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Peng Y, Liang Z, Cai M, Wang J, Li D, Chen Q, Du X, Gu R, Wang G, Schnable PS, Wang J, Li L. ZmPTOX1, a plastid terminal oxidase, contributes to redox homeostasis during seed development and germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:460-477. [PMID: 38678554 DOI: 10.1111/tpj.16776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/24/2024] [Accepted: 03/31/2024] [Indexed: 05/01/2024]
Abstract
Maize plastid terminal oxidase1 (ZmPTOX1) plays a pivotal role in seed development by upholding redox balance within seed plastids. This study focuses on characterizing the white kernel mutant 3735 (wk3735) mutant, which yields pale-yellow seeds characterized by heightened protein but reduced carotenoid levels, along with delayed germination compared to wild-type (WT) seeds. We successfully cloned and identified the target gene ZmPTOX1, responsible for encoding maize PTOX-a versatile plastoquinol oxidase and redox sensor located in plastid membranes. While PTOX's established role involves regulating redox states and participating in carotenoid metabolism in Arabidopsis leaves and tomato fruits, our investigation marks the first exploration of its function in storage organs lacking a photosynthetic system. Through our research, we validated the existence of plastid-localized ZmPTOX1, existing as a homomultimer, and established its interaction with ferredoxin-NADP+ oxidoreductase 1 (ZmFNR1), a crucial component of the electron transport chain (ETC). This interaction contributes to the maintenance of redox equilibrium within plastids. Our findings indicate a propensity for excessive accumulation of reactive oxygen species (ROS) in wk3735 seeds. Beyond its known role in carotenoids' antioxidant properties, ZmPTOX1 also impacts ROS homeostasis owing to its oxidizing function. Altogether, our results underscore the critical involvement of ZmPTOX1 in governing seed development and germination by preserving redox balance within the seed plastids.
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Affiliation(s)
- Yixuan Peng
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Zhi Liang
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Minghao Cai
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Jie Wang
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Delin Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Quanquan Chen
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Xuemei Du
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Riliang Gu
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, 2035 Roy J. Carver Co-Lab, Ames, 50011-3650, Iowa, USA
| | - Jianhua Wang
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
| | - Li Li
- State Key Laboratory of Maize Bio-Breeding, Key Laboratory of Crop Heterosis Utilization, Ministry of Education, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, P. R. China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
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Yang Y, Kong Q, Lim ARQ, Lu S, Zhao H, Guo L, Yuan L, Ma W. Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100328. [PMID: 35605194 PMCID: PMC9482985 DOI: 10.1016/j.xplc.2022.100328] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.
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Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hu Zhao
- 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.
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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3
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Huang Y, Mei G, Fu X, Wang Y, Ruan X, Cao D. Ultrasonic Waves Regulate Antioxidant Defense and Gluconeogenesis to Improve Germination From Naturally Aged Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2022; 13:833858. [PMID: 35419018 PMCID: PMC8996252 DOI: 10.3389/fpls.2022.833858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Soybean seeds contain substantial triacylglycerols and fatty acids that are prone to oxidation during storage, contributing to the dramatic deterioration of seed vigor. This study reports an ultrasonic waves treatment (UWT), which is a physical method capable of promoting the germination ability of the aged soybean seeds by regulating the antioxidant defense and gluconeogenesis. Germination test revealed that UWT significantly increased the germination rate and seedlings' establishment of the soybean seeds stored for 12 months, although insignificantly impacting the vigor of fresh (stored for 1 month) and short-term stored (for 6 months) seeds. Further biochemical analysis revealed that UWT decreased the hydrogen peroxide (H2O2), O2⋅-, and malondialdehyde contents in the aged soybean seeds during early germination. Consistently, UWT prominently elevated the activities of superoxide dismutase, catalase, and acetaldehyde dehydrogenase, and also the corresponding gene expressions. Besides, the soluble sugar content of UWT was significantly higher than that of the untreated aged seeds. Analysis of enzyme activity showed UWT significantly upregulated the activities of several key enzymes in gluconeogenesis and the transcription levels of corresponding genes. Moreover, UWT enhanced the invertase activity within aged seeds, which was responsible for catalyzing sucrose hydrolysis for forming glucose and fructose. In summary, UWT improved germination and seedlings establishment of aged soybean seeds by regulating antioxidant defense and gluconeogenesis. This study expands the application of ultrasonication in agricultural production and further clarifies the physiological and molecular mechanisms of the aged seed germination, aiming to provide theoretical and practical guidance for seed quality and safety.
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Affiliation(s)
- Yutao Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Gaofu Mei
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xujun Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yang Wang
- The Key Laboratory of Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiaoli Ruan
- Zhejiang Nongke Seed Co. Ltd., Hangzhou, China
| | - Dongdong Cao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Bahmanpour S, Keshavarz M, Koohpeyma F, Badr P, Noori A, Dabbaghmanesh MH, Poordast T, Najib FS, Zare N, Namazi N, Jahromi BN. Preserving effect of Loboob (a traditional multi-herbal formulation) on sperm parameters of male rats with busulfan-induced subfertility. JBRA Assist Reprod 2022; 26:574-582. [PMID: 34995049 PMCID: PMC9635600 DOI: 10.5935/1518-0557.20210099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE Male infertility secondary to exposure to gonadotoxic agents during reproductive age is a concerning issue. The aim of this experimental study was to determine the effect of Loboob on sperm parameters. METHODS 55 healthy rats were selected, weighted and divided into five groups consisting of 11 rats each. The control group received no medication. Rats in Treatment Group 1 received 10mg/kg Busulfan and rats in Treatment Groups 2, 3, and 4 received 35,70 and 140 mg/kg Loboob respectively in addition to 10mg/kg Busulfan. Finally, the sperm parameters and weights of the rats were compared using the Kolmogorov-Smirnov, non-parametric Kruskal-Wallis, and Dunn-Bonferroni tests. RESULTS All sperm parameters and weights were significantly decreased among rats receiving Busulfan. All dosages of Loboob were effective to enhance the motility of slow spermatozoa, while only in the rats given 70 and 140 mg/kg of Loboob saw improvements in progressively motile sperm percentages (0.024 and 0.01, respectively). Loboob at a dosage of 140mg/kg improved sperm viability. It did not improve normal morphology sperm or decrease immotile sperm counts. Loboob did not affect mean rat weight. CONCLUSIONS Loboob offered a dose-dependent protective effect on several sperm parameters in rats with busulfan-induced subfertility.
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Affiliation(s)
- Soghra Bahmanpour
- Anatomy Department, School of Medicine, Shiraz University of
Medical Sciences, Shiraz, Iran , Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran
| | - Mojtaba Keshavarz
- Endocrine and Metabolism Research Center, Shiraz University of
Medical Sciences, Shiraz, Iran
| | - Farhad Koohpeyma
- Endocrine and Metabolism Research Center, Shiraz University of
Medical Sciences, Shiraz, Iran
| | - Parmis Badr
- Pharmaceutical Sciences Research Center, Shiraz University of
Medical Sciences, Shiraz, Iran , Phytopharmaceutical Technology and Traditional Medicine Incubator,
Shiraz University of Medical Sciences, Shiraz, Iran
| | - Adel Noori
- Student Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Obstetrics and Gynecology, School of Medicine, Shiraz
University of Medical Sciences, Shiraz, Iran
| | | | - Tahereh Poordast
- Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Obstetrics and Gynecology, School of Medicine, Shiraz
University of Medical Sciences, Shiraz, Iran
| | - Fateme Sadat Najib
- Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Obstetrics and Gynecology, School of Medicine, Shiraz
University of Medical Sciences, Shiraz, Iran
| | - Najaf Zare
- Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Biostatistics, School of Medicine, Shiraz University
of Medical Sciences, Shiraz, Iran
| | - Niloofar Namazi
- Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Obstetrics and Gynecology, School of Medicine, Shiraz
University of Medical Sciences, Shiraz, Iran
| | - Bahia Namavar Jahromi
- Infertility Research Center, Shiraz University of Medical Sciences,
Shiraz, Iran , Department of Obstetrics and Gynecology, School of Medicine, Shiraz
University of Medical Sciences, Shiraz, Iran ,Corresponding author: Bahia Namavar Jahromi Department
of OB-GYN School of Medicine Shiraz University of Medical Sciences Shiraz, Iran.
E-mail:
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Huang Y, Cai S, Ruan X, Xu J, Cao D. CSN improves seed vigor of aged sunflower seeds by regulating the fatty acid, glycometabolism, and abscisic acid metabolism. J Adv Res 2021; 33:1-13. [PMID: 34603775 PMCID: PMC8463905 DOI: 10.1016/j.jare.2021.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/03/2021] [Accepted: 01/29/2021] [Indexed: 11/06/2022] Open
Abstract
Introduction Sunflower seeds possess higher oil content than do cereal crop seeds. Storage of sunflower seeds is accompanied by loss of seed vigor and oxidation of storage and membrane lipids. Objectives This study first reported that compound sodium nitrophenolate (CSN), a new plant growth modulator, improved the germination and seedling emergence of aged sunflower seeds. The present study provide a future reference as to the potential applications of CSN and the regulation mechanism of exogenous substances in increasing aged crop seed vigor. Methods Phenotypic analysis was performed to investigate the effect of CSN on germination and seedling emergence from naturally- and artificially-aged sunflower seeds. The biochemical and enzyme activity analysis were conducted to test the CSN-induced effect on glycometabolism, fatty acid and abscisic acid metabolism. Meanwhile, gene expression analysis was carried out to detect the changes in the transcription level of sunflower seeds during early germination period after CSN treatment. Results CSN application significantly increased the germination rate and seedling emergence rate of sunflower seeds under natural and artificial aging. Biochemical analysis indicated that, CSN treatment significantly enhanced the sucrose and fructose contents in aged sunflower seeds during early germination period. Moreover, the contents of several different fatty acids in CSN-treated sunflower seeds also significantly increased. Enzyme activity analysis revealed that CSN treatment remarkably up-regulated the activities of several critical enzymes related to triacylglycerol hydrolysis. Consequently, the transcription levels of the above key enzymes-related synthetic genes were also significantly up-regulated in CSN treatment. Furthermore, CSN treatment significantly decreased abscisic acid (ABA) content through the regulation of the gene expressions and activities of metabolism related-enzymes. Conclusion Taken together, the contribution of CSN to the improvement of aged sunflower seed germination and seedling emergence might be closely related to the fatty acid, glycometabolism, and ABA metabolism.
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Affiliation(s)
- Yutao Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, China
| | - Shuyu Cai
- School of Architectural Engineering, Shaoxing University Yuanpei College, 312000 Shaoxing, China
| | - Xiaoli Ruan
- Zhejiang Nongke Seed Co. Ltd, 198 Shiqiao Road, Hangzhou 310021, China
| | - Jun Xu
- Bureau of Agriculture and Rural Affairs of Pinhu City, 500 Xinhuabei Road, Pinhu 314200, China
| | - Dongdong Cao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, China
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Huang Y, Lu M, Wu H, Zhao T, Wu P, Cao D. High Drying Temperature Accelerates Sunflower Seed Deterioration by Regulating the Fatty Acid Metabolism, Glycometabolism, and Abscisic Acid/Gibberellin Balance. FRONTIERS IN PLANT SCIENCE 2021; 12:628251. [PMID: 34122464 PMCID: PMC8193951 DOI: 10.3389/fpls.2021.628251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/03/2021] [Indexed: 05/04/2023]
Abstract
Sunflower seed storage is accompanied by the loss of seed vigor. Seed drying is a key link between seed harvest and seed storage; however, to date, the effect of seed drying on sunflower seed deterioration during storage remains unclear. The present study performed hot air drying for sunflower seeds with an initial moisture content of 30% to examine the manner in which drying temperature (35, 40, 45, 50, and 55°C) affects the drying performance and seed vigor following storage process (6 and 12 months). A drying temperature of 40°C was evidently safe for sunflower seeds, whereas the high drying temperatures (HTD, 45, 50, and 55°C) significantly lowered sunflower seed vigor by regulating the fatty acid metabolism, glycometabolism, and abscisic acid (ABA)/gibberellin (GA) balance. HDT significantly increased the seed damage rate and accelerated sunflower seed deterioration during natural and artificial aging process. Further biochemical analysis indicated that HDT significantly increased lipoxygenase and dioxygenase activities, leading to malonaldehyde and reactive oxygen species over-accumulation during storage. During early seed germination, HDT significantly inhibited fatty acid hydrolysis and glycometabolism by decreasing triacylglycerol lipase, CoA-SH oxidase, and invertase activities. Moreover, HDT remarkably increased ABA levels but reduced GA levels by regulating gene expressions and metabolic enzyme activities during early imbibitions. Cumulatively, the seed drying effect on sunflower seed vigor deterioration during the storage process may be strongly related to fatty acid oxidation and hydrolysis metabolism, toxic substance accumulation, and ABA/GA balance.
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Affiliation(s)
- Yutao Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Lu
- Huzhou Keao Seed Co., Ltd., Huzhou, China
| | - Huaping Wu
- Huzhou Keao Seed Co., Ltd., Huzhou, China
| | | | - Pin Wu
- Huzhou Keao Seed Co., Ltd., Huzhou, China
| | - Dongdong Cao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Huzhou Keao Seed Co., Ltd., Huzhou, China
- *Correspondence: Dongdong Cao,
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Gaikwad KB, Rani S, Kumar M, Gupta V, Babu PH, Bainsla NK, Yadav R. Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding. Front Nutr 2020; 7:533453. [PMID: 33324668 PMCID: PMC7725794 DOI: 10.3389/fnut.2020.533453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 01/14/2023] Open
Abstract
Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.
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Affiliation(s)
- Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sushma Rani
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Manjeet Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vikas Gupta
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Prashanth H. Babu
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Naresh Kumar Bainsla
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res 2020; 30:1593-1604. [PMID: 33060172 PMCID: PMC7605251 DOI: 10.1101/gr.255224.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic, and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified 15 loci with potential pleiotropic effects on the proteome. We showed that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein coexpression network, and a reprogramming of the genetic control of the abundance of many proteins, including those involved in stress response. Colocalizations between pQTLs and QTLs for ecophysiological traits, found mostly in the water deficit condition, indicated that this reprogramming may also affect the phenotypic level. Finally, we identified several candidate genes that are potentially responsible for both the coexpression of stress response proteins and the variations of ecophysiological traits under water deficit. Taken together, our findings provide novel insights into the molecular mechanisms of drought tolerance and suggest some pathways for further research and breeding.
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Dharanishanthi V, Ghosh Dasgupta M. Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis. 3 Biotech 2018; 8:315. [PMID: 30023147 DOI: 10.1007/s13205-018-1344-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/09/2018] [Indexed: 12/28/2022] Open
Abstract
Suitability of wood biomass for pulp production is dependent on the cellular architecture and composition of secondary cell wall. Presently, systems genetics approach is being employed to understand the molecular basis of trait variation and co-expression network analysis has enabled holistic understanding of complex trait such as secondary development. Transcription factors (TFs) are reported as key regulators of meristematic growth and wood formation. The hierarchical TF network is a multi-layered system which interacts with downstream structural genes involved in biosynthesis of cellulose, hemicelluloses and lignin. Several TFs have been associated with wood formation in tree species such as Populus, Eucalyptus, Picea and Pinus. However, TF-specific co-expression networks to understand the interaction between these regulators are not reported. In the present study, co-expression network was developed for TFs expressed during wood formation in Eucalyptus tereticornis and ethylene-responsive element-binding factor, EtERF2, was identified as the major hub transcript which co-expressed with other secondary cell wall biogenesis-specific TFs such as EtSND2, EtVND1, EtVND4, EtVND6, EtMYB70, EtGRAS and EtSCL8. This study reveals a probable role of ethylene in determining natural variation in wood properties in Eucalyptus species. Understanding this transcriptional regulation underpinning the complex bio-processing trait of wood biomass will complement the Eucalyptus breeding program through selection of industrially suitable phenotypes by marker-assisted selection.
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Bao B, Chao H, Wang H, Zhao W, Zhang L, Raboanatahiry N, Wang X, Wang B, Jia H, Li M. Stable, Environmental Specific and Novel QTL Identification as Well as Genetic Dissection of Fatty Acid Metabolism in Brassica napus. FRONTIERS IN PLANT SCIENCE 2018; 9:1018. [PMID: 30065738 PMCID: PMC6057442 DOI: 10.3389/fpls.2018.01018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/22/2018] [Indexed: 05/05/2023]
Abstract
Fatty acid (FA) composition is the typical quantitative trait in oil seed crops, of which study is not only closely related to oil content, but is also more critical for the quality improvement of seed oil. The double haploid (DH) population named KN with a high density SNP linkage map was applied for quantitative trait loci (QTL) analysis of FA composition in this study. A total of 406 identified QTL were detected for eight FA components with an average confidence interval (CI) of 2.92 cM, the explained phenotypic variation (PV) value ranged from 1.49 to 45.05%. Totally, 204 consensus and 91 unique QTL were further obtained via meta-analysis method for the purpose of detecting multiple environment expressed and pleiotropic QTL, respectively. Of which, 74 stable expressed and 22 environmental specific QTL were also revealed, respectively. In order to make clear the genetic mechanism of FA metabolism at individual QTL level, conditional QTL analysis was also conducted and more than two thousand conditional QTL which could not be detected under the unconditional mapping were detected, which indicated the complex interrelationship of the QTL controlling FA content in rapeseed. Through comparative genomic analysis and homologous gene annotation, 61 candidates related to acyl lipid metabolism were identified underlying the CI of FA QTL. To further visualize the genetic mechanism of FA metabolism, an intuitive and meticulous network about acyl lipid metabolism was constructed and some closely related candidates were positioned. This study provided a more accurate localization for stable and pleiotropic QTL, and a deeper dissection of the molecular regulatory mechanism of FA metabolism in rapeseed.
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Affiliation(s)
- Binghao Bao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Lina Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaodong Wang
- Provincial Key Laboratory of Agrobiology, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Haibo Jia
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Haibo Jia
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
- Maoteng Li
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Mochida K, Koda S, Inoue K, Nishii R. Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets. FRONTIERS IN PLANT SCIENCE 2018; 9:1770. [PMID: 30555503 PMCID: PMC6281826 DOI: 10.3389/fpls.2018.01770] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023]
Abstract
Statistical and machine learning (ML)-based methods have recently advanced in construction of gene regulatory network (GRNs) based on high-throughput biological datasets. GRNs underlie almost all cellular phenomena; hence, comprehensive GRN maps are essential tools to elucidate gene function, thereby facilitating the identification and prioritization of candidate genes for functional analysis. High-throughput gene expression datasets have yielded various statistical and ML-based algorithms to infer causal relationship between genes and decipher GRNs. This review summarizes the recent advancements in the computational inference of GRNs, based on large-scale transcriptome sequencing datasets of model plants and crops. We highlight strategies to select contextual genes for GRN inference, and statistical and ML-based methods for inferring GRNs based on transcriptome datasets from plants. Furthermore, we discuss the challenges and opportunities for the elucidation of GRNs based on large-scale datasets obtained from emerging transcriptomic applications, such as from population-scale, single-cell level, and life-course transcriptome analyses.
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Affiliation(s)
- Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryuei Nishii
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
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Butardo VM, Anacleto R, Parween S, Samson I, de Guzman K, Alhambra CM, Misra G, Sreenivasulu N. Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis. PLANT PHYSIOLOGY 2017; 173:887-906. [PMID: 27881726 PMCID: PMC5210722 DOI: 10.1104/pp.16.01248] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/21/2016] [Indexed: 05/20/2023]
Abstract
A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.
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Affiliation(s)
- Vito M Butardo
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Roslen Anacleto
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sabiha Parween
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Irene Samson
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Krishna de Guzman
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Crisline Mae Alhambra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Gopal Misra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Nese Sreenivasulu
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
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13
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Kazmi RH, Willems LAJ, Joosen RVL, Khan N, Ligterink W, Hilhorst HWM. Metabolomic analysis of tomato seed germination. Metabolomics 2017; 13:145. [PMID: 29104520 PMCID: PMC5653705 DOI: 10.1007/s11306-017-1284-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Seed germination is inherently related to seed metabolism, which changes throughout its maturation, desiccation and germination processes. The metabolite content of a seed and its ability to germinate are determined by underlying genetic architecture and environmental effects during development. OBJECTIVE This study aimed to assess an integrative approach to explore genetics modulating seed metabolism in different developmental stages and the link between seed metabolic- and germination traits. METHODS We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages. We describe, for the first time in tomato, the use of a so-called generalized genetical genomics (GGG) model to study the interaction between genetics, environment and seed metabolism using 100 tomato recombinant inbred lines (RILs) derived from a cross between Solanum lycopersicum and Solanum pimpinellifolium. RESULTS QTLs were found for over two-thirds of the metabolites within several QTL hotspots. The transition from dry to 6 h imbibed seeds was associated with programmed metabolic switches. Significant correlations varied among individual metabolites and the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways. CONCLUSIONS Extensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance.
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Affiliation(s)
- Rashid H. Kazmi
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Leo A. J. Willems
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ronny V. L. Joosen
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Noorullah Khan
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wilco Ligterink
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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14
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Shasidhar Y, Vishwakarma MK, Pandey MK, Janila P, Variath MT, Manohar SS, Nigam SN, Guo B, Varshney RK. Molecular Mapping of Oil Content and Fatty Acids Using Dense Genetic Maps in Groundnut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2017; 8:794. [PMID: 28588591 PMCID: PMC5438992 DOI: 10.3389/fpls.2017.00794] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/27/2017] [Indexed: 05/04/2023]
Abstract
Enhancing seed oil content with desirable fatty acid composition is one of the most important objectives of groundnut breeding programs globally. Genomics-assisted breeding facilitates combining multiple traits faster, however, requires linked markers. In this context, we have developed two different F2 mapping populations, one for oil content (OC-population, ICGV 07368 × ICGV 06420) and another for fatty acid composition (FA-population, ICGV 06420 × SunOleic 95R). These two populations were phenotyped for respective traits and genotyped using Diversity Array Technology (DArT) and DArTseq genotyping platforms. Two genetic maps were developed with 854 (OC-population) and 1,435 (FA-population) marker loci with total map distance of 3,526 and 1,869 cM, respectively. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data identified eight QTLs for oil content including two major QTLs, qOc-A10 and qOc-A02, with 22.11 and 10.37% phenotypic variance explained (PVE), respectively. For seven different fatty acids, a total of 21 QTLs with 7.6-78.6% PVE were identified and 20 of these QTLs were of major effect. Two mutant alleles, ahFAD2B and ahFAD2A, also had 18.44 and 10.78% PVE for palmitic acid, in addition to oleic (33.8 and 17.4% PVE) and linoleic (41.0 and 19.5% PVE) acids. Furthermore, four QTL clusters harboring more than three QTLs for fatty acids were identified on the three LGs. The QTLs identified in this study could be further dissected for candidate gene discovery and development of diagnostic markers for breeding improved groundnut varieties with high oil content and desirable oil quality.
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Affiliation(s)
- Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Department of Genetics, Osmania UniversityHyderabad, India
| | | | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
| | - Murali T. Variath
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Shyam N. Nigam
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, Agricultural Research Service (USDA), TiftonGA, USA
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Agriculture and Environment, University of Western Australia, CrawleyWA, Australia
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
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Abstract
One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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16
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Gacek K, Bayer PE, Bartkowiak-Broda I, Szala L, Bocianowski J, Edwards D, Batley J. Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:2062. [PMID: 28163710 PMCID: PMC5247464 DOI: 10.3389/fpls.2016.02062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/26/2016] [Indexed: 05/03/2023]
Abstract
Fatty acids and their composition in seeds determine oil value for nutritional or industrial purposes and also affect seed germination as well as seedling establishment. To better understand the genetic basis of seed fatty acid biosynthesis in oilseed rape (Brassica napus L.) we applied a genome-wide association study, using 91,205 single nucleotide polymorphisms (SNPs) characterized across a mapping population with high-resolution skim genotyping by sequencing (SkimGBS). We identified a cluster of loci on chromosome A05 associated with oleic and linoleic seed fatty acids. The delineated genomic region contained orthologs of the Arabidopsis thaliana genes known to play a role in regulation of seed fatty acid biosynthesis such as Fatty acyl-ACP thioesterase B (FATB) and Fatty Acid Desaturase (FAD5). This approach allowed us to identify potential functional genes regulating fatty acid composition in this important oil producing crop and demonstrates that this approach can be used as a powerful tool for dissecting complex traits for B. napus improvement programs.
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Affiliation(s)
- Katarzyna Gacek
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Philipp E. Bayer
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
| | - Iwona Bartkowiak-Broda
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Laurencja Szala
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznan University of Life SciencesPoznan, Poland
| | - David Edwards
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
| | - Jacqueline Batley
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
- *Correspondence: Jacqueline Batley
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17
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Qu C, Zhao H, Fu F, Zhang K, Yuan J, Liu L, Wang R, Xu X, Lu K, Li JN. Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1691. [PMID: 27881992 PMCID: PMC5102069 DOI: 10.3389/fpls.2016.01691] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/26/2016] [Indexed: 05/18/2023]
Abstract
Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue UniversityWest Lafayette, IN, USA
| | - Kai Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Jianglian Yuan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Jia-Na Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Jia-na Li
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18
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Basnet RK, Duwal A, Tiwari DN, Xiao D, Monakhos S, Bucher J, Visser RGF, Groot SPC, Bonnema G, Maliepaard C. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:1032. [PMID: 26648948 PMCID: PMC4664704 DOI: 10.3389/fpls.2015.01032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/06/2015] [Indexed: 05/03/2023]
Abstract
The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.
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Affiliation(s)
- Ram K. Basnet
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- Centre for BioSystems GenomicsWageningen, Netherlands
| | - Anita Duwal
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
| | - Dev N. Tiwari
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
| | - Dong Xiao
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Horticultural College, Nanjing Agricultural UniversityNanjing, China
| | - Sokrat Monakhos
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- Russian State Agrarian University, Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
| | - Richard G. F. Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- Centre for BioSystems GenomicsWageningen, Netherlands
| | | | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- Centre for BioSystems GenomicsWageningen, Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Chris Maliepaard
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