1
|
Cui C, Zhang K, Chai L, Zheng B, Zhang J, Jiang J, Tan C, Li H, Chen D, Jiang L. Unraveling the mechanism of flower color variation in Brassica napus by integrated metabolome and transcriptome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1419508. [PMID: 38933465 PMCID: PMC11199733 DOI: 10.3389/fpls.2024.1419508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Brassica napus is one of the most important oil crops in the world. Breeding oilseed rape with colorful flowers can greatly enhance the ornamental value of B. napus and thus improve the economic benefits of planting. As water-soluble flavonoid secondary metabolites, anthocyanins are very important for the synthesis and accumulation of pigments in the petals of plants, giving them a wide range of bright colors. Despite the documentation of over 60 distinct flower shades in B. napus, the intricacies underlying flower color variation remain elusive. Particularly, the mechanisms driving color development across varying flower color backgrounds necessitate further comprehensive investigation. This research undertook a comprehensive exploration through the integration of transcriptome and metabolome analyses to pinpoint pivotal genes and metabolites underpinning an array of flower colors, including beige, beige-red, yellow, orange-red, deep orange-red, white, light-purple, and purple. First, we used a two-way BLAST search to find 275 genes in the reference genome of B. napus Darmor v10 that were involved in making anthocyanins. The subsequent scrutiny of RNA-seq outcomes underscored notable upregulation in the structural genes F3H and UGT, alongside the MYB75, GL3, and TTG1 transcriptional regulators within petals, showing anthocyanin accumulation. By synergizing this data with a weighted gene co-expression network analysis, we identified CHS, F3H, MYB75, MYB12, and MYB111 as the key players driving anthocyanin synthesis in beige-red, orange-red, deep orange-red, light-purple, and purple petals. By integrating transcriptome and weighted gene co-expression network analysis findings with anthocyanin metabolism data, it is hypothesized that the upregulation of MYB75, which, in turn, enhances F3H expression, plays a pivotal role in the development of pigmented oilseed rape flowers. These findings help to understand the transcriptional regulation of anthocyanin biosynthesis in B. napus and provide valuable genetic resources for breeding B. napus varieties with novel flower colors.
Collapse
Affiliation(s)
- Cheng Cui
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ka Zhang
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Liang Chai
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Benchuan Zheng
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jinfang Zhang
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Jiang
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Chen Tan
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, China
| | - Haojie Li
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, China
| | - Liangcai Jiang
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| |
Collapse
|
2
|
Cai Y, Liang Y, Shi H, Cui J, Prakash S, Zhang J, Anaokar S, Chai J, Schwender J, Lu C, Yu XH, Shanklin J. Creating yellow seed Camelina sativa with enhanced oil accumulation by CRISPR-mediated disruption of Transparent Testa 8. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38859598 DOI: 10.1111/pbi.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/26/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024]
Abstract
Camelina (Camelina sativa L.), a hexaploid member of the Brassicaceae family, is an emerging oilseed crop being developed to meet the increasing demand for plant oils as biofuel feedstocks. In other Brassicas, high oil content can be associated with a yellow seed phenotype, which is unknown for camelina. We sought to create yellow seed camelina using CRISPR/Cas9 technology to disrupt its Transparent Testa 8 (TT8) transcription factor genes and to evaluate the resulting seed phenotype. We identified three TT8 genes, one in each of the three camelina subgenomes, and obtained independent CsTT8 lines containing frameshift edits. Disruption of TT8 caused seed coat colour to change from brown to yellow reflecting their reduced flavonoid accumulation of up to 44%, and the loss of a well-organized seed coat mucilage layer. Transcriptomic analysis of CsTT8-edited seeds revealed significantly increased expression of the lipid-related transcription factors LEC1, LEC2, FUS3, and WRI1 and their downstream fatty acid synthesis-related targets. These changes caused metabolic remodelling with increased fatty acid synthesis rates and corresponding increases in total fatty acid (TFA) accumulation from 32.4% to as high as 38.0% of seed weight, and TAG yield by more than 21% without significant changes in starch or protein levels compared to parental line. These data highlight the effectiveness of CRISPR in creating novel enhanced-oil germplasm in camelina. The resulting lines may directly contribute to future net-zero carbon energy production or be combined with other traits to produce desired lipid-derived bioproducts at high yields.
Collapse
Affiliation(s)
- Yuanheng Cai
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Yuanxue Liang
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Hai Shi
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jodie Cui
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Shreyas Prakash
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jianhui Zhang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Sanket Anaokar
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jin Chai
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Jorg Schwender
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Xiao-Hong Yu
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| |
Collapse
|
3
|
Akanmu AO, Asemoloye MD, Marchisio MA, Babalola OO. Adoption of CRISPR-Cas for crop production: present status and future prospects. PeerJ 2024; 12:e17402. [PMID: 38860212 PMCID: PMC11164064 DOI: 10.7717/peerj.17402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time. Methods This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security. Results The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops. Conclusion Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.
Collapse
Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | - Michael Dare Asemoloye
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| |
Collapse
|
4
|
Zhang W, Higgins EE, Robinson SJ, Clarke WE, Boyle K, Sharpe AG, Fobert PR, Parkin IAP. A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds. FRONTIERS IN PLANT SCIENCE 2024; 15:1393621. [PMID: 38903439 PMCID: PMC11188405 DOI: 10.3389/fpls.2024.1393621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 06/22/2024]
Abstract
Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.
Collapse
Affiliation(s)
- Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Erin E. Higgins
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Stephen J. Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Wayne E. Clarke
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - Pierre R. Fobert
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada
| | - Isobel A. P. Parkin
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| |
Collapse
|
5
|
Tao B, Ma Y, Wang L, He C, Chen J, Ge X, Zhao L, Wen J, Yi B, Tu J, Fu T, Shen J. Developmental pleiotropy of SDP1 from seedling to mature stages in B. napus. PLANT MOLECULAR BIOLOGY 2024; 114:49. [PMID: 38642182 DOI: 10.1007/s11103-024-01447-8] [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: 12/22/2023] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
Rapeseed, an important oil crop, relies on robust seedling emergence for optimal yields. Seedling emergence in the field is vulnerable to various factors, among which inadequate self-supply of energy is crucial to limiting seedling growth in early stage. SUGAR-DEPENDENT1 (SDP1) initiates triacylglycerol (TAG) degradation, yet its detailed function has not been determined in B. napus. Here, we focused on the effects of plant growth during whole growth stages and energy mobilization during seedling establishment by mutation in BnSDP1. Protein sequence alignment and haplotypic analysis revealed the conservation of SDP1 among species, with a favorable haplotype enhancing oil content. Investigation of agronomic traits indicated bnsdp1 had a minor impact on vegetative growth and no obvious developmental defects when compared with wild type (WT) across growth stages. The seed oil content was improved by 2.0-2.37% in bnsdp1 lines, with slight reductions in silique length and seed number per silique. Furthermore, bnsdp1 resulted in lower seedling emergence, characterized by a shrunken hypocotyl and poor photosynthetic capacity in the early stages. Additionally, impaired seedling growth, especially in yellow seedlings, was not fully rescued in medium supplemented with exogenous sucrose. The limited lipid turnover in bnsdp1 was accompanied by induced amino acid degradation and PPDK-dependent gluconeogenesis pathway. Analysis of the metabolites in cotyledons revealed active amino acid metabolism and suppressed lipid degradation, consistent with the RNA-seq results. Finally, we proposed strategies for applying BnSDP1 in molecular breeding. Our study provides theoretical guidance for understanding trade-off between oil accumulation and seedling energy mobilization in B. napus.
Collapse
Affiliation(s)
- Baolong Tao
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Yina Ma
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Liqin Wang
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Chao He
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Junlin Chen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Xiaoyu Ge
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Lun Zhao
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jing Wen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Bin Yi
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jinxing Tu
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Tingdong Fu
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jinxiong Shen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China.
| |
Collapse
|
6
|
Zhao W, Li X, Wen J, Li Q, Bian S, Ren Y. BrTTG1 regulates seed coat proanthocyanidin formation through a direct interaction with structural gene promoters of flavonoid pathway and glutathione S-transferases in Brassica rapa L. FRONTIERS IN PLANT SCIENCE 2024; 15:1372477. [PMID: 38638349 PMCID: PMC11024264 DOI: 10.3389/fpls.2024.1372477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/18/2024] [Indexed: 04/20/2024]
Abstract
Introduction Seed coat color is a significant agronomic trait in horticultural crops such as Brassica rapa which is characterized by brown or yellow seed coat coloration. Previous Brassica rapa studies have shown that BrTTG1 is responsible for seed coat proanthocyanidin formation, which is dependent on the MYB-bHLH-WD40 complex, whereas some studies have reported that TRANSPARENT TESTA GLABRA 1 (TTG1) directly interacts with the structural gene promoters of the flavonoid pathway. Methods Herein, the brown-seeded inbred B147 and ttg1 yellow-seeded inbred B80 mutants were used as plant materials for gene expression level analysis, gene promoter clone and transient overexpression. Results The analysis identified eleven structural genes involved in the flavonoid biosynthesis pathway, which are potentially responsible for BrTTG1- dependent seed coat proanthocyanidin formation. The promoters of these genes were cloned and cis-acting elements were identified. Yeast one-hybrid and dual-luciferase assays confirmed that BrTTG1 directly and independently interacted with proCHS-Bra008792, proDFR-Bra027457, proTT12-Bra003361, proTT19-Bra008570, proTT19-Bra023602 and proAHA10-Bra016610. A TTG1-binding motif (RTWWGTRGM) was also identified. Overexpression of TTG1 in the yellow-seed B. rapa inbred induced proanthocyanidin accumulation by increasing the expression levels of related genes. Discussion Our study unveiled, for the first time, the direct interaction between TTG1 and the promoters of the flavonoid biosynthesis pathway structural genes and glutathione S-transferases in Brassica rapa. Additionally, we have identified a novel TTG1-binding motif, providing a basis for further exploration into the function of TTG1 and the accumulation of proanthocyanidins in seed coats.
Collapse
Affiliation(s)
- Wenju Zhao
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
| | - Xiaojuan Li
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
| | - Junqin Wen
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Qinghai, Xining, China
| | - Quanhui Li
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Qinghai, Xining, China
| | - Shuanling Bian
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
| | - Yanjing Ren
- Qinghai University, Academy of Agriculture and Forestry Sciences of Qinghai Province, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai, Xining, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Qinghai, Xining, China
| |
Collapse
|
7
|
Lu N. Revisiting decade-old questions in proanthocyanidin biosynthesis: current understanding and new challenges. FRONTIERS IN PLANT SCIENCE 2024; 15:1373975. [PMID: 38595764 PMCID: PMC11002137 DOI: 10.3389/fpls.2024.1373975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Proanthocyanidins (PAs), one of the most abundant natural polymers found in plants, are gaining increasing attention because of their beneficial effects for agriculture and human health. The study of PA biosynthesis has been active for decades, and progress has been drastically accelerated since the discovery of key enzymes such as Anthocyanidin Reductase (ANR), Leucoanthocyanidin Reductase (LAR), and key transcription factors such as Transparent Testa 2 (TT2) and Transparent Testa 8 (TT8) in the early 2000s. Scientists raised some compelling questions regarding PA biosynthesis about two decades ago in the hope that addressing these questions would lead to an enhanced understanding of PA biosynthesis in plants. These questions focus on the nature of starter and extension units for PA biosynthesis, the stereochemistry of PA monomers and intermediates, and how and where the polymerization or condensation steps work subcellularly. Here, I revisit these long-standing questions and provide an update on progress made toward answering them. Because of advanced technologies in genomics, bioinformatics and metabolomics, we now have a much-improved understanding of functionalities of key enzymes and identities of key intermediates in the PA biosynthesis and polymerization pathway. Still, several questions, particularly the ones related to intracellular PA transportation and deposition, as well as enzyme subcellular localization, largely remain to be explored. Our increasing understanding of PA biosynthesis in various plant species has led to a new set of compelling open questions, suggesting future research directions to gain a more comprehensive understanding of PA biosynthesis.
Collapse
Affiliation(s)
- Nan Lu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| |
Collapse
|
8
|
Chen XY, Wu HX, Zhang XH, Guo RH, Li K, Fu YL, Huang Z, Xu AX, Dong JG, Yu CY. Comparative Transcriptomics Uncovers Upstream Factors Regulating BnFAD3 Expression and Affecting Linolenic Acid Biosynthesis in Yellow-Seeded Rapeseed ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:760. [PMID: 38592766 PMCID: PMC10974354 DOI: 10.3390/plants13060760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 04/10/2024]
Abstract
α-Linolenic acid (ALA) is an important nutrient component in rapeseed oil, and rapeseed breeders want to either restrain or enhance the function of fatty acid desaturases (FADs) in the ALA biosynthesis pathway. To determine the reason for the upregulation of rapeseed BnFAD genes in two high-ALA accessions, R8Q10 and YH25005, we compared their transcriptome profiles in the seed at 24 days after pollination (DAP) with those of two low-ALA lines, A28 and SW. The expression levels of twenty-eight important genes in the seed samples at 20, 27, and 34 DAP were also investigated using an RT-qPCR. The expression levels of genes involved in flavonoid and proanthocyanidin synthesis, including BnCHS, BnCHI, BnDFR, BnFLS1, BnLDOX, BnBAN, BnTT10, and BnTT12 and genes encoding the transcription factors BnTT1, BnTT2, BnTT8, and BnTT16 were lower in R8Q10 and YH25005 than in A28 and SW. The expression levels of genes encoding master transcription factors in embryo development, such as BnLEC1, BnABI3, BnFUS3, BnL1L, BnAREB3, and BnbZIP67, were elevated significantly in the two high-ALA accessions. Combined with previous results in the Arabidopsis and rapeseed literature, we speculated that the yellow-seededness genes could elevate the activity of BnLEC1, BnABI3, BnFUS3, and BnbZIP67, etc., by reducing the expression levels of several transparent testa homologs, resulting in BnFAD3 and BnFAD7 upregulation and the acceleration of ALA synthesis. Yellow-seededness is a favorable factor to promote ALA synthesis in the two high-ALA accessions with the yellow-seeded trait. These findings provide initial insights into the transcriptomic differences between high-/low-ALA germplasms and a theoretic basis for seed quality breeding.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Cheng-Yu Yu
- College of Agronomy, Northwest A&F University, Taicheng Road 3, Yangling 712100, China (Z.H.); (A.-X.X.)
| |
Collapse
|
9
|
Tan Z, Han X, Dai C, Lu S, He H, Yao X, Chen P, Yang C, Zhao L, Yang QY, Zou J, Wen J, Hong D, Liu C, Ge X, Fan C, Yi B, Zhang C, Ma C, Liu K, Shen J, Tu J, Yang G, Fu T, Guo L, Zhao H. Functional genomics of Brassica napus: Progresses, challenges, and perspectives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:484-509. [PMID: 38456625 DOI: 10.1111/jipb.13635] [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: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024]
Abstract
Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.
Collapse
Affiliation(s)
- Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Xu Han
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanzi He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
10
|
Amin F, Al-Huqail AA, Ullah S, Khan MN, Kaplan A, Ali B, Iqbal M, Elsaid FG, Ercisli S, Malik T, Al-Robai SA, Abeed AHA. Mitigation effect of alpha-tocopherol and thermo-priming in Brassica napus L. under induced mercuric chloride stress. BMC PLANT BIOLOGY 2024; 24:108. [PMID: 38347449 PMCID: PMC10863246 DOI: 10.1186/s12870-024-04767-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024]
Abstract
Soil pollution with heavy metals has grown to be a big hassle, leading to the loss in farming production particularly in developing countries like Pakistan, where no proper channel is present for irrigation and extraction of these toxic heavy metals. The present study aims to ameliorate the damages caused by heavy metal ions (Hg-Mercury) on rapeseed (Brassica napus L.) via a growth regulator (α-tocopherol 150 mg/L) and thermopriming technique at 4 °C and 50 °C to maintain plant agronomical and physiological characteristics. In pot experiments, we designed total of 11 treatments viz.( T0 (control), T1 (Hg4ppm), T2 (Hg8ppm), T3 (Hg4ppm + 4 °C), T4 (Hg4ppm + 4 °C + tocopherol (150 m/L)), T5 (Hg4ppm + 50 °C), T6 (Hg4ppm + 50 °C + tocopherol (150 mg/L)), T7 (Hg8ppm + 4 °C), T8 (Hg8ppm + 4 °C + tocopherol (150 mg/L)), T9 (Hg8ppm + 50 °C), T10 (Hg8ppm + 50 °C + tocopherol (150 mg/L) the results revealed that chlorophyll content at p < 0.05 with growth regulator and antioxidant enzymes such as catalase, peroxidase, and malondialdehyde enhanced up to the maximum level at T5 = Hg4ppm + 50 °C (50 °C thermopriming under 4 ppm mercuric chloride stress), suggesting that high temperature initiate the antioxidant system to reduce photosystem damage. However, protein, proline, superoxide dismutase at p < 0.05, and carotenoid, soluble sugar, and ascorbate peroxidase were increased non-significantly (p > 0.05) 50 °C thermopriming under 8 ppm high mercuric chloride stress (T9 = Hg8ppm + 50 °C) representing the tolerance of selected specie by synthesizing osmolytes to resist oxidation mechanism. Furthermore, reduction in % MC (moisture content) is easily improved with foliar application of α-tocopherol and 50 °C thermopriming and 4 ppm heavy metal stress at T6 = Hg4ppm + 50 °C + α-tocopherol (150 mg/L), with a remarkable increase in plant vigor and germination energy. It has resulted that the inhibitory effect of only lower concentration (4 ppm) of heavy metal stress was ameliorated by exogenous application of α-tocopherol and thermopriming technique by synthesizing high levels of proline and antioxidant activities in maintaining seedling growth and development on heavy metal contaminated soil.
Collapse
Affiliation(s)
- Fazal Amin
- Department of Botany, University of Peshawar, Peshawar, 25120, Pakistan
| | - Arwa Abdulkreem Al-Huqail
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sami Ullah
- Department of Botany, University of Peshawar, Peshawar, 25120, Pakistan.
| | - Muhammad Nauman Khan
- Department of Botany, Islamia College, Peshawar, 25120, Pakistan
- Biology Laboratory, University Public School, University of Peshawar, Peshawar, 25120, Pakistan
| | - Alevcan Kaplan
- Department of Crop and Animal Production, Sason Vocational School, Batman University, Batman, 72060, Turkey
| | - Baber Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Majid Iqbal
- Institute of Geographic Sciences and Natural Resources Research, University of Chinese Academy of Sciences, Beijing, 100040, China
| | - Fahmy Gad Elsaid
- Biology Department, College of Science, King Khalid University, 61421, Abha, Al-Faraa, Asir, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, 25240, Turkey
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, 378, Jimma, Ethiopia.
| | - Sami Asir Al-Robai
- Department of Biology, Faculty of Science, Al-Baha University, 1988, Al-Baha, Saudi Arabia
| | - Amany H A Abeed
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71516, Egypt
| |
Collapse
|
11
|
Li H, Yu K, Zhang Z, Yu Y, Wan J, He H, Fan C. Targeted mutagenesis of flavonoid biosynthesis pathway genes reveals functional divergence in seed coat colour, oil content and fatty acid composition in Brassica napus L. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:445-459. [PMID: 37856327 PMCID: PMC10826991 DOI: 10.1111/pbi.14197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/08/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Yellow-seed is widely accepted as a good-quality trait in Brassica crops. Previous studies have shown that the flavonoid biosynthesis pathway is essential for the development of seed colour, but its function in Brassica napus, an important oil crop, is poorly understood. To systematically explore the gene functions of the flavonoid biosynthesis pathway in rapeseed, several representative TRANSPARENT TESTA (TT) genes, including three structural genes (BnaTT7, BnaTT18, BnaTT10), two regulatory genes (BnaTT1, BnaTT2) and a transporter (BnaTT12), were selected for targeted mutation by CRISPR/Cas9 in the present study. Seed coat colour, lignin content, seed quality and yield-related traits were investigated in these Bnatt mutants together with Bnatt8 generated previously. These Bnatt mutants produced seeds with an elevated seed oil content and decreased pigment and lignin accumulation in the seed coat without any serious defects in the yield-related traits. In addition, the fatty acid (FA) composition was also altered to different degrees, i.e., decreased oleic acid and increased linoleic acid and α-linolenic acid, in all Bnatt mutants except Bnatt18. Furthermore, gene expression analysis revealed that most of BnaTT mutations resulted in the down-regulation of key genes related to flavonoid and lignin synthesis, and the up-regulation of key genes related to lipid synthesis and oil body formation, which may contribute to the phenotype. Collectively, our study generated valuable resources for breeding programs, and more importantly demonstrated the functional divergence and overlap of flavonoid biosynthesis pathway genes in seed coat colour, oil content and FA composition of rapeseed.
Collapse
Affiliation(s)
- Huailin Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Kaidi Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Zilu Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Yalun Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Jiakai Wan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Hanzi He
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| |
Collapse
|
12
|
Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
Collapse
Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
| |
Collapse
|
13
|
Li S, Dong Y, Li D, Shi S, Zhao N, Liao J, Liu Y, Chen H. Eggplant transcription factor SmMYB5 integrates jasmonate and light signaling during anthocyanin biosynthesis. PLANT PHYSIOLOGY 2024; 194:1139-1165. [PMID: 37815242 DOI: 10.1093/plphys/kiad531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 10/11/2023]
Abstract
Low light conditions severely suppress anthocyanin synthesis in fruit skins, leading to compromised fruit quality in eggplant (Solanum melongena L.) production. In this study, we found that exogenous methyl-jasmonate (MeJA) application can effectively rescue the poor coloration of the eggplant pericarp under low light conditions. However, the regulatory relationship between jasmonate and light signaling for regulating anthocyanin synthesis remains unclear. Here, we identified a JA response factor, SmMYB5, as an anthocyanin positive regulator by applying RNA-sequencing and characterization of transgenic plants. Firstly, we resolved that SmMYB5 can interact with TRANSPARENT TESTA8 (SmTT8), an anthocyanin-promoted BASIC HELIX-LOOP-HELIX (bHLH) transcription factor, to form the SmMYB5-SmTT8 complex and activate CHALCONE SYNTHASE (SmCHS), FLAVANONE-3-HYDROXYLASE (SmF3H), and ANTHOCYANIN SYNTHASE (SmANS) promoters by direct binding. Secondly, we revealed that JA signaling repressors JASMONATE ZIM DOMAIN5 (SmJAZ5) and SmJAZ10 can interfere with the stability and transcriptional activity of SmMYB5-SmTT8 by interacting with SmMYB5. JA can partially rescue the transcriptional activation of SmF3H and SmANS promoters by inducing SmJAZ5/10 degradation. Thirdly, we demonstrated that the protein abundance of SmMYB5 is regulated by light. CONSTITUTIVELY PHOTOMORPHOGENIC1 (SmCOP1) interacts with SmMYB5 to trigger SmMYB5 degradation via the 26S proteasome pathway. Finally, we delineated a light-dependent JA-SmMYB5 signaling pathway that promotes anthocyanin synthesis in eggplant fruit skins. These results provide insights into the mechanism of the integration of JA and light signals in regulating secondary metabolite synthesis in plants.
Collapse
Affiliation(s)
- Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanxiao Dong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Na Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielei Liao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
14
|
Wang Y, Lu H, Liu X, Liu L, Zhang W, Huang Z, Li K, Xu A. Identification of Yellow Seed Color Genes Using Bulked Segregant RNA Sequencing in Brassica juncea L. Int J Mol Sci 2024; 25:1573. [PMID: 38338852 PMCID: PMC10855766 DOI: 10.3390/ijms25031573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/19/2023] [Accepted: 12/29/2023] [Indexed: 02/12/2024] Open
Abstract
Yellow seed breeding is an effective method to improve oil yield and quality in rapeseed (Brassica napus L.). However, naturally occurring yellow-seeded genotypes have not been identified in B. napus. Mustard (Brassica juncea L.) has some natural, yellow-seeded germplasms, yet the molecular mechanism underlying this trait remains unclear. In this study, a BC9 population derived from the cross of yellow seed mustard "Wuqi" and brown seed mustard "Wugong" was used to analyze the candidate genes controlling the yellow seed color of B. juncea. Subsequently, yellow-seeded (BY) and brown-seeded (BB) bulks were constructed in the BC9 population and subjected to bulked segregant RNA sequencing (BSR-Seq). A total of 511 differentially expressed genes (DEGs) were identified between the brown and yellow seed bulks. Enrichment analysis revealed that these DEGs were involved in the phenylpropanoid biosynthetic process and flavonoid biosynthetic process, including key genes such as 4CL, C4H, LDOX/TT18, PAL1, PAL2, PAL4, TT10, TT12, TT4, TT8, BAN, DFR/TT3, F3H/TT6, TT19, and CHI/TT5. In addition, 111,540 credible single-nucleotide polymorphisms (SNPs) and 86,319 INDELs were obtained and used for quantitative trait locus (QTL) identification. Subsequently, two significant QTLs on chromosome A09, namely, qSCA09-3 and qSCA09-7, were identified by G' analysis, and five DEGs (BjuA09PAL2, BjuA09TT5, BjuA09TT6, BjuA09TT4, BjuA09TT3) involved in the flavonoid pathway were identified as hub genes based on the protein-to-protein network. Among these five genes, only BjuA09PAL2 and BjuA09F3H had SNPs between BY and BB bulks. Interestingly, the majority of SNPs in BjuA09PAL2 were consistent with the SNPs identified between the high-quality assembled B. juncea reference genome "T84-66" (brown-seed) and "AU213" (yellow-seed). Therefore, BjuA09PAL2, which encodes phenylalanine lyase, was considered as the candidate gene associated with yellow seed color of B. juncea. The identification of a novel gene associated with the yellow seed coloration of B. juncea through this study may play a significant role in enhancing yellow seed breeding in rapeseed.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Keqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China
| |
Collapse
|
15
|
Dai G, Liu Y, Shen W, Zhu B, Chen L, Chen D, Tan C. Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus. BMC PLANT BIOLOGY 2024; 24:52. [PMID: 38229007 DOI: 10.1186/s12870-023-04718-6] [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: 12/13/2023] [Accepted: 12/31/2023] [Indexed: 01/18/2024]
Abstract
BACKGROUND MYB transcription factors are splay a vital role in plant biology, with previous research highlighting the significant impact of the R2R3-MYB-like transcription factor MYB5 on seed mucilage biosynthesis, trichome branching, and seed coat development. However, there is a dearth of studies investigating its role in the regulation of proanthocyanidin (PA) biosynthesis. RESULTS In this study, a total of 51 MYB5 homologous genes were identified across 31 species belonging to the Brassicaceae family, with particular emphasis on Brassica napus for subsequent investigation. Through phylogenetic analysis, these genes were categorized into four distinct subclasses. Protein sequence similarity and identity analysis demonstrated a high degree of conservation of MYB5 among species within the Brassicaceae family. Additionally, the examination of selection pressure revealed that MYB5 predominantly underwent purifying selection during its evolutionary history, as indicated by the Ka/Ks values of all MYB5 homologous gene pairs being less than one. Notably, we observed a higher rate of non-synonymous mutations in orthologous genes compared to paralogous genes, and the Ka/Ks value displayed a stronger correlation with Ka. In B. napus, an examination of expression patterns in five tissues revealed that MYB5 exhibited particularly high expression in the black seed coat. The findings from the WGCNA demonstrated a robust correlation between MYB5 and BAN(ANR) associated with PA biosynthesis in the black seed coat, providing further evidence of their close association and co-expression. Furthermore, the results obtained from of the analysis of protein interaction networks offer supplementary support for the proposition that MYB5 possesses the capability to interact with transcriptional regulatory proteins, specifically TT8 and TT2, alongside catalytic enzymes implicated in the synthesis of PAs, thereby making a contribution to the biosynthesis of PAs. These findings imply a plausible and significant correlation between the nuique expression pattern of MYB5 and the pigmentation of rapeseed coats. Nevertheless, additional research endeavors are imperative to authenticate and substantiate these findings. CONCLUSIONS This study offers valuable insights into the genetic evolution of Brassicaceae plants, thereby serving as a significant reference for the genetic enhancement of Brassicaceae seed coat color.
Collapse
Affiliation(s)
- Guoqiang Dai
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Yi Liu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Wenjie Shen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Bo Zhu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Lunlin Chen
- Nanchang Branch of National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
| | - Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
| | - Chen Tan
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
| |
Collapse
|
16
|
Jia C, Lai Q, Zhu Y, Feng J, Dan X, Zhang Y, Long Z, Wu J, Wang Z, Qumu X, Wang R, Wang J. Intergrative metabolomic and transcriptomic analyses reveal the potential regulatory mechanism of unique dihydroxy fatty acid biosynthesis in the seeds of an industrial oilseed crop Orychophragmus violaceus. BMC Genomics 2024; 25:29. [PMID: 38172664 PMCID: PMC10765717 DOI: 10.1186/s12864-023-09906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Orychophragmus violaceus is a potentially important industrial oilseed crop due to the two 24-carbon dihydroxy fatty acids (diOH-FA) that was newly identified from its seed oil via a 'discontinuous elongation' process. Although many research efforts have focused on the diOH-FA biosynthesis mechanism and identified the potential co-expressed diacylglycerol acyltranferase (DGAT) gene associated with triacylglycerol (TAG)-polyestolides biosynthesis, the dynamics of metabolic changes during seed development of O. violaceus as well as its associated regulatory network changes are poorly understood. RESULTS In this study, by combining metabolome and transcriptome analysis, we identified that 1,003 metabolites and 22,479 genes were active across four stages of seed development, which were further divided into three main clusters based on the patterns of metabolite accumulation and/or gene expression. Among which, cluster2 was mostly related to diOH-FA biosynthesis pathway. We thus further constructed transcription factor (TF)-structural genes regulatory map for the genes associated with the flavonoids, fatty acids and diOH-FA biosynthesis pathway in this cluster. In particular, several TF families such as bHLH, B3, HD-ZIP, MYB were found to potentially regulate the metabolism associated with the diOH-FA pathway. Among which, multiple candidate TFs with promising potential for increasing the diOH-FA content were identified, and we further traced the evolutionary history of these key genes among species of Brassicaceae. CONCLUSION Taken together, our study provides new insight into the gene resources and potential relevant regulatory mechanisms of diOH-FA biosynthesis uniquely in seeds of O. violaceus, which will help to promote the downstream breeding efforts of this potential oilseed crop and advance the bio-lubricant industry.
Collapse
Affiliation(s)
- Changfu Jia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qiang Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiman Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiajun Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuming Dan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yulin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiqin Long
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiali Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zeng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiner Qumu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Rui Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Jing Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| |
Collapse
|
17
|
Cheng H, Cai S, Hao M, Cai Y, Wen Y, Huang W, Mei D, Hu Q. Targeted mutagenesis of BnTTG1 homologues generated yellow-seeded rapeseed with increased oil content and seed germination under abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108302. [PMID: 38171134 DOI: 10.1016/j.plaphy.2023.108302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Yellow seed is one desirable trait with great potential to improve seed oil quality and yield. The present study surveys the redundant role of BnTTG1 genes in the proanthocyanidins (PA) biosynthesis, oil content and abiotic stress resistance. Stable yellow seed mutants were generated after mutating BnTTG1 by CRISPR/Cas9 genome editing system. Yellow seed phenotype could be obtained only when both functional homologues of BnTTG1 were simultaneously knocked out. Homozygous mutants of BnTTG1 homologues showed decreased thickness and PA accumulation in seed coat. Transcriptome and qRT-PCR analysis indicated that BnTTG1 mutation inhibited the expression of genes involved in phenylpropanoid and flavonoid biosynthetic pathways. Increased seed oil content and alteration of fatty acid (FA) composition were observed in homozygous mutants of BnTTG1 with enriched expression of genes involved in FA biosynthesis pathway. In addition, target mutation of BnTTG1 accelerated seed germination rate under salt and cold stresses. Enhanced seed germination capacity in BnTTG1 mutants was correlated with the change of expression level of ABA responsive genes. Overall, this study elucidated the redundant role of BnTTG1 in regulating seed coat color and established an efficient approach for generating yellow-seeded oilseed rape genetic resources with increase oil content, modified FA composition and resistance to multiple abiotic stresses.
Collapse
Affiliation(s)
- Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Shengli Cai
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Yating Cai
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Yunfei Wen
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Wei Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China; Hubei Hongshan Laboratory, Wuhan, China.
| |
Collapse
|
18
|
Rauf S, Fatima S, Ortiz R. Modification of Fatty Acid Profile and Oil Contents Using Gene Editing in Oilseed Crops for a Changing Climate. GM CROPS & FOOD 2023; 14:1-12. [PMID: 37551783 PMCID: PMC10761075 DOI: 10.1080/21645698.2023.2243041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Mutation breeding based on various chemical and physical mutagens induces and disrupts non-target loci. Hence, large populations were required for visual screening, but desired plants were rare and it was a further laborious task to identify desirable mutants. Generated mutant had high defect due to non-targeted mutation, with poor agronomic performance. Mutation techniques were augmented by targeted induced local lesions in genome (TILLING) facilitating the selection of desirable germplasm. On the other hand, gene editing through CRISPR/Cas9 allows knocking down genes for site-directed mutation. This handy technique has been exploited for the modification of fatty acid profile. High oleic acid genetic stocks were obtained in a broad range of crops. Moreover, genes involved in the accumulation of undesirable seed components such as starch, polysaccharide, and flavors were knocked down to enhance seed quality, which helps to improve oil contents and reduces the anti-nutritional component.
Collapse
Affiliation(s)
- Saeed Rauf
- Department of Plant Breeding & Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Seerat Fatima
- Department of Plant Breeding & Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
19
|
Jolliffe JB, Pilati S, Moser C, Lashbrooke JG. Beyond skin-deep: targeting the plant surface for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6468-6486. [PMID: 37589495 PMCID: PMC10662250 DOI: 10.1093/jxb/erad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.
Collapse
Affiliation(s)
- Jenna Bryanne Jolliffe
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Stefania Pilati
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige, 38098, Italy
| | - Justin Graham Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| |
Collapse
|
20
|
Rudenko NN, Vetoshkina DV, Marenkova TV, Borisova-Mubarakshina MM. Antioxidants of Non-Enzymatic Nature: Their Function in Higher Plant Cells and the Ways of Boosting Their Biosynthesis. Antioxidants (Basel) 2023; 12:2014. [PMID: 38001867 PMCID: PMC10669185 DOI: 10.3390/antiox12112014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Plants are exposed to a variety of abiotic and biotic stresses leading to increased formation of reactive oxygen species (ROS) in plant cells. ROS are capable of oxidizing proteins, pigments, lipids, nucleic acids, and other cell molecules, disrupting their functional activity. During the process of evolution, numerous antioxidant systems were formed in plants, including antioxidant enzymes and low molecular weight non-enzymatic antioxidants. Antioxidant systems perform neutralization of ROS and therefore prevent oxidative damage of cell components. In the present review, we focus on the biosynthesis of non-enzymatic antioxidants in higher plants cells such as ascorbic acid (vitamin C), glutathione, flavonoids, isoprenoids, carotenoids, tocopherol (vitamin E), ubiquinone, and plastoquinone. Their functioning and their reactivity with respect to individual ROS will be described. This review is also devoted to the modern genetic engineering methods, which are widely used to change the quantitative and qualitative content of the non-enzymatic antioxidants in cultivated plants. These methods allow various plant lines with given properties to be obtained in a rather short time. The most successful approaches for plant transgenesis and plant genome editing for the enhancement of biosynthesis and the content of these antioxidants are discussed.
Collapse
Affiliation(s)
- Natalia N. Rudenko
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (D.V.V.); (M.M.B.-M.)
| | - Daria V. Vetoshkina
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (D.V.V.); (M.M.B.-M.)
| | - Tatiana V. Marenkova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia;
| | - Maria M. Borisova-Mubarakshina
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (D.V.V.); (M.M.B.-M.)
| |
Collapse
|
21
|
Gu J, Chen J, Zhao C, Hong D. Mutating BnEOD1s via CRISPR-Cas9 increases the seed size and weight in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:79. [PMID: 37954031 PMCID: PMC10632315 DOI: 10.1007/s11032-023-01430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Seed weight, which is highly correlated to seed size, is a critical agronomic trait that determines the yield of Brassica napus. However, there have been limited researches on the genes involved in regulating seed size. In Arabidopsis thaliana, ENHANCER OF DA1 (EOD1), an E3 ubiquitin ligase gene, has been identified as a significant negative regulator in controlling organ size, but the function of its homologs in rapeseed remains unknown. Only two homologous of EOD1, BnaEOD1.A04 and BnaEOD1.C04, have been found in B. napus and were mutated using the CRISPR-Cas9 system. Three T-DNA-free lines, T2-157-1-C8, T2-390-2-B8, and T2-397-2-E2, were identified from the homozygous T2 mutant lines. The BnaEOD1.A04 showed a similar type of editing in these mutants, whereas the BnaEOD1.C04 in T2-397-2-E2 was only missing 26 amino acids, and the translation was not prematurely terminated, which was different from the other two mutants. In parallel, mutation of BnaEOD1s resulted in a noteworthy increase in both seed size and seed weight in the three editing lines. Additionally, there was a significant decline in the number of seeds per silique (SPS) and silique length (SL) in T2-157-1-C8 and T2-390-2-B8, but T2-397-2-E2 did not show any significant changes in the SPS and SL, possibly due to distinct types of editing in the three lines. The above results indicate the conserved function of EOD1 homologs and provides promising germplasm for breeding novel high-yield rapeseed varieties by improving seed size and thousand-seed weight. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01430-z.
Collapse
Affiliation(s)
- Jianwei Gu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000 China
| | - Jiayin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chenqi Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
22
|
Matinvafa MA, Makani S, Parsasharif N, Zahed MA, Movahed E, Ghiasvand S. CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology. 3 Biotech 2023; 13:383. [PMID: 37920190 PMCID: PMC10618153 DOI: 10.1007/s13205-023-03786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/09/2023] [Indexed: 11/04/2023] Open
Abstract
The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.
Collapse
Affiliation(s)
- Mohammad Ali Matinvafa
- Department of Biotechnology & Environment, Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Shadi Makani
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Negin Parsasharif
- Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY USA
| | - Saeedeh Ghiasvand
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Hamedan, Iran
| |
Collapse
|
23
|
Yu L, Liu D, Yin F, Yu P, Lu S, Zhang Y, Zhao H, Lu C, Yao X, Dai C, Yang QY, Guo L. Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes. BMC Biol 2023; 21:202. [PMID: 37775748 PMCID: PMC10543336 DOI: 10.1186/s12915-023-01705-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Brassica napus is an important oilseed crop providing high-quality vegetable oils for human consumption and non-food applications. However, the regulation between embryo and seed coat for the synthesis of oil and phenylpropanoid compounds remains largely unclear. RESULTS Here, we analyzed the transcriptomes in developing seeds at 2-day intervals from 14 days after flowering (DAF) to 64 DAF. The 26 high-resolution time-course transcriptomes are clearly clustered into five distinct groups from stage I to stage V. A total of 2217 genes including 136 transcription factors, are specifically expressed in the seed and show high temporal specificity by being expressed only at certain stages of seed development. Furthermore, we analyzed the co-expression networks during seed development, which mainly included master regulatory transcription factors, lipid, and phenylpropane metabolism genes. The results show that the phenylpropane pathway is prominent during seed development, and the key enzymes in the phenylpropane metabolic pathway, including TT5, BAN, and the transporter TT19, were directly or indirectly related to many key enzymes and transcription factors involved in oil accumulation. We identified candidate genes that may regulate seed oil content based on the co-expression network analysis combined with correlation analysis of the gene expression with seed oil content and seed coat content. CONCLUSIONS Overall, these results reveal the transcriptional regulation between lipid and phenylpropane accumulation during B. napus seed development. The established co-expression networks and predicted key factors provide important resources for future studies to reveal the genetic control of oil accumulation in B. napus seeds.
Collapse
Affiliation(s)
- Liangqian Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feifan Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, 59717, USA
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Yazhouwan National Laboratory, Sanya, 572025, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Yazhouwan National Laboratory, Sanya, 572025, China.
| |
Collapse
|
24
|
Mackon E, Jeazet Dongho Epse Mackon GC, Yao Y, Guo Y, Ma Y, Dai X, Jandan TH, Liu P. Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice ( Oryza sativa. L) caryopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1211326. [PMID: 37727854 PMCID: PMC10505814 DOI: 10.3389/fpls.2023.1211326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/11/2023] [Indexed: 09/21/2023]
Abstract
Introduction Anthocyanins are plants' secondary metabolites belonging to the flavonoid class with potential health-promoting properties. They are greatly employed in the food industry as natural alternative food colorants for dairy and ready-to-eat desserts and pH indicators. These tremendous advantages make them economically important with increasing market trends. Black rice is a rich source of anthocyanin that can be used to ensure food and nutritional security around the world. However, research on anthocyanin accumulation and gene expression during rice caryopsis development is lacking. Methods In this study, we combined high-performance liquid chromatography (HPLC) and transcriptome analysis to profile the changes in anthocyanin content and gene expression dynamics at three developmental stages (milky, doughy, and mature). Results Our results showed that anthocyanin accumulation started to be visible seven days after flowering (DAF), increased rapidly from milky (11 DAF) to dough stage, then started decreasing after the peak was attained at 18 DAF. RNA-seq showed that 519 out of 14889, 477 out of 17914, and 1614 out of 18810 genes were uniquely expressed in the milky, doughy, and mature stages, respectively. We performed three pairwise comparisons: milky vs. dough, milky vs. mature, and dough vs. mature, and identified 6753, 9540, and 2531 DEGs, respectively. The DEGs' abundance was higher in milky vs. mature, with 5527 up-regulated genes and 4013 down-regulated genes, while it was smaller in dough vs. mature, with 1419 up-regulated genes and 1112 down-regulated DEGs. This result was consistent with the changes in anthocyanin profiling, and the expression of structural, regulatory, and transporter genes involved in anthocyanin biosynthesis showed their highest expression at the dough stage. Through the gene expression profile and protein interaction network, we deciphered six main contributors of the anthocyanin peak observed at dough stage, including OsANS, OsDFR, OsGSTU34, OsMYB3, OsbHLH015, and OsWD40-50. Discussion This study is the first to report the investigation of anthocyanin and gene expression at three developmental stages of black rice caryopsis. The findings of this study could aid in predicting the best harvesting time to achieve maximum anthocyanin content and the best time to collect samples for various gene expression analysis, laying the groundwork for future research into the molecular mechanisms underlying rice caryopsis coloration.
Collapse
Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | | | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xianggui Dai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Tahir Hussain Jandan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| |
Collapse
|
25
|
Qu C, Zhu M, Hu R, Niu Y, Chen S, Zhao H, Li C, Wang Z, Yin N, Sun F, Chen Z, Shen S, Shang G, Zhou Y, Yan X, Wei L, Liu L, Yi B, Lian J, Li J, Tang Z, Liang Y, Xu X, Wang R, Yin J, Wan H, Du H, Qian W, Chai Y, Zhou Q, He Y, Zhong S, Qiu X, Yu H, Lam HM, Lu K, Fu F, Li J. Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus. Nat Commun 2023; 14:5194. [PMID: 37626056 PMCID: PMC10457299 DOI: 10.1038/s41467-023-40838-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Yellow-seed trait is a desirable breeding characteristic of rapeseed (Brassica napus) that could greatly improve seed oil yield and quality. However, the underlying mechanisms controlling this phenotype in B. napus plants are difficult to discern because of their complexity. Here, we assemble high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821). Combining in-depth fine mapping of a quantitative trait locus (QTL) for seed color with other omics data reveal BnA09MYB47a, encoding an R2R3-MYB-type transcription factor, as the causal gene of a major QTL controlling the yellow-seed trait. Functional studies show that sequence variation of BnA09MYB47a underlies the functional divergence between the yellow- and black-seeded B. napus. The black-seed allele BnA09MYB47aZY821, but not the yellow-seed allele BnA09MYB47aGH06, promotes flavonoid biosynthesis by directly activating the expression of BnTT18. Our discovery suggests a possible approach to breeding B. napus for improved commercial value and facilitates flavonoid biosynthesis studies in Brassica crops.
Collapse
Affiliation(s)
- Cunmin Qu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meichen Zhu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ran Hu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yongchao Niu
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Si Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Huiyan Zhao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chengxiang Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Zhen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Nengwen Yin
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Fujun Sun
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhiyou Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Shulin Shen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guoxia Shang
- National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Yan Zhou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xingying Yan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lijuan Wei
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liezhao Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | | | - Jiang Li
- Biozeron Shenzhen, Inc, Shenzhen, China
| | - Zhanglin Tang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ying Liang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xinfu Xu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rui Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiaming Yin
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Huafang Wan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hai Du
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Qian
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yourong Chai
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qingyuan Zhou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yajun He
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Qiu
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Hao Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Hon-Ming Lam
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kun Lu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Fuyou Fu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Canada.
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| |
Collapse
|
26
|
Huang H, Ahmar S, Samad RA, Qin P, Yan T, Zhao Q, Xie K, Zhang C, Fan C, Zhou Y. A novel type of Brassica napus with higher stearic acid in seeds developed through genome editing of BnaSAD2 family. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:187. [PMID: 37572171 DOI: 10.1007/s00122-023-04414-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/23/2023] [Indexed: 08/14/2023]
Abstract
KEY MESSAGE Modifications of multiple copies of the BnaSAD2 gene family with genomic editing technology result in higher stearic acid content in the seed of polyploidy rapeseed. Solid fats from vegetable oils are widely used in food processing industry. Accumulating data showed that stearic acid is more favorite as the major composite among the saturate fatty acids in solid fats in considerations of its effects on human health. Rapeseed is the third largest oil crop worldwide, and has potential to be manipulated to produce higher saturated fatty acids as raw materials of solid fats. Toward that end, we identified four SAD2 gene family members in B. napus genome and established spatiotemporal expression pattern of the BnaSAD2 members. Genomic editing technology was applied to mutate all the copies of BnaSAD2 in this allopolyploid species and mutants at multiple alleles were generated and characterized to understand the effect of each BnaSAD2 member on blocking desaturation of stearic acid. Mutations occurred at BnaSAD2.A3 resulted in more dramatic changes of fatty acid profile than ones on BnaSAD2.C3, BnaSAD2.A5 and BnaSAD2.C4. The content of stearic acid in mutant seeds with single locus increased dramatically with a range of 3.1-8.2%. Furthermore, combination of different mutated alleles of BnaSAD2 resulted in more dramatic changes in fatty acid profiles and the double mutant at BnaSAD2.A3 and BnaSAD2.C3 showed the most dramatic phenotypic changes compared with its single mutants and other double mutants, leading to 11.1% of stearic acid in the seeds. Our results demonstrated that the members of BnaSAD2 have differentiated in their efficacy as a Δ9-Stearoyl-ACP-Desaturase and provided valuable rapeseed germplasm for breeding high stearic rapeseed oil.
Collapse
Affiliation(s)
- Huibin Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rana Abdul Samad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pin Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tong Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
27
|
Li F, Gong Y, Mason AS, Liu Q, Huang J, Ma M, Xiao M, Wang H, Fu D. Research progress and applications of colorful Brassica crops. PLANTA 2023; 258:45. [PMID: 37462779 DOI: 10.1007/s00425-023-04205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
MAIN CONCLUSION We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.
Collapse
Affiliation(s)
- Fuyan Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yingying Gong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Qian Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Juan Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Miao Ma
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huadong Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
28
|
Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
Collapse
Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
| |
Collapse
|
29
|
Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
Collapse
Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
30
|
Li L, Tian Z, Chen J, Tan Z, Zhang Y, Zhao H, Wu X, Yao X, Wen W, Chen W, Guo L. Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis. Genome Biol 2023; 24:141. [PMID: 37337206 DOI: 10.1186/s13059-023-02984-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. RESULTS Using a widely targeted metabolomics analysis in a natural population of 388 B. napus inbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus. CONCLUSIONS This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops.
Collapse
Affiliation(s)
- Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaowei Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| |
Collapse
|
31
|
Liu F, Chen H, Yang L, You L, Ju J, Yang S, Wang X, Liu Z. QTL Mapping and Transcriptome Analysis Reveal Candidate Genes Regulating Seed Color in Brassica napus. Int J Mol Sci 2023; 24:ijms24119262. [PMID: 37298213 DOI: 10.3390/ijms24119262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Yellow seeds are desirable in rapeseed breeding because of their higher oil content and better nutritional quality than black seeds. However, the underlying genes and formation mechanism of yellow seeds remain unclear. Here, a novel yellow-seeded rapeseed line (Huangaizao, HAZ) was crossed with a black-seeded rapeseed line (Zhongshuang11, ZS11) to construct a mapping population of 196 F2 individuals, based on which, a high-density genetic linkage map was constructed. This map, comprising 4174 bin markers, was 1618.33 cM in length and had an average distance of 0.39 cM between its adjacent markers. To assess the seed color of the F2 population, three methods (imaging, spectrophotometry, and visual scoring) were used and a common major quantitative trait locus (QTL) on chromosome A09, explaining 10.91-21.83% of the phenotypic variance, was detected. Another minor QTL, accounting for 6.19-6.69% of the phenotypic variance, was detected on chromosome C03, only by means of imaging and spectrophotometry. Furthermore, a dynamic analysis of the differential expressions between the parental lines showed that flavonoid biosynthesis-related genes were down-regulated in the yellow seed coats at 25 and 35 days after flowering. A coexpression network between the differentially expressed genes identified 17 candidate genes for the QTL intervals, including a flavonoid structure gene, novel4557 (BnaC03.TT4), and two transcription factor genes, namely, BnaA09G0616800ZS (BnaA09.NFYA8) and BnaC03G0060200ZS (BnaC03.NAC083), that may regulate flavonoid biosynthesis. Our study lays a foundation for further identifying the genes responsible for and understanding the regulatory mechanism of yellow seed formation in Brassica napus.
Collapse
Affiliation(s)
- Fangying Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Liu Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Liang You
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Jianye Ju
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shujie Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
32
|
Mackon E, Mackon GCJDE, Guo Y, Ma Y, Yao Y, Liu P. Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111746. [PMID: 37230190 DOI: 10.1016/j.plantsci.2023.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.
Collapse
Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University.
| | | | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| |
Collapse
|
33
|
He J, Zhang K, Yan S, Tang M, Zhou W, Yin Y, Chen K, Zhang C, Li M. Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library. Genome Res 2023; 33:798-809. [PMID: 37290935 PMCID: PMC10317123 DOI: 10.1101/gr.277650.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/19/2023] [Indexed: 06/10/2023]
Abstract
The recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the genome complexity, it is a big challenge to accomplish large-scale targeted mutagenesis in polyploid plants. Here, we demonstrate the feasibility of using a pooled CRISPR library to achieve genome-scale targeted editing in an allotetraploid crop of Brassica napus A total of 18,414 sgRNAs were designed to target 10,480 genes of interest, and afterward, 1104 regenerated transgenic plants harboring 1088 sgRNAs were obtained. Editing interrogation results revealed that 93 of the 178 genes were identified as mutated, thus representing an editing efficiency of 52.2%. Furthermore, we have discovered that Cas9-mediated DNA cleavages tend to occur at all the target sites guided by the same individual sgRNA, a novel finding in polyploid plants. Finally, we show the strong capability of reverse genetic screening for various traits with the postgenotyped plants. Several genes, which might dominate the fatty acid profile and seed oil content and have yet to be reported, were unveiled from the forward genetic studies. Our research provides valuable resources for functional genomics, elite crop breeding, and a good reference for high-throughput targeted mutagenesis in other polyploid plants.
Collapse
Affiliation(s)
- Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Mi Tang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| |
Collapse
|
34
|
Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
Collapse
Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
35
|
Ali E, Zhang K. CRISPR-mediated technology for seed oil improvement in rapeseed: Challenges and future perspectives. FRONTIERS IN PLANT SCIENCE 2023; 14:1086847. [PMID: 37025135 PMCID: PMC10070842 DOI: 10.3389/fpls.2023.1086847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Rapeseed not only provide considerable amount of edible oil with high nutritional properties but can also be used as a raw material for biofuel production in many industries. It is therefore in high demand to bring genetic changes in order to fulfill the need of human and of industries. Though traditional breeding techniques such as hybridization and mutagenesis remained the top methods for long time to create improved varieties in oilseed rape. Clustered regularly interspaced short palindromic repeats (CRISPR) is becoming one of the most valuable gene editing technologies that allow precise genome engineering, and open new ways for research in plant functional genomics. Though CRISPR has been used in many other crops for genetic improvement it is expected to be an effective tool for genome editing and molecular design in oilseed rape for seed oil improvement. This mini review will discuss and summarize the past and ongoing research and development in rapeseed in terms of seed oil improvement and fatty acid composition using CRISPR technology. In addition, the factors that hinder the efficiency of this tool and how to eliminate those factors will be briefly summarized. The improvement of CRISPR technology for getting better results in oilseed rape will also be considered here. This minireview will open new windows for researchers in Brassica napus oil improvement research and genetic improvement using CRISPR technology.
Collapse
Affiliation(s)
- Essa Ali
- *Correspondence: Kewei Zhang, ; Essa Ali,
| | | |
Collapse
|
36
|
Chen D, Chen H, Dai G, Zhang H, Liu Y, Shen W, Zhu B, Cui C, Tan C. Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics 2023; 24:103. [PMID: 36894869 PMCID: PMC9999611 DOI: 10.1186/s12864-023-09170-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/07/2023] [Indexed: 03/11/2023] Open
Abstract
Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.
Collapse
Affiliation(s)
- Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Haidong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Guoqiang Dai
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Haimei Zhang
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Yi Liu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Wenjie Shen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Bo Zhu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chendu, 610066, China.
| | - Chen Tan
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
| |
Collapse
|
37
|
Guan M, Shi X, Chen S, Wan Y, Tang Y, Zhao T, Gao L, Sun F, Yin N, Zhao H, Lu K, Li J, Qu C. Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed. FRONTIERS IN PLANT SCIENCE 2023; 14:1154208. [PMID: 36993847 PMCID: PMC10042178 DOI: 10.3389/fpls.2023.1154208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Yellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapeseed with different backgrounds. The differentially expressed genes (DEGs) during seed development showed significant characteristics, these genes were mainly enriched for the Gene Ontology (GO) terms carbohydrate metabolic process, lipid metabolic process, photosynthesis, and embryo development. Moreover, 1206 and 276 DEGs, which represent candidates to be involved in seed coat color, were identified between yellow- and black-seeded rapeseed during the middle and late stages of seed development, respectively. Based on gene annotation, GO enrichment analysis, and protein-protein interaction network analysis, the downregulated DEGs were primarily enriched for the phenylpropanoid and flavonoid biosynthesis pathways. Notably, 25 transcription factors (TFs) involved in regulating flavonoid biosynthesis pathway, including known (e.g., KNAT7, NAC2, TTG2 and STK) and predicted TFs (e.g., C2H2-like, bZIP44, SHP1, and GBF6), were identified using integrated gene regulatory network (iGRN) and weight gene co-expression networks analysis (WGCNA). These candidate TF genes had differential expression profiles between yellow- and black-seeded rapeseed, suggesting they might function in seed color formation by regulating genes in the flavonoid biosynthesis pathway. Thus, our results provide in-depth insights that facilitate the exploration of candidate gene function in seed development. In addition, our data lay the foundation for revealing the roles of genes involved in the yellow-seeded trait in rapeseed.
Collapse
Affiliation(s)
- Mingwei Guan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Xiangtian Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Si Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Yuanyuan Wan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Yunshan Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Tian Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Lei Gao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Fujun Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Nengwen Yin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Huiyan Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| |
Collapse
|
38
|
Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
Collapse
Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| |
Collapse
|
39
|
May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
Collapse
Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
| |
Collapse
|
40
|
Zhang Y, Qin Y, Li D, Wang W, Gao X, Hao C, Feng H, Wang Y, Li T. Fine mapping and cloning of a novel BrSCC1 gene for seed coat color in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:11. [PMID: 36658295 DOI: 10.1007/s00122-023-04287-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
A novel BrSCC1 gene for seed coat color was fine mapped within a 41.1-kb interval on chromosome A03 in Brassica rapa and functionally validated by ectopic expression analysis. Yellow seed is a valuable breeding trait that can be potentiality applied for improving seed quality and oil productivity in oilseed Brassica crops. However, only few genes for yellow seed have been identified in B. rapa. We previously identified a minor quantitative trait locus (QTL), qSC3.1, for seed coat color on chromosome A03 in B. rapa. In order to isolate the seed coat color gene, a brown-seeded chromosome segment substitution line, CSSL-38, harboring the qSC3.1, was selected and crossed with the yellow-seeded recurrent parent, a rapid cycling inbred line of B. rapa (RcBr), to construct the secondary F2 population. Metabolite identification suggested that seed coat coloration in CSSL-38 was independent of proanthocyanidins (PAs) accumulation. Genetic analysis revealed that yellow seed was controlled by a single recessive gene, Seed Coat Color 1 (BrSCC1). Utilizing bulked segregant analysis (BSA)-seq and secondary F2 and F2:3 recombinants analysis, BrSCC1 was fine mapped within a 41.1-kb interval. By integrating gene expression profiling, genome sequence comparison, metabolite analysis, and functional validation through ectopic expression in Arabidopsis, the BraA03g040800.3C gene was confirmed to be BrSCC1, which positively correlated with the seed coat coloration. Our study provides a novel gene resource for the genetic improvement of yellow seeds in oilseed B. rapa.
Collapse
Affiliation(s)
- Yinghuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yao Qin
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Dongxiao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China.
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China
| |
Collapse
|
41
|
Chen YY, Lu HQ, Jiang KX, Wang YR, Wang YP, Jiang JJ. The Flavonoid Biosynthesis and Regulation in Brassica napus: A Review. Int J Mol Sci 2022; 24:ijms24010357. [PMID: 36613800 PMCID: PMC9820570 DOI: 10.3390/ijms24010357] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
Brassica napus is an important crop for edible oil, vegetables, biofuel, and animal food. It is also an ornamental crop for its various petal colors. Flavonoids are a group of secondary metabolites with antioxidant activities and medicinal values, and are important to plant pigmentation, disease resistance, and abiotic stress responses. The yellow seed coat, purple leaf and inflorescence, and colorful petals of B. napus have been bred for improved nutritional value, tourism and city ornamentation. The putative loci and genes regulating flavonoid biosynthesis in B. napus have been identified using germplasms with various seed, petal, leaf, and stem colors, or different flavonoid contents under stress conditions. This review introduces the advances of flavonoid profiling, biosynthesis, and regulation during development and stress responses of B. napus, and hopes to help with the breeding of B. napus with better quality, ornamental value, and stress resistances.
Collapse
Affiliation(s)
- Yuan-Yuan Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Hai-Qin Lu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Kai-Xuan Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yi-Ran Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - You-Ping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Jin-Jin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| |
Collapse
|
42
|
Channaoui S, Mazouz H, Labhilili M, El Fechtali M, Nabloussi A. Inheritance of dwarfism and narrow lobed-leaf in two rapeseed ( Brassica napus L.) mutant lines. Heliyon 2022; 8:e12649. [PMID: 36619419 PMCID: PMC9813704 DOI: 10.1016/j.heliyon.2022.e12649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/05/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
There is a need for dwarf and narrow lobed-leaves rapeseed cultivars to reduce transpiration under drought prone areas. A dwarf mutant line 'H2M-1' and a mutant with reduced lobed-leaf 'H2M-2' were developed. To exploit these mutated traits properly in an effective breeding program, one should understand their mode of inheritance. There are conflicting findings for plant dwarfism and limited studies for leaf size in mutant genetic backgrounds. Therefore, the objective of this study was to investigate the inheritance of dwarfism and narrow lobed-leaf mutated traits. Plants of the wild-type variety 'INRA-CZH2' were reciprocally crossed with plants of the line 'H2M-1' and plants of the line 'H2M-2'. A genetic study was conducted by analyzing segregation of mutated traits in F1, F2 and BC1F1 generations. The results revealed that two recessive genes with dominant epistasis action controlled the heredity of plant height in the dwarf line, whereas only a single recessive gene is involved in determining reduced lobed-leaf in the line H2M-2. Thus, there is a possibility to easily and quickly transfer these characters into rapeseed breeding germplasm or varieties towards the development of suitable cultivars for areas marked by increasing drought stress.
Collapse
Affiliation(s)
- Souhail Channaoui
- Plant Breeding and Plant Genetic Resources Conservation Research Unit, Regional Agricultural Research Center of Meknes, National Institute of Agricultural Research, PO. Box 415, Rabat 10090, Morocco,Laboratory of Plant Biotechnology and Molecular Biology, Department of Biology, Faculty of Science, University Moulay Ismail, PO. Box 11201 Zitoune Meknes 50100, Morocco
| | - Hamid Mazouz
- Laboratory of Plant Biotechnology and Molecular Biology, Department of Biology, Faculty of Science, University Moulay Ismail, PO. Box 11201 Zitoune Meknes 50100, Morocco
| | - Mustapha Labhilili
- Plant Biotechnology Research Unit, Regional Agricultural Research Center of Meknes, National Institute of Agricultural Research, PO. Box 415, Rabat 10090, Morocco
| | - Mohamed El Fechtali
- Plant Breeding and Plant Genetic Resources Conservation Research Unit, Regional Agricultural Research Center of Meknes, National Institute of Agricultural Research, PO. Box 415, Rabat 10090, Morocco
| | - Abdelghani Nabloussi
- Plant Breeding and Plant Genetic Resources Conservation Research Unit, Regional Agricultural Research Center of Meknes, National Institute of Agricultural Research, PO. Box 415, Rabat 10090, Morocco,Corresponding author.
| |
Collapse
|
43
|
Farooq Z, Nouman Riaz M, Farooq MS, Li Y, Wang H, Ahmad M, Tu J, Ma C, Dai C, Wen J, Shen J, Fu T, Yang S, Wang B, Yi B. Induction of Male Sterility by Targeted Mutation of a Restorer-of-Fertility Gene with CRISPR/Cas9-Mediated Genome Editing in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2022; 11:3501. [PMID: 36559613 PMCID: PMC9785856 DOI: 10.3390/plants11243501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Brassica napus L. (canola, oil seed rape) is one of the world's most important oil seed crops. In the last four decades, the discovery of cytoplasmic male-sterility (CMS) systems and the restoration of fertility (Rf) genes in B. napus has improved the crop traits by heterosis. The homologs of Rf genes, known as the restoration of fertility-like (RFL) genes, have also gained importance because of their similarities with Rf genes. Such as a high non-synonymous/synonymous codon replacement ratio (dN/dS), autonomous gene duplications, and a possible engrossment in fertility restoration. B. napus contains 53 RFL genes on chromosomes A9 and C8. Our research aims to study the function of BnaRFL11 in fertility restoration using the CRISPR/Cas9 genome editing technique. A total of 88/108 (81.48%) T0 lines, and for T1, 110/145 (75%) lines carried T-DNA insertions. Stable mutations were detected in the T0 and T1 generations, with an average allelic mutation transmission rate of 81%. We used CRISPR-P software to detect off-target 50 plants sequenced from the T0 generation that showed no off-target mutation, signifying that if the designed sgRNA is specific for the target, the off-target effects are negligible. We also concluded that the mutagenic competence of the designed sgRNAs mediated by U6-26 and U6-29 ranged widely from 31% to 96%. The phenotypic analysis of bnarfl11 revealed defects in the floral structure, leaf size, branch number, and seed production. We discovered a significant difference between the sterile line and fertile line flower development after using a stereomicroscope and scanning electron microscope. The pollen visibility test showed that the pollen grain had utterly degenerated. The cytological observations of homozygous mutant plants showed an anther abortion stage similar to nap-CMS, with a Orf222, Orf139, Ap3, and nad5c gene upregulation. The bnarfl11 shows vegetative defects, including fewer branches and a reduced leaf size, suggesting that PPR-encoding genes are essential for the plants' vegetative and reproductive growth. Our results demonstrated that BnaRFL11 has a possible role in fertility restoration. The current study's findings suggest that CRISPR/Cas9 mutations may divulge the functions of genes in polyploid species and provide agronomically desirable traits through a targeted mutation.
Collapse
Affiliation(s)
- Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Muhammad Nouman Riaz
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Shoaib Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mayra Ahmad
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Benqi Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and Technology, Wuhan 430065, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
44
|
Editing of a Novel Cd Uptake-Related Gene CUP1 Contributes to Reducing Cd Accumulations in Arabidopsis thaliana and Brassica napus. Cells 2022; 11:cells11233888. [PMID: 36497146 PMCID: PMC9739810 DOI: 10.3390/cells11233888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Brassica napus is a Cd hyperaccumulator, which is a serious threat to food and fodder safety. However, no related studies on developing Cd-safe B. napus have been reported yet. Here, we screened out a novel Cd uptake-related gene, AtCUP1, from the major facilitator superfamily in Arabidopsis thaliana. The mutation of AtCUP1 decreased Cd accumulation, both in roots and shoots of A. thaliana. Furthermore, the disruption of the AtCUP1 gene by the CRISPR/Cas9 system significantly reduced Cd accumulation in A. thaliana. Interestingly, the disruption of the BnCUP1 gene, an orthologous gene of AtCUP1, by the CRISPR/Cas9 system also diminished Cd accumulation in both roots and shoots of B. napus based on the hydroponics assay. Furthermore, for the field experiment, the Cd accumulations of BnCUP1-edited lines were reduced by 52% in roots and 77% in shoots compared to that of wild-type (WT) lines, and the biomass and yield of BnCUP1-edited lines increased by 42% and 47% of that of WT, respectively. Noteworthily, agronomic characteristics of B. napus were not apparently affected by BnCUP1-editing. Thus, BnCUP1-edited lines are excellent non-transgenic germplasm resources for reducing Cd accumulation without a distinct compromise in yield, which could be applied to agricultural production in Cd-contaminated soils.
Collapse
|
45
|
Hoffman NE. USDA's revised biotechnology regulation's contribution to increasing agricultural sustainability and responding to climate change. FRONTIERS IN PLANT SCIENCE 2022; 13:1055529. [PMID: 36507369 PMCID: PMC9726801 DOI: 10.3389/fpls.2022.1055529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Biotechnology can provide a valuable tool to meet UN Sustainable Development Goals and U.S. initiatives to find climate solutions and improve agricultural sustainability. The literature contains hundreds of examples of crops that may serve this purpose, yet most remain un-launched due to high regulatory barriers. Recently the USDA revised its biotechnology regulations to make them more risk-proportionate, science-based, and streamlined. Here, we review some of the promising leads that may enable agriculture to contribute to UN sustainability goals. We further describe and discuss how the revised biotechnology regulation would hypothetically apply to these cases.
Collapse
|
46
|
Liu Z, Liu H, Zheng L, Xu F, Wu Y, Pu L, Zhang G. Enolase2 regulates seed fatty acid accumulation via mediating carbon partitioning in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2022; 174:e13797. [PMID: 36251672 DOI: 10.1111/ppl.13797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
In many higher plants, fatty acid (FA) biosynthesis is coordinately regulated at multiple levels by intricate regulatory networks. However, the factors and their regulatory mechanisms underlying seed oil accumulation are still limited. Here, we identified that loss of glycolytic metalloenzyme enolase2 (AtENO2) activity increased the contents of total FAs and salicylic acid (SA) but reduced the accumulation of flavonoids and mucilage by regulating the expression of key genes involved in their biosynthesis pathway in Arabidopsis thaliana seeds. AtENO2 physically interacts with the transcription factor AtTGA5, which may participate in the regulation of SA levels. Non-targeted metabolomics analysis of eno2- and WT also showed that the levels of three flavonoids, quercetin-3-galactoside, quercitrin, and epicatechin, were significantly decreased in eno2- , and the flavonoid biosynthesis pathway was also enriched in the KEGG analysis. Meanwhile, the mutation of AtENO2 delayed silique ripening, thereby prolonging silique photosynthesis time, allowing siliques to generate more photosynthesis products for FA biosynthesis. These results reveal a molecular mechanism by AtENO2 to regulate seed oil accumulation in A. thaliana, providing potential targets for improving crop seed oil quality.
Collapse
Affiliation(s)
- Zijin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Huimin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lamei Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Yu Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Genfa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
47
|
Patel MK, Chaudhary R, Taak Y, Pardeshi P, Nanjundan J, Vinod KK, Saini N, Vasudev S, Yadava DK. Seed coat colour of Indian mustard [ Brassica juncea (L.) Czern. and Coss.] is associated with Bju.TT8 homologs identifiable by targeted functional markers. FRONTIERS IN PLANT SCIENCE 2022; 13:1012368. [PMID: 36275533 PMCID: PMC9581272 DOI: 10.3389/fpls.2022.1012368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Seed coat colour is an important trait in Indian mustard. Breeding for seed coat colour needs precise knowledge of mode of inheritance and markers linked to it. The present study was focussed on genetics and development of functional markers for seed coat colour. F1s (direct and reciprocal) and F2 populations were developed by crossing two contrasting parents for seed coat colour (DRMRIJ-31, brown seeded and RLC-3, yellow seeded). Phenotypic results have shown that the seed coat colour trait was under the influence of maternal effect and controlled by digenic-duplicate gene action. Further, Bju.TT8 homologs of both parents (DRMRIJ-31 and RLC-3) were cloned and sequenced. Sequencing results of Bju.TT8 homologs revealed that in RLC-3, gene Bju.ATT8 had an insertion of 1279bp in the 7th exon; whereas, gene Bju.BTT8 had an SNP (C→T) in the 7th exon. These two mutations were found to be associated with yellow seed coat colour. Using sequence information, functional markers were developed for both Bju.TT8 homologs, validated on F2 population and were found highly reliable with no recombination between the markers and the phenotype. Further, these markers were subjected to a germplasm assembly of Indian mustard, and their allelic combination for the seed coat colour genes has been elucidated. The comparative genomics of TT8 genes revealed high degree of similarity between and across the Brassica species, and the respective diploid progenitors in tetraploid Brassica species are the possible donors of TT8 homologs. This study will help in the marker-assisted breeding for seed coat colour, and aid in understanding seed coat colour genetics more precisely.
Collapse
Affiliation(s)
- Manoj Kumar Patel
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajat Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Yashpal Taak
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priya Pardeshi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Joghee Nanjundan
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, Regional Research Station, Wellington, India
| | - K. K. Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Navinder Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sujata Vasudev
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - D. K. Yadava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
48
|
Gao Q, Song W, Li X, Xiang C, Chen G, Xiang G, Liu X, Zhang G, Li X, Yang S, Zhai C, Zhao Y. Genome-wide identification of bHLH transcription factors: Discovery of a candidate regulator related to flavonoid biosynthesis in Erigeron breviscapus. FRONTIERS IN PLANT SCIENCE 2022; 13:977649. [PMID: 36186051 PMCID: PMC9515989 DOI: 10.3389/fpls.2022.977649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Erigeron breviscapus is a Compositae plant, and its rich flavonoids have shown strong preventative and curative effects in the treatment of cardio- and cerebrovascular diseases. bHLH genes play a crucial role in plant growth and development. There are 116 EbbHLH genes in E. breviscapus, and each gene has been named based on its chromosome location. Our phylogenetic analysis divided these genes into 18 subfamilies. To further investigate its function, EbbHLH80 was isolated from E. breviscapus leaves. Next, transcriptomic and metabolomic analyses of tobacco leaves were performed. Among 421 differentially accumulated compounds, 98 flavonoids were identified. In addition, differentially expressed genes were identified using RNA-seq, and further analysis suggested that EbbHLH80-OE could not only regulate the expression of some structural genes in the flavonoid biosynthesis pathway to achieve flavonoid accumulation but also be involved in the regulation of a series of downstream pathways, such as stress response, ABA and ethylene signal transduction, to affect plant growth and development. The results of our analysis provide new insights into the function of EbbHLH80 and lay the foundation for future functional studies on E. breviscapus.
Collapse
Affiliation(s)
- Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Geng Chen
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiangyu Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiaoning Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Chenxi Zhai
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, United States
| | - Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
49
|
Yao L, Zhang H, Liu Y, Ji Q, Xie J, Zhang R, Huang L, Mei K, Wang J, Gao W. Engineering of triterpene metabolism and overexpression of the lignin biosynthesis gene PAL promotes ginsenoside Rg 3 accumulation in ginseng plant chassis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1739-1754. [PMID: 35731022 DOI: 10.1111/jipb.13315] [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: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
The ginsenoside Rg3 found in Panax species has extensive pharmacological properties, in particular anti-cancer effects. However, its natural yield in Panax plants is limited. Here, we report a multi-modular strategy to improve yields of Rg3 in a Panax ginseng chassis, combining engineering of triterpene metabolism and overexpression of a lignin biosynthesis gene, phenylalanine ammonia lyase (PAL). We first performed semi-rational design and site mutagenesis to improve the enzymatic efficiency of Pq3-O-UGT2, a glycosyltransferase that directly catalyzes the biosynthesis of Rg3 from Rh2 . Next, we used clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing to knock down the branch pathway of protopanaxatriol-type ginsenoside biosynthesis to enhance the metabolic flux of the protopanaxadiol-type ginsenoside Rg3 . Overexpression of PAL accelerated the formation of the xylem structure, significantly improving ginsenoside Rg3 accumulation (to 6.19-fold higher than in the control). We combined overexpression of the ginsenoside aglycon synthetic genes squalene epoxidase, Pq3-O-UGT2, and PAL with CRISPR/Cas9-based knockdown of CYP716A53v2 to improve ginsenoside Rg3 accumulation. Finally, we produced ginsenoside Rg3 at a yield of 83.6 mg/L in a shake flask (7.0 mg/g dry weight, 21.12-fold higher than with wild-type cultures). The high-production system established in this study could be a potential platform to produce the ginsenoside Rg3 commercially for pharmaceutical use.
Collapse
Affiliation(s)
- Lu Yao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Yirong Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Qiushuang Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ru Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
50
|
Wei X, Pu A, Liu Q, Hou Q, Zhang Y, An X, Long Y, Jiang Y, Dong Z, Wu S, Wan X. The Bibliometric Landscape of Gene Editing Innovation and Regulation in the Worldwide. Cells 2022; 11:cells11172682. [PMID: 36078090 PMCID: PMC9454589 DOI: 10.3390/cells11172682] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Gene editing (GE) has become one of the mainstream bioengineering technologies over the past two decades, mainly fueled by the rapid development of the CRISPR/Cas system since 2012. To date, plenty of articles related to the progress and applications of GE have been published globally, but the objective, quantitative and comprehensive investigations of them are relatively few. Here, 13,980 research articles and reviews published since 1999 were collected by using GE-related queries in the Web of Science. We used bibliometric analysis to investigate the competitiveness and cooperation of leading countries, influential affiliations, and prolific authors. Text clustering methods were used to assess technical trends and research hotspots dynamically. The global application status and regulatory framework were also summarized. This analysis illustrates the bottleneck of the GE innovation and provides insights into the future trajectory of development and application of the technology in various fields, which will be helpful for the popularization of gene editing technology.
Collapse
Affiliation(s)
- Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| | - Aqing Pu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Qianqian Liu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yong Zhang
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yan Long
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Zhenying Dong
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
- Beijing Beike Institute of Precision Medicine and Health Technology, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| |
Collapse
|