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Patwa N, Penning BW. Genetics of a diverse soft winter wheat population for pre-harvest sprouting, agronomic, and flour quality traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1137808. [PMID: 37346135 PMCID: PMC10280069 DOI: 10.3389/fpls.2023.1137808] [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: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Soft winter wheat has been adapted to the north-central, north-western, and south-central United States over hundreds of years for optimal yield, height, heading date, and pathogen and pest resistance. Environmental factors like weather affect abiotic traits such as pre-harvest sprouting resistance. However, pre-harvest sprouting has rarely been a target for breeding. Owing to changing weather patterns from climate change, pre-harvest sprouting resistance is needed to prevent significant crop losses not only in the United States, but worldwide. Twenty-two traits including age of breeding line as well as agronomic, flour quality, and pre-harvest sprouting traits were studied in a population of 188 lines representing genetic diversity over 200 years of soft winter wheat breeding. Some traits were correlated with one another by principal components analysis and Pearson's correlations. A genome-wide association study using 1,978 markers uncovered a total of 102 regions encompassing 226 quantitative trait nucleotides. Twenty-six regions overlapped multiple traits with common significant markers. Many of these traits were also found to be correlated by Pearson's correlation and principal components analyses. Most pre-harvest sprouting regions were not co-located with agronomic traits and thus useful for crop improvement against climate change without affecting crop performance. Six different genome-wide association statistical models (GLM, MLM, MLMM, FarmCPU, BLINK, and SUPER) were utilized to search for reasonable models to analyze soft winter wheat populations with increased markers and/or breeding lines going forward. Some flour quality and agronomic traits seem to have been selected over time, but not pre-harvest sprouting. It appears possible to select for pre-harvest sprouting resistance without impacting flour quality or the agronomic value of soft winter wheat.
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Ullah S, Randhawa IAS, Trethowan R. Genome-wide association study of multiple traits linked to heat tolerance in emmer-derived hexaploid wheat genotypes. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:29. [PMID: 37309354 PMCID: PMC10236052 DOI: 10.1007/s11032-021-01222-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/17/2021] [Indexed: 06/13/2023]
Abstract
Heat stress tolerance in plants is a complex trait controlled by multiple genes of minor effect which are influenced by the environment and this makes breeding and selection complicated. Emmer wheat (Triticum dicoccon Schrank) carries valuable diversity that can be used to improve the heat tolerance of modern bread wheat. A diverse set of emmer-based genotypes was developed by crossing emmer wheat with hexaploid wheat. These materials, along with their hexaploid recurrent parents and commercial cultivars, were evaluated at optimum (E1) and heat stressed (E2) sowing times in the field for three consecutive years (2014-2016). The material was genotyped using the Infinium iSelect SNP 90K SNP Assay. The phenotypic data were combined across years within each sowing time and best linear unbiased estimators calculated for each genotype in each environment. These estimates were used for GWAS analysis. Significant phenotypic and genotypic variation was observed for all traits. A total of 125 and 142 marker-trait associations (MTAs) were identified in E1 and E2, respectively. The highest number of MTAs were observed on the A genome (106), followed by the B (105) and D (56) genomes. MTAs with pleiotropic effects within and across the environments were observed. Many of the MTAs found were reported previously for various traits, and a few significant MTAs under heat stress were new and linked to emmer genome. Genomic regions identified on chromosomes 2B and 3A had a significant positive impact on grain yield under stress with a 7% allelic effect. Genomic regions on chromosomes 1A and 4B contributed 11% and 9% of the variation for thousand kernel weight (TKW) under heat stress respectively. Following fine mapping, these regions could be used for marker-assisted selection to improve heat tolerance in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01222-3.
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Affiliation(s)
- Smi Ullah
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Narrabri, New South Wales 2390 Australia
| | - Imtiaz A. S. Randhawa
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343 Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Narrabri, New South Wales 2390 Australia
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Cobbitty, New South Wales 2570 Australia
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3
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Zhou W, Shi M, Deng C, Lu S, Huang F, Wang Y, Kai G. The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza. HORTICULTURE RESEARCH 2021; 8:10. [PMID: 33384411 DOI: 10.1038/s41438-020-00443-445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/30/2020] [Accepted: 10/17/2020] [Indexed: 05/25/2023]
Abstract
Water-soluble phenolic acids are major bioactive compounds in the medicinal plant species Salvia miltiorrhiza. Phenolic acid biosynthesis is induced by methyl jasmonate (MeJA) in this important Chinese herb. Here, we investigated the mechanism underlying this induction by analyzing a transcriptome library of S. miltiorrhiza in response to MeJA. Global transcriptome analysis identified the MeJA-responsive R2R3-MYB transcription factor-encoding gene SmMYB1. Overexpressing SmMYB1 significantly promoted phenolic acid accumulation and upregulated the expression of genes encoding key enzymes in the phenolic acid biosynthesis pathway, including cytochrome P450-dependent monooxygenase (CYP98A14). Dual-luciferase (dual-LUC) assays and/or an electrophoretic mobility shift assays (EMSAs) indicated that SmMYB1 activated the expression of CYP98A14, as well as the expression of genes encoding anthocyanin biosynthesis pathway enzymes, including chalcone isomerase (CHI) and anthocyanidin synthase (ANS). In addition, SmMYB1 was shown to interact with SmMYC2 to additively promote CYP98A14 expression compared to the action of SmMYB1 alone. Taken together, these results demonstrate that SmMYB1 is an activator that improves the accumulation of phenolic acids and anthocyanins in S. miltiorrhiza. These findings lay the foundation for in-depth studies of the molecular mechanism underlying MeJA-mediated phenolic acid biosynthesis and for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.
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Affiliation(s)
- Wei Zhou
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Min Shi
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Changping Deng
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Sunjie Lu
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Fenfen Huang
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Yao Wang
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Guoyin Kai
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China.
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.
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4
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Zhou W, Shi M, Deng C, Lu S, Huang F, Wang Y, Kai G. The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza. HORTICULTURE RESEARCH 2021; 8:10. [PMID: 33384411 PMCID: PMC7775463 DOI: 10.1038/s41438-020-00443-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/30/2020] [Accepted: 10/17/2020] [Indexed: 05/24/2023]
Abstract
Water-soluble phenolic acids are major bioactive compounds in the medicinal plant species Salvia miltiorrhiza. Phenolic acid biosynthesis is induced by methyl jasmonate (MeJA) in this important Chinese herb. Here, we investigated the mechanism underlying this induction by analyzing a transcriptome library of S. miltiorrhiza in response to MeJA. Global transcriptome analysis identified the MeJA-responsive R2R3-MYB transcription factor-encoding gene SmMYB1. Overexpressing SmMYB1 significantly promoted phenolic acid accumulation and upregulated the expression of genes encoding key enzymes in the phenolic acid biosynthesis pathway, including cytochrome P450-dependent monooxygenase (CYP98A14). Dual-luciferase (dual-LUC) assays and/or an electrophoretic mobility shift assays (EMSAs) indicated that SmMYB1 activated the expression of CYP98A14, as well as the expression of genes encoding anthocyanin biosynthesis pathway enzymes, including chalcone isomerase (CHI) and anthocyanidin synthase (ANS). In addition, SmMYB1 was shown to interact with SmMYC2 to additively promote CYP98A14 expression compared to the action of SmMYB1 alone. Taken together, these results demonstrate that SmMYB1 is an activator that improves the accumulation of phenolic acids and anthocyanins in S. miltiorrhiza. These findings lay the foundation for in-depth studies of the molecular mechanism underlying MeJA-mediated phenolic acid biosynthesis and for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.
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Grants
- This work was supported by National Key R&G Program of China (2018YFC1706200), National Natural Science Fund (81522049, 31571735, 31270007), the ‘Dawn’ Program of Shanghai Education Commission (16SG38), Shanghai Science and Technology Committee Project (17JC1404300, 15430502700), Zhejiang Provincial Ten Thousands Program for Leading Talents of Science and Technology Innovation (2018R52050), Zhejiang Natural Science Fund (LY20H280008), Zhejiang Provincial Program for the Cultivation of High-level Innovative Health talents, Pre-research Projects of Zhejiang Chinese Medical University (2018ZG30).
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Affiliation(s)
- Wei Zhou
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Min Shi
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Changping Deng
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Sunjie Lu
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Fenfen Huang
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Yao Wang
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Guoyin Kai
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China.
- Institute of Plant Biotechnology, School of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.
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Deblieck M, Fatiukha A, Grundman N, Merchuk-Ovnat L, Saranga Y, Krugman T, Pillen K, Serfling A, Makalowski W, Ordon F, Perovic D. GenoTypeMapper: graphical genotyping on genetic and sequence-based maps. PLANT METHODS 2020; 16:123. [PMID: 32944061 PMCID: PMC7488165 DOI: 10.1186/s13007-020-00665-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. RESULTS We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. CONCLUSIONS In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.
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Affiliation(s)
- Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andrii Fatiukha
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Norbert Grundman
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Lianne Merchuk-Ovnat
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Yehoshua Saranga
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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Kidane YG, Gesesse CA, Hailemariam BN, Desta EA, Mengistu DK, Fadda C, Pè ME, Dell'Acqua M. A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1380-1393. [PMID: 30575264 PMCID: PMC6576139 DOI: 10.1111/pbi.13062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 05/11/2023]
Abstract
The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi-parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre-breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.
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Affiliation(s)
- Yosef G. Kidane
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Bioversity InternationalAddis AbabaEthiopia
| | - Cherinet A. Gesesse
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Amhara Regional Agricultural Research Institute (ARARI)Adet Agricultural Research CenterBahir DarEthiopia
| | | | - Ermias A. Desta
- Amhara Regional Agricultural Research Institute (ARARI)Adet Agricultural Research CenterBahir DarEthiopia
| | - Dejene K. Mengistu
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Department of Dryland Crop and Horticultural SciencesMekelle UniversityMekelleEthiopia
| | | | - Mario Enrico Pè
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
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Cao W, Wang Y, Shi M, Hao X, Zhao W, Wang Y, Ren J, Kai G. Transcription Factor SmWRKY1 Positively Promotes the Biosynthesis of Tanshinones in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2018; 9:554. [PMID: 29755494 PMCID: PMC5934499 DOI: 10.3389/fpls.2018.00554] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/09/2018] [Indexed: 05/20/2023]
Abstract
Tanshinones, one group of bioactive diterpenes, were widely used in the treatment of cardiovascular diseases. WRKYs play important roles in plant metabolism, but their regulation mechanism in Salvia miltiorrhiza remains elusive. In this study, one WRKY transcription factor SmWRKY1 was isolated and functionally characterized from S. miltiorrhiza. Multiple sequence alignment and phylogenetic tree analysis showed SmWRKY1 shared high homology with other plant WRKYs such as CrWRKY1. SmWRKY1 was found predominantly expressed in leaves and stems, and was responsive to salicylic acid (SA), methyl jasmonate (MeJA), and nitric oxide (NO) treatment. Subcellular localization analysis found that SmWRKY1 was localized in the nucleus. Over-expression of SmWRKY1 significantly elevated the transcripts of genes coding for enzymes in the MEP pathway especially 1-deoxy-D-xylulose-5-phosphate synthase (SmDXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (SmDXR), resulted in over fivefold increase in tanshinones production in transgenic lines (up to 13.7 mg/g DW) compared with the control lines. A dual-luciferase (Dual-LUC) assay showed that SmWRKY1 can positively regulate SmDXR expression by binding to its promoter. Our work revealed that SmWRKY1 participated in the regulation of tanshinones biosynthesis and acted as a positive regulator through activating SmDXR in the MEP pathway, thus provided a new insight to further explore the regulation mechanism of tanshinones biosynthesis.
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Affiliation(s)
- Wenzhi Cao
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Wang
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Min Shi
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaolong Hao
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Weiwei Zhao
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yu Wang
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Ren
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Guoyin Kai
- Institute of Plant Biotechnology, Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
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Zhou W, Huang Q, Wu X, Zhou Z, Ding M, Shi M, Huang F, Li S, Wang Y, Kai G. Comprehensive transcriptome profiling of Salvia miltiorrhiza for discovery of genes associated with the biosynthesis of tanshinones and phenolic acids. Sci Rep 2017; 7:10554. [PMID: 28874707 PMCID: PMC5585387 DOI: 10.1038/s41598-017-10215-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/07/2017] [Indexed: 12/14/2022] Open
Abstract
Tanshinones and phenolic acids are crucial bioactive compounds biosynthesized in Salvia miltiorrhiza. Methyl jasmonate (MeJA) is an effective elicitor to enhance the production of phenolic acids and tanshinones simultaneously, while yeast extract (YE) is used as a biotic elicitor that only induce tanshinones accumulation. However, little was known about the different molecular mechanism. To identify the downstream and regulatory genes involved in tanshinone and phenolic acid biosynthesis, we conducted comprehensive transcriptome profiling of S. miltiorrhiza hairy roots treated with either MeJA or YE. Total 55588 unigenes were assembled from about 1.72 billion clean reads, of which 42458 unigenes (76.4%) were successfully annotated. The expression patterns of 19 selected genes in the significantly upregulated unigenes were verified by quantitative real-time PCR. The candidate downstream genes and other cytochrome P450s involved in the late steps of tanshinone and phenolic acid biosynthesis pathways were screened from the RNA-seq dataset based on co-expression pattern analysis with specific biosynthetic genes. Additionally, 375 transcription factors were identified to exhibit a significant up-regulated expression pattern in response to induction. This study can provide us a valuable gene resource for elucidating the molecular mechanism of tanshinones and phenolic acids biosynthesis in hairy roots of S. miltiorrhiza.
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Affiliation(s)
- Wei Zhou
- College of pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China.,The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang, 311300, China
| | - Qiang Huang
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao Wu
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zewen Zhou
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang, 311300, China
| | - Min Shi
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Fenfen Huang
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shen Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang, 311300, China
| | - Yao Wang
- Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Guoyin Kai
- College of pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China. .,Laboratory of Plant Biotechnology, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China.
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9
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Lucas SJ, Salantur A, Yazar S, Budak H. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 2017; 17:667-685. [PMID: 28550605 DOI: 10.1007/s10142-017-0563-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.
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Affiliation(s)
- Stuart J Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey.
| | - Ayten Salantur
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Selami Yazar
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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