL, which was validated by transmission electron microscopy, showing that HOCL accumulates considerable more oil bodies in the seed cells. Markedly higher silique chlorophyll content was observed in HOCL consistently over the three consecutive years, implying a higher potential of photosynthetic capacity in siliques of HOCL. As a consequence, HOCL exhibited significantly higher content of fructose, glucose, sucrose, and starch mainly at 20 to 45 DAA, a key stage of seed lipid deposition. Moreover, seed sugar content was usually higher than silique indicating the importance of sugar transportation from siliques to seeds as substrate for lipid biosynthesis. The much lower silique cellulose content in HOCL was beneficial for lipid synthesis rather than consuming excessive carbohydrate for cell wall. CONCLUSIONS Superior physiological characteristics of siliques in HOCL showed advantage to produce more photosynthetic assimilates, which were highly correlated to seed oil contents.
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Affiliation(s)
- Shuijin Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 P.R. China
| | - Zhong-Hua Chen
- School of Science and Health, University of Western Sydney, Penrith, 2751NSW Australia
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 P.R. China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 P.R. China
| | - Baogang Lin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 P.R. China
| | - Dongqing Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 P.R. China
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De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. G3-GENES GENOMES GENETICS 2014; 4:2147-57. [PMID: 25193496 PMCID: PMC4232540 DOI: 10.1534/g3.114.013409] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coconut palm (Cocos nucifera) is a symbol of the tropics and a source of numerous edible and nonedible products of economic value. Despite its nutritional and industrial significance, coconut remains under-represented in public repositories for genomic and transcriptomic data. We report de novo transcript assembly from RNA-seq data and analysis of gene expression in seed tissues (embryo and endosperm) and leaves of a dwarf coconut variety. Assembly of 10 GB sequencing data for each tissue resulted in 58,211 total unigenes in embryo, 61,152 in endosperm, and 33,446 in leaf. Within each unigene pool, 24,857 could be annotated in embryo, 29,731 could be annotated in endosperm, and 26,064 could be annotated in leaf. A KEGG analysis identified 138, 138, and 139 pathways, respectively, in transcriptomes of embryo, endosperm, and leaf tissues. Given the extraordinarily large size of coconut seeds and the importance of small RNA-mediated epigenetic regulation during seed development in model plants, we used homology searches to identify putative homologs of factors required for RNA-directed DNA methylation in coconut. The findings suggest that RNA-directed DNA methylation is important during coconut seed development, particularly in maturing endosperm. This dataset will expand the genomics resources available for coconut and provide a foundation for more detailed analyses that may assist molecular breeding strategies aimed at improving this major tropical crop.
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Yu E, Fan C, Yang Q, Li X, Wan B, Dong Y, Wang X, Zhou Y. Identification of heat responsive genes in Brassica napus siliques at the seed-filling stage through transcriptional profiling. PLoS One 2014; 9:e101914. [PMID: 25013950 PMCID: PMC4094393 DOI: 10.1371/journal.pone.0101914] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, global transcription profiles of 20 d-old siliques of B. napus were analyzed after heat stress using a Brassica 95k EST microarray. The up-regulated genes included many HSF/HSP transcripts and other heat-related marker genes, such as ROF2, DREB2a, MBF1c and Hsa32, reflecting the conservation of key heat resistance factors among plants. Other up-regulated genes were preferentially expressed in heat-stressed silique walls or seeds, including some transcription factors and potential developmental regulators. In contrast, down-regulated genes differed between the silique wall and seeds and were largely tied to the biological functions of each tissue, such as glucosinolate metabolism in the silique wall and flavonoid synthesis in seeds. Additionally, a large proportion (one-third) of these differentially expressed genes had unknown functions. Based on these gene expression profiles, Arabidopsis mutants for eight heat-induced Brassica homologous genes were treated with different heat stress methods, and thermotolerance varied with each mutation, heat stress regimen and plant development stage. At least two of the eight mutants exhibited sensitivity to the heat treatments, suggesting the importance of the respective genes in responding to heat stress. In summary, this study elucidated the molecular bases of the heat responses in siliques during later reproductive stages and provides valuable information and gene resources for the genetic improvement of heat tolerance in oilseed rape breeding.
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Affiliation(s)
- Erru Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaodong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Bingxi Wan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanni Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, Saint Louis, Missouri, United States of America
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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Microarray expression analysis of the main inflorescence in Brassica napus. PLoS One 2014; 9:e102024. [PMID: 25007212 PMCID: PMC4090195 DOI: 10.1371/journal.pone.0102024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/13/2014] [Indexed: 01/13/2023] Open
Abstract
The effect of the number of pods on the main inflorescence (NPMI) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. Here, we sought to identify patterns of gene expression that determine the NPMI during inflorescence differentiation. We monitored gene expression profiles in the main inflorescence of two B. napus F6 RIL pools, each composed of nine lines with a low or high NPMI, and their parental lines, Zhongshuang 11 (ZS11) and 73290, using a Brassica 90K elements oligonucleotide array. We identified 4,805 genes that were differentially expressed (≥1.5 fold-change) between the low- and high-NPMI samples. Of these, 82.8% had been annotated and 17.2% shared no significant homology with any known genes. About 31 enriched GO clusters were identified amongst the differentially expressed genes (DEGs), including those involved in hormone responses, development regulation, carbohydrate metabolism, signal transduction, and transcription regulation. Furthermore, 92.8% of the DEGs mapped to chromosomes that originated from B. rapa and B. oleracea, and 1.6% of the DEGs co-localized with two QTL intervals (PMI10 and PMI11) known to be associated with the NPMI. Overexpression of BnTPI, which co-localized with PMI10, in Arabidopsis suggested that this gene increases the NPMI. This study provides insight into the molecular factors underlying inflorescence architecture, NPMI determination and, consequently, seed yield in B. napus.
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Lorenz C, Rolletschek H, Sunderhaus S, Braun HP. Brassica napus seed endosperm - metabolism and signaling in a dead end tissue. J Proteomics 2014; 108:382-426. [PMID: 24906024 DOI: 10.1016/j.jprot.2014.05.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 02/04/2023]
Abstract
UNLABELLED Oilseeds are an important element of human nutrition and of increasing significance for the production of industrial materials. The development of the seeds is based on a coordinated interplay of the embryo and its surrounding tissue, the endosperm. This study aims to give insights into the physiological role of endosperm for seed development in the oilseed crop Brassica napus. Using protein separation by two-dimensional (2D) isoelectric focusing (IEF)/SDS polyacrylamide gel electrophoresis (PAGE) and protein identification by mass spectrometry three proteome projects were carried out: (i) establishment of an endosperm proteome reference map, (ii) proteomic characterization of endosperm development and (iii) comparison of endosperm and embryo proteomes. The endosperm proteome reference map comprises 930 distinct proteins, including enzymes involved in genetic information processing, carbohydrate metabolism, environmental information processing, energy metabolism, cellular processes and amino acid metabolism. To investigate dynamic changes in protein abundance during seed development, total soluble proteins were extracted from embryo and endosperm fractions at defined time points. Proteins involved in sugar converting and recycling processes, ascorbate metabolism, amino acid biosynthesis and redox balancing were found to be of special importance for seed development in B. napus. Implications for the seed filling process and the function of the endosperm for seed development are discussed. BIOLOGICAL SIGNIFICANCE The endosperm is of key importance for embryo development during seed formation in plants. We present a broad study for characterizing endosperm proteins in the oilseed plant B. napus. Furthermore, a project on the biochemical interplay between the embryo and the endosperm during seed development is presented. We provide evidence that the endosperm includes a complete set of enzymes necessary for plant primary metabolism. Combination of our results with metabolome data will further improve systems-level understanding of the seed filling process and provide rational strategies for plant bioengineering.
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Affiliation(s)
- Christin Lorenz
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Stephanie Sunderhaus
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany.
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10
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Venglat P, Xiang D, Wang E, Datla R. Genomics of seed development: Challenges and opportunities for genetic improvement of seed traits in crop plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Huang D, Koh C, Feurtado JA, Tsang EWT, Cutler AJ. MicroRNAs and their putative targets in Brassica napus seed maturation. BMC Genomics 2013; 14:140. [PMID: 23448243 PMCID: PMC3602245 DOI: 10.1186/1471-2164-14-140] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 02/21/2013] [Indexed: 01/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) are 20–21 nucleotide RNA molecules that suppress the transcription of target genes and may also inhibit translation. Despite the thousands of miRNAs identified and validated in numerous plant species, only small numbers have been identified from the oilseed crop plant Brassica napus (canola) – especially in seeds. Results Using next-generation sequencing technologies, we performed a comprehensive analysis of miRNAs during seed maturation at 9 time points from 10 days after flowering (DAF) to 50 DAF using whole seeds and included separate analyses of radicle, hypocotyl, cotyledon, embryo, endosperm and seed coat tissues at 4 selected time points. We identified more than 500 conserved miRNA or variant unique sequences with >300 sequence reads and also found 10 novel miRNAs. Only 27 of the conserved miRNA sequences had been previously identified in B. napus (miRBase Release 18). More than 180 MIRNA loci were identified/annotated using the B. rapa genome as a surrogate for the B.napus A genome. Numerous miRNAs were expressed in a stage- or tissue-specific manner suggesting that they have specific functions related to the fine tuning of transcript abundance during seed development. miRNA targets in B. napus were predicted and their expression patterns profiled using microarray analyses. Global correlation analysis of the expression patterns of miRNAs and their targets revealed complex miRNA-target gene regulatory networks during seed development. The miR156 family was the most abundant and the majority of the family members were primarily expressed in the embryo. Conclusions Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and complex relationships between expression of miRNAs and targets were identified in this study. Several key miRNA-target expression patterns were identified and new roles of miRNAs in regulating seed development are suggested. miR156, miR159, miR172, miR167, miR158 and miR166 are the major contributors to the network controlling seed development and maturation through their pivotal roles in plant development. miR156 may regulate the developmental transition to germination.
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Affiliation(s)
- Daiqing Huang
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon S7N 0W9, Canada
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Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:189-217. [PMID: 23451786 DOI: 10.1146/annurev-arplant-050312-120215] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size--an important yield-related characteristic--as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding.
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Affiliation(s)
- Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
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Wang L, Shen W, Kazachkov M, Chen G, Chen Q, Carlsson AS, Stymne S, Weselake RJ, Zou J. Metabolic interactions between the Lands cycle and the Kennedy pathway of glycerolipid synthesis in Arabidopsis developing seeds. THE PLANT CELL 2012; 24:4652-69. [PMID: 23150634 PMCID: PMC3531858 DOI: 10.1105/tpc.112.104604] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/12/2012] [Accepted: 10/17/2012] [Indexed: 05/18/2023]
Abstract
It has been widely accepted that the primary function of the Lands cycle is to provide a route for acyl remodeling to modify fatty acid (FA) composition of phospholipids derived from the Kennedy pathway. Lysophosphatidylcholine acyltransferase (LPCAT) is an evolutionarily conserved key enzyme in the Lands cycle. In this study, we provide direct evidence that the Arabidopsis thaliana LPCATs, LPCAT1 and LPCAT2, participate in the Lands cycle in developing seeds. In spite of a substantially reduced initial rate of nascent FA incorporation into phosphatidylcholine (PC), the PC level in the double mutant lpcat1 lpcat2-2 remained unchanged. LPCAT deficiency triggered a compensatory response of de novo PC synthesis and a concomitant acceleration of PC turnover that were attributable at least in part to PC deacylation. Acyl-CoA profile analysis revealed complicated metabolic alterations rather than merely reduced acyl group shuffling from PC in the mutant. Shifts in FA stereo-specific distribution in triacylglycerol of the mutant seed suggested a preferential retention of saturated acyl chains at the stereospecific numbering (sn)-1 position from PC and likely a channeling of lysophosphatidic acid, derived from PC, into the Kennedy pathway. Our study thus illustrates an intricate relationship between the Lands cycle and the Kennedy pathway.
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Affiliation(s)
- Liping Wang
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Wenyun Shen
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Michael Kazachkov
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Guanqun Chen
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Qilin Chen
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Anders S. Carlsson
- Department of Plant Breeding and Biotechnology, Swedish University of Agricultural Sciences, S 230 53 Alnarp, Sweden
| | - Sten Stymne
- Department of Plant Breeding and Biotechnology, Swedish University of Agricultural Sciences, S 230 53 Alnarp, Sweden
| | - Randall J. Weselake
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Jitao Zou
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
- Address correspondence to
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Graeber K, Linkies A, Wood AT, Leubner-Metzger G. A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study. THE PLANT CELL 2011; 23:2045-63. [PMID: 21666000 PMCID: PMC3160028 DOI: 10.1105/tpc.111.084103] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 05/06/2011] [Accepted: 05/27/2011] [Indexed: 05/20/2023]
Abstract
Comparative biology includes the comparison of transcriptome and quantitative real-time RT-PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and divergent processes. Transcript abundance analysis of target genes by qRT-PCR requires a highly accurate and robust workflow. This includes reference genes with high expression stability (i.e., low intersample transcript abundance variation) for correct target gene normalization. Cross-species qRT-PCR for proper comparative transcript quantification requires reference genes suitable for different species. We addressed this issue using tissue-specific transcriptome data sets of germinating Lepidium sativum seeds to identify new candidate reference genes. We investigated their expression stability in germinating seeds of L. sativum and Arabidopsis thaliana by qRT-PCR, combined with in silico analysis of Arabidopsis and Brassica napus microarray data sets. This revealed that reference gene expression stability is higher for a given developmental process between distinct species than for distinct developmental processes within a given single species. The identified superior cross-species reference genes may be used for family-wide comparative qRT-PCR analysis of Brassicaceae seed germination. Furthermore, using germinating seeds, we exemplify optimization of the qRT-PCR workflow for challenging tissues regarding RNA quality, transcript stability, and tissue abundance. Our work therefore can serve as a guideline for moving beyond Arabidopsis by establishing high-quality cross-species qRT-PCR.
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Affiliation(s)
- Kai Graeber
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
| | - Ada Linkies
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
| | - Andrew T.A. Wood
- University of Nottingham, Division of Statistics, School of Mathematical Sciences, University Park, Nottingham NG7 2RD, United Kingdom
| | - Gerhard Leubner-Metzger
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, D-79104 Freiburg, Germany
- Address correspondence to
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Chen X, Truksa M, Shah S, Weselake RJ. A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus. Anal Biochem 2010; 405:138-40. [DOI: 10.1016/j.ab.2010.05.032] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/25/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
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Jiang Y, Deyholos MK. Transcriptome analysis of secondary-wall-enriched seed coat tissues of canola (Brassica napus L.). PLANT CELL REPORTS 2010; 29:327-42. [PMID: 20145934 DOI: 10.1007/s00299-010-0824-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/15/2010] [Accepted: 01/18/2010] [Indexed: 05/23/2023]
Abstract
The seed coat of Brassica napus (canola, oilseed rape) is derived from ovule integuments and contains a layer of palisade cells, which have thick secondary walls. Because cellulosic walls and other indigestible components of the seed coat contribute negatively to the value of oilseeds, efforts are underway to alter seed development. To facilitate these efforts, and to better understand the biology of seed coats, we used a 90,000 element microarray to identify genes whose transcripts were expressed in developing seed coats of B. napus. After dissecting seed coats into three layers, and comparing transcript expression in the middle fraction (which contained the palisade-enriched tissue and bulk of inner integument) to transcript expression in developing hypocotyls, we identified 674 genes whose transcripts were more abundant in the middle fraction of the seed coat. Among these were well-characterized markers of seed coat identity and many genes associated with metabolism of cell wall polysaccharides, flavonoids and various cell wall proteins and transcription factors. Conversely, we identified 1,203 genes whose transcripts were more abundant in the hypocotyl tissue as compared to seed coat, including xylem-specific markers, such as XCP1 and XCP2. We validated 21 of the differentially expressed transcripts using quantitative RT-PCR. The results define a set of transcripts that are highly enriched in the developing seed coat of B. napus.
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Affiliation(s)
- Yuanqing Jiang
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Canada
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