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Shekhawat PK, Goyal A, Akhatar J, Sharma S, Kaur N, Bharti B, Mittal M, Sardana VK, Chhuneja P, Banga SS, Atri C. Genetic analysis of the variation for mineral accumulation in the leaves and seeds of natural germplasm of Brassica rapa L. (AA) and the its derived forms extracted from an allotetraploid B.juncea L.(AABB). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108084. [PMID: 37832370 DOI: 10.1016/j.plaphy.2023.108084] [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: 06/18/2023] [Revised: 09/16/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
Brassica rapa L. (2n = 20; AA) is a vegetable and oilseed crop that is grown all over the world. Its leaves, shoots, and seeds store significant amounts of minerals. We used inductively coupled plasma-optical emission spectroscopy (ICP-OES) to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines, of which 92 represented natural (NR) B. rapa and the remaining 103 were derived (DR) from a set of mother genotypes originally extracted from an allotetraploid B. juncea (2n = 36; AABB). The inbred lines differed for the composition of leaf and seed minerals. Leaf concentrations of N, K, Zn, and Se were higher in the DR subpanel as compared to NR subpanel, along with high seed accumulations of K and Se. DArT genotyping and genome wide association mapping led to the identification of SNPs associated with leaf and seed mineral compositions. Chromosomes A03, A05, and A10 harboured the most associated loci. Annotations of the regions adjacent to respective GWAS peaks allowed prediction of genes known for acquisition, transport, and accumulation of minerals and heavy metal detoxification. Transcriptome analysis revealed differential expression patterns of the predicted candidates, with most genes either down-regulated in derived genotypes relative to natural forms or their expression being comparable between the two. General downregulation may be a consequence of extracting B. rapa from allotetraploid B. juncea through genome resection. Some of the identified SNPs may be used as DNA markers for breeding programmes designed to modify the leaf and seed mineral compositions.
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Affiliation(s)
- Pooja Kanwar Shekhawat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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Lou H, Zheng S, Chen W, Yu W, Jiang H, Farag MA, Xiao J, Wu J, Song L. Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel. J Adv Res 2023:S2090-1232(23)00007-3. [PMID: 36639025 DOI: 10.1016/j.jare.2023.01.007] [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: 10/18/2021] [Revised: 12/21/2022] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations. OBJECTIVES As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis. METHODS We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes. RESULTS We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (-log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson's correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1. CONCLUSION Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini st., Cairo P.B. 11562, Egypt
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo - Ourense Campus, E-32004 Ourense, Spain.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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Koprivova A, Elkatmis B, Gerlich SC, Trick M, Harper AL, Bancroft I, Kopriva S. Natural Variation in OASC Gene for Mitochondrial O-Acetylserine Thiollyase Affects Sulfate Levels in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 12:35. [PMID: 36616163 PMCID: PMC9824738 DOI: 10.3390/plants12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Sulfur plays a vital role in the primary and secondary metabolism of plants, and carries an important function in a large number of different compounds. Despite this importance, compared to other mineral nutrients, relatively little is known about sulfur sensing and signalling, as well as about the mechanisms controlling sulfur metabolism and homeostasis. Sulfur contents in plants vary largely not only among different species, but also among accessions of the same species. We previously used associative transcriptomics to identify several genes potentially controlling variation in sulfate content in the leaves of Brassica napus, including an OASC gene for mitochondrial O-acetylserine thiollyase (OAS-TL), an enzyme involved in cysteine synthesis. Here, we show that loss of OASC in Arabidopsis thaliana lowers not only sulfate, but also glutathione levels in the leaves. The reduced accumulation is caused by lower sulfate uptake and translocation to the shoots; however, the flux through the pathway is not affected. In addition, we identified a single nucleotide polymorphism in the OASC gene among A. thaliana accessions that is linked to variation in sulfate content. Both genetic and transgenic complementation confirmed that the exchange of arginine at position 81 for lysine in numerous accessions resulted in a less active OASC and a lower sulfate content in the leaves. The mitochondrial isoform of OAS-TL is, thus, after the ATPS1 isoform of sulfurylase and the APR2 form of APS reductase 2, the next metabolic enzyme with a role in regulation of sulfate content in Arabidopsis.
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Affiliation(s)
- Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Büsra Elkatmis
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Silke C. Gerlich
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Andrea L. Harper
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
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Nitrogen Assimilation Related Genes in Brassicanapus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses. PLANTS 2021; 10:plants10102160. [PMID: 34685969 PMCID: PMC8539475 DOI: 10.3390/plants10102160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) is an essential macronutrient for plants. However, little is known about the molecular regulation of N assimilation in Brassica napus, one of the most important oil crops worldwide. Here, we carried out a comprehensive genome-wide analysis of the N assimilation related genes (NAGs) in B. napus. A total of 67 NAGs were identified encoding major enzymes involved in N assimilation, including asparagine synthetase (AS), glutamate dehydrogenase (GDH), glutamine oxoglutarate aminotransferase (GOGAT), glutamine synthetase (GS), nitrite reductase (NiR), nitrate reductase (NR). The syntenic analysis revealed that segmental duplication and whole-genome duplication were the main expansion pattern during gene evolution. Each NAG family showed different degrees of differentiation in characterization, gene structure, conserved motifs and cis-elements. Furthermore, diverse responses of NAG to multiple nutrient stresses were observed. Among them, more NAGs were regulated by N deficiency and ammonium toxicity than by phosphorus and potassium deprivations. Moreover, 12 hub genes responding to N starvation were identified, which may play vital roles in N utilization. Taken together, our results provide a basis for further functional research of NAGs in rapeseed N assimilation and also put forward new points in their responses to contrasting nutrient stresses.
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Cruz DF, De Meyer S, Ampe J, Sprenger H, Herman D, Van Hautegem T, De Block J, Inzé D, Nelissen H, Maere S. Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol Syst Biol 2020; 16:e9667. [PMID: 33346944 PMCID: PMC7751767 DOI: 10.15252/msb.20209667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
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Affiliation(s)
- Daniel Felipe Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Sam De Meyer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Joke Ampe
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Heike Sprenger
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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Huang Y, Hussain MA, Luo D, Xu H, Zeng C, Havlickova L, Bancroft I, Tian Z, Zhang X, Cheng Y, Zou X, Lu G, Lv Y. A Brassica napus Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:971. [PMID: 32676095 PMCID: PMC7333310 DOI: 10.3389/fpls.2020.00971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Cold treatment (vernalization) is required for winter crops such as rapeseed (Brassica napus L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the Arabidopsis gene AT2G29300.2 encoding a tropinone reductase (BnTR1), was further confirmed to be closely linked to transpiration rate. Ectopic expressing BnTR1 in Arabidopsis plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic Arabidopsis plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that BnTR1 is a good target gene for the genetic improvement of LT tolerance in plant.
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Affiliation(s)
- Yong Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dan Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongzhi Xu
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Chuan Zeng
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Lenka Havlickova
- Centre for Novel Agricultural Products (CNAP) M119, Department of Biology, University of York, York, United Kingdom
| | - Ian Bancroft
- Centre for Novel Agricultural Products (CNAP) M119, Department of Biology, University of York, York, United Kingdom
| | - Zhitao Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xuekun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guangyuan Lu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Wang W, Ding G, White PJ, Wang M, Zou J, Xu F, Hammond JP, Shi L. Genetic dissection of the shoot and root ionomes of Brassica napus grown with contrasting phosphate supplies. ANNALS OF BOTANY 2020; 126:119-140. [PMID: 32221530 PMCID: PMC7304470 DOI: 10.1093/aob/mcaa055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Mineral elements have many essential and beneficial functions in plants. Phosphorus (P) deficiency can result in changes in the ionomes of plant organs. The aims of this study were to characterize the effects of P supply on the ionomes of shoots and roots, and to identify chromosomal quantitative trait loci (QTLs) for shoot and root ionomic traits, as well as those affecting the partitioning of mineral elements between shoot and root in Brassica napus grown with contrasting P supplies. METHODS Shoot and root concentrations of 11 mineral elements (B, Ca, Cu, Fe, K, Mg, Mn, Na, P, S and Zn) were investigated by inductively coupled plasma optical emission spectrometry (ICP-OES) in a Brassica napus double haploid population grown at an optimal (OP) and a low phosphorus supply (LP) in an agar system. Shoot, root and plant contents, and the partitioning of mineral elements between shoot and root were calculated. KEY RESULTS The tissue concentrations of B, Ca, Cu, K, Mg, Mn, Na, P and Zn were reduced by P starvation, while the concentration of Fe was increased by P starvation in the BnaTNDH population. A total of 133 and 123 QTLs for shoot and root ionomic traits were identified at OP and LP, respectively. A major QTL cluster on chromosome C07 had a significant effect on shoot Mg and S concentrations at LP and was narrowed down to a 2.1 Mb region using an advanced backcross population. CONCLUSIONS The tissue concentration and partitioning of each mineral element was affected differently by P starvation. There was a significant difference in mineral element composition between shoots and roots. Identification of the genes underlying these QTLs will enhance our understanding of processes affecting the uptake and partitioning of mineral elements in Brassica napus.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - John P Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
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Hejna O, Havlickova L, He Z, Bancroft I, Curn V. Analysing the genetic architecture of clubroot resistance variation in Brassica napus by associative transcriptomics. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2019; 39:112. [PMID: 31396013 PMCID: PMC6647481 DOI: 10.1007/s11032-019-1021-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/08/2019] [Indexed: 06/01/2023]
Abstract
Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus. A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.
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Affiliation(s)
- Ondrej Hejna
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Lenka Havlickova
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Vladislav Curn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
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Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains. Proc Natl Acad Sci U S A 2019; 116:15735-15744. [PMID: 31311863 PMCID: PMC6681745 DOI: 10.1073/pnas.1818604116] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants in their natural ecosystems interact with numerous microorganisms, but how they influence their microbiota is still elusive. We observed that sulfatase activity in soil, which can be used as a measure of rhizosphere microbial activity, is differently affected by Arabidopsis accessions. Following a genome-wide association analysis of the variation in sulfatase activity we identified a candidate gene encoding an uncharacterized cytochrome P450, CYP71A27 Loss of this gene resulted in 2 different and independent microbiota-specific phenotypes: A lower sulfatase activity in the rhizosphere and a loss of plant growth-promoting effect by Pseudomonas sp. CH267. On the other hand, tolerance to leaf pathogens was not affected, which agreed with prevalent expression of CYP71A27 in the root vasculature. The phenotypes of cyp71A27 mutant were similar to those of cyp71A12 and cyp71A13, known mutants in synthesis of camalexin, a sulfur-containing indolic defense compound. Indeed, the cyp71A27 mutant accumulated less camalexin in the roots upon elicitation with silver nitrate or flagellin. Importantly, addition of camalexin complemented both the sulfatase activity and the loss of plant growth promotion by Pseudomonas sp. CH267. Two alleles of CYP71A27 were identified among Arabidopsis accessions, differing by a substitution of Glu373 by Gln, which correlated with the ability to induce camalexin synthesis and to gain fresh weight in response to Pseudomonas sp. CH267. Thus, CYP71A27 is an additional component in the camalexin synthesis pathway, contributing specifically to the control of plant microbe interactions in the root.
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Wang X, Xu P, Yin L, Ren Y, Li S, Shi Y, Alcock TD, Xiong Q, Qian W, Chi X, Pandey MK, Varshney RK, Yuan M. Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.). PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:518-529. [PMID: 30100671 PMCID: PMC6061501 DOI: 10.1007/s11105-018-1088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs.
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Affiliation(s)
- Xiaohua Wang
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Ping Xu
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Liang Yin
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yan Ren
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Shuangling Li
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yanmao Shi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Thomas D. Alcock
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Qing Xiong
- College of Computer and Information Science, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaoyuan Chi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Mei Yuan
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
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12
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Alcock TD, Havlickova L, He Z, Wilson L, Bancroft I, White PJ, Broadley MR, Graham NS. Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2018; 9:1487. [PMID: 30386356 PMCID: PMC6198146 DOI: 10.3389/fpls.2018.01487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/25/2018] [Indexed: 05/06/2023]
Abstract
Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in B. napus.
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Affiliation(s)
- Thomas D. Alcock
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | | | - Zhesi He
- Department of Biology, University of York, York, United Kingdom
| | - Lolita Wilson
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Ian Bancroft
- Department of Biology, University of York, York, United Kingdom
| | - Philip J. White
- The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| | - Martin R. Broadley
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Neil S. Graham
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- *Correspondence: Neil S. Graham
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13
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Miller CN, Harper AL, Trick M, Wellner N, Werner P, Waldron KW, Bancroft I. Dissecting the complex regulation of lodging resistance in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:30. [PMID: 29568228 PMCID: PMC5842258 DOI: 10.1007/s11032-018-0781-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 01/29/2018] [Indexed: 05/17/2023]
Abstract
Lodging continues to be a major cause of yield loss in important crop species such as Brassica napus. Understanding the genetic regulation of lodging resistance is therefore of key interest to breeders worldwide. Current strategies aimed at minimising lodging risk involve the incorporation of dwarfing genes or the application of plant growth regulators. However, despite these efforts, lodging continues to be a persistent problem and it is therefore of high interest that novel, complimentary strategies for lodging control are implemented. One approach would be to focus on understanding the genetic properties underlying stem mechanical strength. With this in mind, we screened a training genetic diversity panel of B. napus accession for variation in stem mechanical strength and related traits. Using Associative Transcriptomics, we identified molecular markers for a suite of valuable traits. Using an independent test genetic diversity panel, we show that the methods employed are robust for identification of predictive markers. Furthermore, based on conserved synteny with Arabidopsis thaliana, we are able to provide a biological context to the marker associations detected and provide evidence for a role in pectin methylesterification in contributing to stem mechanical strength in Brassicaceae.
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Affiliation(s)
| | - Andrea L. Harper
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Biology, University of York, York, YO10 5DD UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Nikolaus Wellner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Peter Werner
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | - Keith W. Waldron
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Biology, University of York, York, YO10 5DD UK
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14
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Linn J, Ren M, Berkowitz O, Ding W, van der Merwe MJ, Whelan J, Jost R. Root Cell-Specific Regulators of Phosphate-Dependent Growth. PLANT PHYSIOLOGY 2017; 174:1969-1989. [PMID: 28465462 PMCID: PMC5490885 DOI: 10.1104/pp.16.01698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/01/2017] [Indexed: 05/07/2023]
Abstract
Cellular specialization in abiotic stress responses is an important regulatory feature driving plant acclimation. Our in silico approach of iterative coexpression, interaction, and enrichment analyses predicted root cell-specific regulators of phosphate starvation response networks in Arabidopsis (Arabidopsis thaliana). This included three uncharacterized genes termed Phosphate starvation-induced gene interacting Root Cell Enriched (PRCE1, PRCE2, and PRCE3). Root cell-specific enrichment of 12 candidates was confirmed in promoter-GFP lines. T-DNA insertion lines of 11 genes showed changes in phosphate status and growth responses to phosphate availability compared with the wild type. Some mutants (cbl1, cipk2, prce3, and wdd1) displayed strong biomass gain irrespective of phosphate supply, while others (cipk14, mfs1, prce1, prce2, and s6k2) were able to sustain growth under low phosphate supply better than the wild type. Notably, root or shoot phosphate accumulation did not strictly correlate with organ growth. Mutant response patterns markedly differed from those of master regulators of phosphate homeostasis, PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHOSPHATE2 (PHO2), demonstrating that negative growth responses in the latter can be overcome when cell-specific regulators are targeted. RNA sequencing analysis highlighted the transcriptomic plasticity in these mutants and revealed PHR1-dependent and -independent regulatory circuits with gene coexpression profiles that were highly correlated to the quantified physiological traits. The results demonstrate how in silico prediction of cell-specific, stress-responsive genes uncovers key regulators and how their manipulation can have positive impacts on plant growth under abiotic stress.
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Affiliation(s)
- Joshua Linn
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Meiyan Ren
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Wona Ding
- College of Science and Technology, Ningbo University, Ningbo, 315211 Zhejiang Province, People's Republic of China
| | - Margaretha J van der Merwe
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Western Australia, WA 6009, Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
| | - Ricarda Jost
- Department of Animal, Plant, and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, VIC 3083, Australia
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15
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Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS. Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. FRONTIERS IN PLANT SCIENCE 2017; 8:1968. [PMID: 29187860 PMCID: PMC5694822 DOI: 10.3389/fpls.2017.01968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 05/07/2023]
Abstract
Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young Brassica napus plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes ACA8 and MGT7. Further candidate genes were selected from seven loci and the mineral composition of whole Arabidopsis thaliana shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.
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Affiliation(s)
- Thomas D. Alcock
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | | | - Zhesi He
- Department of Biology, University of York, York, United Kingdom
| | - Ian Bancroft
- Department of Biology, University of York, York, United Kingdom
| | - Philip J. White
- The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| | - Martin R. Broadley
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | - Neil S. Graham
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Neil S. Graham,
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16
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Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc Natl Acad Sci U S A 2016; 113:E7996-E8005. [PMID: 27864511 DOI: 10.1073/pnas.1616564113] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.
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17
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Thomas CL, Alcock TD, Graham NS, Hayden R, Matterson S, Wilson L, Young SD, Dupuy LX, White PJ, Hammond JP, Danku JMC, Salt DE, Sweeney A, Bancroft I, Broadley MR. Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit. BMC PLANT BIOLOGY 2016; 16:214. [PMID: 27716103 PMCID: PMC5050600 DOI: 10.1186/s12870-016-0902-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/25/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a 'pouch and wick' system (n = ~24 replicates per genotype). The mineral composition of 3-6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS). RESULTS Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues. CONCLUSIONS High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits.
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Affiliation(s)
- C. L. Thomas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - T. D. Alcock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - N. S. Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - R. Hayden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. Matterson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - S. D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - L. X. Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - P. J. White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - J. P. Hammond
- School of Agriculture, Policy and Development and the Centre for Food Security, University of Reading, Whiteknights, PO Box 237, Reading, RG6 6AR UK
| | - J. M. C. Danku
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - D. E. Salt
- University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU UK
| | - A. Sweeney
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - I. Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - M. R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
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18
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Koprivova A, Kopriva S. Sulfur metabolism and its manipulation in crops. J Genet Genomics 2016; 43:623-629. [PMID: 27582269 DOI: 10.1016/j.jgg.2016.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/12/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Anna Koprivova
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany.
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19
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Koprivova A, Kopriva S. Hormonal control of sulfate uptake and assimilation. PLANT MOLECULAR BIOLOGY 2016; 91:617-27. [PMID: 26810064 DOI: 10.1007/s11103-016-0438-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/11/2016] [Indexed: 05/23/2023]
Abstract
Plant hormones have a plethora of functions in control of plant development, stress response, and primary metabolism, including nutrient homeostasis. In the plant nutrition, the interplay of hormones with responses to nitrate and phosphate deficiency is well described, but relatively little is known about the interaction between phytohormones and regulation of sulfur metabolism. As for other nutrients, sulfate deficiency results in modulation of root architecture, where hormones are expected to play an important role. Accordingly, sulfate deficiency induces genes involved in metabolism of tryptophane and auxin. Also jasmonate biosynthesis is induced, pointing to the need of increase the defense capabilities of the plants when sulfur is limiting. However, hormones affect also sulfate uptake and assimilation. The pathway is coordinately induced by jasmonate and the key enzyme, adenosine 5'-phosphosulfate reductase, is additionally regulated by ethylene, abscisic acid, nitric oxid, and other phytohormones. Perhaps the most intriguing link between hormones and sulfate assimilation is the fact that the main regulator of the response to sulfate starvation, SULFATE LIMITATION1 (SLIM1) belongs to the family of ethylene related transcription factors. We will review the current knowledge of interplay between phytohormones and control of sulfur metabolism and discuss the main open questions.
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Affiliation(s)
- Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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20
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Koprivova A, Kopriva S. Sulfation pathways in plants. Chem Biol Interact 2016; 259:23-30. [PMID: 27206694 DOI: 10.1016/j.cbi.2016.05.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 11/27/2022]
Abstract
Plants take up sulfur in the form of sulfate. Sulfate is activated to adenosine 5'-phosphosulfate (APS) and reduced to sulfite and then to sulfide when it is assimilated into amino acid cysteine. Alternatively, APS is phosphorylated to 3'-phosphoadenosine 5'-phosphosulfate (PAPS), and sulfate from PAPS is transferred onto diverse metabolites in its oxidized form. Traditionally, these pathways are referred to as primary and secondary sulfate metabolism, respectively. However, the synthesis of PAPS is essential for plants and even its reduced provision leads to dwarfism. Here the current knowledge of enzymes involved in sulfation pathways of plants will be summarized, the similarities and differences between different kingdoms will be highlighted, and major open questions in the research of plant sulfation will be formulated.
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Affiliation(s)
- Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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21
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Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, Wang L, Fellgett A, Sollars ESA, Janacek SH, Downie JA, Buggs RJA, Kjær ED, Bancroft I. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics. Sci Rep 2016; 6:19335. [PMID: 26757823 PMCID: PMC4725942 DOI: 10.1038/srep19335] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/07/2015] [Indexed: 11/24/2022] Open
Abstract
Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback.
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Affiliation(s)
| | - Lea Vig McKinney
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | - Lene Rostgaard Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | | | - Yi Li
- Department of Biology, University of York, York, UK
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, UK
| | - Fiona Fraser
- Department of Crop Genetics, John Innes Centre, Norwich, UK
| | - Lihong Wang
- Department of Biology, University of York, York, UK
| | | | | | | | - J. Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Richard. J. A. Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Erik Dahl Kjær
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Denmark
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
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22
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Kopriva S, Calderwood A, Weckopp SC, Koprivova A. Plant sulfur and Big Data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:1-10. [PMID: 26706053 DOI: 10.1016/j.plantsci.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 05/20/2023]
Abstract
Sulfur is an essential mineral nutrient for plants, therefore, the pathways of its uptake and assimilation have been extensively studied. Great progress has been made in elucidation of the individual genes and enzymes and their regulation. Sulfur assimilation has been intensively investigated by -omics technologies and has been target of several genome wide genetic approaches. This brought a significant step in our understanding of the regulation of the pathway and its integration in cellular metabolism. However, the large amount of information derived from other experiments not directly targeting sulfur has also brought new and exciting insights into processes affecting sulfur homeostasis. In this review we will integrate the findings of the targeted experiments with those that brought unintentional progress in sulfur research, and will discuss how to synthesize the large amount of information available in various repositories into a meaningful dissection of the regulation of a specific metabolic pathway. We then speculate how this might be used to further advance knowledge on control of sulfur metabolism and what are the main questions to be answered.
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Affiliation(s)
- Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | | | - Silke C Weckopp
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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23
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Pilbeam DJ. Breeding crops for improved mineral nutrition under climate change conditions. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3511-21. [PMID: 25614661 DOI: 10.1093/jxb/eru539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Improvements in understanding how climate change may influence chemical and physical processes in soils, how this may affect nutrient availability, and how plants may respond to changed availability of nutrients will influence crop breeding programmes. The effects of increased atmospheric CO2 and warmer temperatures, both individually and combined, on soil microbial activity, including mycorrhizas and N-fixing organisms, are evaluated, together with their implications for nutrient availability. Potential changes to plant growth, and the combined effects of soil and plant changes on nutrient uptake, are discussed. The organization of research on the efficient use of macro- and micronutrients by crops under climate change conditions is outlined, including analysis of QTLs for nutrient efficiency. Suggestions for how the information gained can be used in plant breeding programmes are given.
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Koprivova A, Kopriva S. Molecular mechanisms of regulation of sulfate assimilation: first steps on a long road. FRONTIERS IN PLANT SCIENCE 2014; 5:589. [PMID: 25400653 PMCID: PMC4212615 DOI: 10.3389/fpls.2014.00589] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/10/2014] [Indexed: 05/19/2023]
Abstract
The pathway of sulfate assimilation, which provides plants with the essential nutrient sulfur, is tightly regulated and coordinated with the demand for reduced sulfur. The responses of metabolite concentrations, enzyme activities and mRNA levels to various signals and environmental conditions have been well described for the pathway. However, only little is known about the molecular mechanisms of this regulation. To date, nine transcription factors have been described to control transcription of genes of sulfate uptake and assimilation. In addition, other levels of regulation contribute to the control of sulfur metabolism. Post-transcriptional regulation has been shown for sulfate transporters, adenosine 5'phosphosulfate reductase, and cysteine synthase. Several genes of the pathway are targets of microRNA miR395. In addition, protein-protein interaction is increasingly found in the center of various regulatory circuits. On top of the mechanisms of regulation of single genes, we are starting to learn more about mechanisms of adaptation, due to analyses of natural variation. In this article, the summary of different mechanisms of regulation will be accompanied by identification of the major gaps in knowledge and proposition of possible ways of filling them.
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Affiliation(s)
| | - Stanislav Kopriva
- *Correspondence: Stanislav Kopriva, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany e-mail:
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