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Abstract
The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.
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Yan J, Aboshi T, Teraishi M, Strickler SR, Spindel JE, Tung CW, Takata R, Matsumoto F, Maesaka Y, McCouch SR, Okumoto Y, Mori N, Jander G. The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice. THE PLANT CELL 2015; 27:1265-78. [PMID: 25901084 PMCID: PMC4558700 DOI: 10.1105/tpc.15.00058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/19/2015] [Accepted: 04/03/2015] [Indexed: 05/18/2023]
Abstract
Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth of Arabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice.
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Affiliation(s)
- Jian Yan
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Takako Aboshi
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | | | | | - Jennifer E Spindel
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853
| | - Chih-Wei Tung
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853
| | - Ryo Takata
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | - Fuka Matsumoto
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | - Yoshihiro Maesaka
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | - Naoki Mori
- Graduate School of Agriculture, Kyoto University, Kyoto 808-8502, Japan
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
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153
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Sestili F, Palombieri S, Botticella E, Mantovani P, Bovina R, Lafiandra D. TILLING mutants of durum wheat result in a high amylose phenotype and provide information on alternative splicing mechanisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:127-133. [PMID: 25711820 DOI: 10.1016/j.plantsci.2015.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 05/20/2023]
Abstract
The amylose/amylopectin ratio has a major influence over the properties of starch and determines its optimal end use. Here, high amylose durum wheat has been bred by combining knock down alleles at the two homoelogous genes encoding starch branching enzyme IIa (SBEIIa-A and SBEIIa-B). The complete silencing of these genes had a number of pleiotropic effects on starch synthesis: it affected the transcriptional activity of SBEIIb, ISA1 (starch debranching enzyme) and all of the genes encoding starch synthases (SSI, SSIIa, SSIII and GBSSI). The starch produced by grain of the double SBEIIa mutants was high in amylose (up to ∼1.95 fold that of the wild type) and contained up to about eight fold more resistant starch. A single nucleotide polymorphism adjacent to the splice site at the end of exon 10 of the G364E mutant copies of both SBEIIa-A and SBEIIa-B resulted in the loss of a conserved exonic splicing silencer element. Its starch was similar to that of the SBEIIa double mutant. G364E SBEIIa pre-mRNA was incorrectly processed, resulting in the formation of alternative, but non-functional splicing products.
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Affiliation(s)
- Francesco Sestili
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Via S Camillo de Lellis SNC, 01100 Viterbo, Italy.
| | - Samuela Palombieri
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Via S Camillo de Lellis SNC, 01100 Viterbo, Italy.
| | - Ermelinda Botticella
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Via S Camillo de Lellis SNC, 01100 Viterbo, Italy.
| | - Paola Mantovani
- Società Produttori Sementi Spa, Via Macero 1, 40050 Argelato, Bologna, Italy.
| | - Riccardo Bovina
- Società Produttori Sementi Spa, Via Macero 1, 40050 Argelato, Bologna, Italy; Department of Agricultural Science (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Domenico Lafiandra
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Via S Camillo de Lellis SNC, 01100 Viterbo, Italy.
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154
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Abstract
Tomato (Solanum lycopersicum), along with many other economically valuable species, belongs to the Solanaceae family. Understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. Such changes can implicate the affected gene as participating in plant defense. Testing the involvement of these candidate genes in defense has relied largely on posttranscriptional gene silencing, particularly virus-induced gene silencing. We discuss how functional genomics has played a key role in our current understanding of the defense response in tomato and related species and what are the challenges and opportunities for the future.
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155
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Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
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156
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Scanning the effects of ethyl methanesulfonate on the whole genome of Lotus japonicus using second-generation sequencing analysis. G3-GENES GENOMES GENETICS 2015; 5:559-67. [PMID: 25660167 PMCID: PMC4390572 DOI: 10.1534/g3.114.014571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two individually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes; however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.
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157
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Dorn KM, Fankhauser JD, Wyse DL, Marks MD. A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop. DNA Res 2015; 22:121-31. [PMID: 25632110 PMCID: PMC4401323 DOI: 10.1093/dnares/dsu045] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/21/2014] [Indexed: 12/30/2022] Open
Abstract
Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.
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Affiliation(s)
- Kevin M Dorn
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | | | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - M David Marks
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
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159
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Chemical and Radiation Mutagenesis: Induction and Detection by Whole Genome Sequencing. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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160
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Brutnell TP, Bennetzen JL, Vogel JP. Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:465-85. [PMID: 25621515 DOI: 10.1146/annurev-arplant-042811-105528] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The family of grasses encompasses the world's most important food, feed, and bioenergy crops, yet we are only now beginning to develop the genetic resources to explore the diversity of form and function that underlies economically important traits. Two emerging model systems, Brachypodium distachyon and Setaria viridis, promise to greatly accelerate the process of gene discovery in the grasses and to serve as bridges in the exploration of panicoid and pooid grasses, arguably two of the most important clades of plants from a food security perspective. We provide both a historical view of the development of plant model systems and highlight several recent reports that are providing these developing communities with the tools for gene discovery and pathway engineering.
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161
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Teichmann T, Muhr M. Shaping plant architecture. FRONTIERS IN PLANT SCIENCE 2015; 6:233. [PMID: 25914710 PMCID: PMC4390985 DOI: 10.3389/fpls.2015.00233] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/23/2015] [Indexed: 05/18/2023]
Abstract
Plants exhibit phenotypical plasticity. Their general body plan is genetically determined, but plant architecture and branching patterns are variable and can be adjusted to the prevailing environmental conditions. The modular design of the plant facilitates such morphological adaptations. The prerequisite for the formation of a branch is the initiation of an axillary meristem. Here, we review the current knowledge about this process. After its establishment, the meristem can develop into a bud which can either become dormant or grow out and form a branch. Many endogenous factors, such as photoassimilate availability, and exogenous factors like nutrient availability or shading, have to be integrated in the decision whether a branch is formed. The underlying regulatory network is complex and involves phytohormones and transcription factors. The hormone auxin is derived from the shoot apex and inhibits bud outgrowth indirectly in a process termed apical dominance. Strigolactones appear to modulate apical dominance by modification of auxin fluxes. Furthermore, the transcription factor BRANCHED1 plays a central role. The exact interplay of all these factors still remains obscure and there are alternative models. We discuss recent findings in the field along with the major models. Plant architecture is economically significant because it affects important traits of crop and ornamental plants, as well as trees cultivated in forestry or on short rotation coppices. As a consequence, plant architecture has been modified during plant domestication. Research revealed that only few key genes have been the target of selection during plant domestication and in breeding programs. Here, we discuss such findings on the basis of various examples. Architectural ideotypes that provide advantages for crop plant management and yield are described. We also outline the potential of breeding and biotechnological approaches to further modify and improve plant architecture for economic needs.
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Affiliation(s)
- Thomas Teichmann
- *Correspondence: Thomas Teichmann, Plant Cell Biology, Georg-August-Universität Göttingen, Julia-Lermontowa-Weg 3, Göttingen, Germany
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162
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Fraenkel R, Kovalski I, Troadec C, Bendahmane A, Perl-Treves R. Development and evaluation of a cucumber TILLING population. BMC Res Notes 2014; 7:846. [PMID: 25425033 PMCID: PMC4256834 DOI: 10.1186/1756-0500-7-846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 11/18/2014] [Indexed: 01/23/2023] Open
Abstract
Background Ordered collections of mutants serve as invaluable tools in biological research. TILLING (Targeting Induced Local Lesions IN Genomes) provides an efficient method to discover, in mutagenized populations, the possible phenotypes controlled by gene sequences whose function is unknown. This method can replace transgenic techniques for the functional validation of cloned genes, especially in the case of transformation-recalcitrant plants such as cucumber. Results We report the development of a TILLING cucumber population, generated by EMS mutagenesis in the Poinsett76 genetic background. The population was evaluated by screening for morphological mutations, and a range of developmental, pigmentation and spontaneous lesion mutants were observed. Suitability for detecting single nucleotide polymorphism in selected genes has been tested by screening a sample of amplicons, with detection rate of 1 SNP in ~1 Mbp. Conclusion The population described in this Research Note represents a useful asset in cucumber research, to be exploited for forward genetic screens and functional genomics purposes.
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Affiliation(s)
| | | | | | | | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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163
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Nicaise V. Crop immunity against viruses: outcomes and future challenges. FRONTIERS IN PLANT SCIENCE 2014; 5:660. [PMID: 25484888 PMCID: PMC4240047 DOI: 10.3389/fpls.2014.00660] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/04/2014] [Indexed: 05/02/2023]
Abstract
Viruses cause epidemics on all major cultures of agronomic importance, representing a serious threat to global food security. As strict intracellular pathogens, they cannot be controlled chemically and prophylactic measures consist mainly in the destruction of infected plants and excessive pesticide applications to limit the population of vector organisms. A powerful alternative frequently employed in agriculture relies on the use of crop genetic resistances, approach that depends on mechanisms governing plant-virus interactions. Hence, knowledge related to the molecular bases of viral infections and crop resistances is key to face viral attacks in fields. Over the past 80 years, great advances have been made on our understanding of plant immunity against viruses. Although most of the known natural resistance genes have long been dominant R genes (encoding NBS-LRR proteins), a vast number of crop recessive resistance genes were cloned in the last decade, emphasizing another evolutive strategy to block viruses. In addition, the discovery of RNA interference pathways highlighted a very efficient antiviral system targeting the infectious agent at the nucleic acid level. Insidiously, plant viruses evolve and often acquire the ability to overcome the resistances employed by breeders. The development of efficient and durable resistances able to withstand the extreme genetic plasticity of viruses therefore represents a major challenge for the coming years. This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant-virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants. In addition, I will discuss the current outcomes of the actions employed to control viral diseases in fields and the future investigations that need to be undertaken to develop sustainable broad-spectrum crop resistances against viruses.
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Affiliation(s)
- Valérie Nicaise
- Fruit Biology and Pathology, Virology Laboratory, Institut National de la Recherche Agronomique, University of BordeauxUMR 1332, Villenave d’Ornon, France
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164
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Kornienko AV, Podvigina OA, Zhuzhzhalova TP, Fedulova TP, Bogomolov MA, Oshevnev VP, Butorina AK. High-priority research directions in genetics and the breeding of the sugar beet (Beta vulgaris L.) in the 21st century. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414110064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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165
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First TILLING platform in Cucurbita pepo: a new mutant resource for gene function and crop improvement. PLoS One 2014; 9:e112743. [PMID: 25386735 PMCID: PMC4227871 DOI: 10.1371/journal.pone.0112743] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022] Open
Abstract
Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding.
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166
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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167
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Micol-Ponce R, Aguilera V, Ponce MR. A genetic screen for suppressors of a hypomorphic allele of Arabidopsis ARGONAUTE1. Sci Rep 2014; 4:5533. [PMID: 24985352 PMCID: PMC4078309 DOI: 10.1038/srep05533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/13/2014] [Indexed: 12/28/2022] Open
Abstract
ARGONAUTE1 (AGO1) encodes a key component of the complexes mediating microRNA (miRNA) function in Arabidopsis. To study the regulation, action and interactions of AGO1, we conducted a genetic screen to identify second-site mutations modifying the morphological phenotype of ago1-52, a partial loss-of-function allele of AGO1. Unlike null ago1 mutations, the hypomorphic ago1-52 allele does not cause lethality or sterility; however, ago1-52 does produce a morphological phenotype clearly distinct from wild type. In our screen for modifiers of ago1-52, we identified suppressor mutations that partially restore wild-type morphology in the ago1-52 background and we termed these mas (morphology of argonaute1-52 suppressed). We focused on 23 of these putative suppressors. Linkage analysis of the mas mutations together with sequencing of the AGO1 gene in genomic DNA and cDNA from ago1-52 mas plants indicated that 22 of the mas lines contain extragenic suppressors, and one contains an intragenic suppressor that affects splicing of ago1-52. In the presence of the wild-type allele of AGO1, most of the mas mutations cause a mild or no mutant phenotype on their own, indicating that the ago1-52 mutant may provide a sensitized background for examining the interactions of AGO1.
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Affiliation(s)
- Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
- These authors contributed equally to this work
| | - Verónica Aguilera
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
- These authors contributed equally to this work
- Current address: Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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168
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Lai D, Abou Hachem M, Robson F, Olsen CE, Wang TL, Møller BL, Takos AM, Rook F. The evolutionary appearance of non-cyanogenic hydroxynitrile glucosides in the Lotus genus is accompanied by the substrate specialization of paralogous β-glucosidases resulting from a crucial amino acid substitution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:299-311. [PMID: 24861854 DOI: 10.1111/tpj.12561] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 05/02/2014] [Accepted: 05/13/2014] [Indexed: 05/14/2023]
Abstract
Lotus japonicus, like several other legumes, biosynthesizes the cyanogenic α-hydroxynitrile glucosides lotaustralin and linamarin. Upon tissue disruption these compounds are hydrolysed by a specific β-glucosidase, resulting in the release of hydrogen cyanide. Lotus japonicus also produces the non-cyanogenic γ- and β-hydroxynitrile glucosides rhodiocyanoside A and D using a biosynthetic pathway that branches off from lotaustralin biosynthesis. We previously established that BGD2 is the only β-glucosidase responsible for cyanogenesis in leaves. Here we show that the paralogous BGD4 has the dominant physiological role in rhodiocyanoside degradation. Structural modelling, site-directed mutagenesis and activity assays establish that a glycine residue (G211) in the aglycone binding site of BGD2 is essential for its ability to hydrolyse the endogenous cyanogenic glucosides. The corresponding valine (V211) in BGD4 narrows the active site pocket, resulting in the exclusion of non-flat substrates such as lotaustralin and linamarin, but not of the more planar rhodiocyanosides. Rhodiocyanosides and the BGD4 gene only occur in L. japonicus and a few closely related species associated with the Lotus corniculatus clade within the Lotus genus. This suggests the evolutionary scenario that substrate specialization for rhodiocyanosides evolved from a promiscuous activity of a progenitor cyanogenic β-glucosidase, resembling BGD2, and required no more than a single amino acid substitution.
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Affiliation(s)
- Daniela Lai
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
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169
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Sanchez-Moran E, Armstrong SJ. Meiotic chromosome synapsis and recombination in Arabidopsis thaliana: new ways of integrating cytological and molecular approaches. Chromosome Res 2014; 22:179-90. [DOI: 10.1007/s10577-014-9426-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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170
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Kemen AC, Honkanen S, Melton RE, Findlay KC, Mugford ST, Hayashi K, Haralampidis K, Rosser SJ, Osbourn A. Investigation of triterpene synthesis and regulation in oats reveals a role for β-amyrin in determining root epidermal cell patterning. Proc Natl Acad Sci U S A 2014; 111:8679-84. [PMID: 24912185 PMCID: PMC4060722 DOI: 10.1073/pnas.1401553111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Sterols have important functions in membranes and signaling. Plant sterols are synthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene to cycloartenol. Plants also convert 2,3-oxidosqualene to other sterol-like cyclization products, including the simple triterpene β-amyrin. The function of β-amyrin per se is unknown, but this molecule can serve as an intermediate in the synthesis of more complex triterpene glycosides associated with plant defense. β-Amyrin is present at low levels in the roots of diploid oat (Avena strigosa). Oat roots also synthesize the β-amyrin-derived triterpene glycoside avenacin A-1, which provides protection against soil-borne diseases. The genes for the early steps in avenacin A-1 synthesis [saponin-deficient 1 and 2 (Sad1 and Sad2)] have been recruited from the sterol pathway by gene duplication and neofunctionalization. Here we show that Sad1 and Sad2 are regulated by an ancient root developmental process that is conserved across diverse species. Sad1 promoter activity is dependent on an L1 box motif, implicating sterol/lipid-binding class IV homeodomain leucine zipper transcription factors as potential regulators. The metabolism of β-amyrin is blocked in sad2 mutants, which therefore accumulate abnormally high levels of this triterpene. The accumulation of elevated levels of β-amyrin in these mutants triggers a "superhairy" root phenotype. Importantly, this effect is manifested very early in the establishment of the root epidermis, causing a greater proportion of epidermal cells to be specified as root hair cells rather than nonhair cells. Together these findings suggest that simple triterpenes may have widespread and as yet largely unrecognized functions in plant growth and development.
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Affiliation(s)
| | - Suvi Honkanen
- Departments of Metabolic Biology andInstitute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom; and
| | | | - Kim C Findlay
- Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk NR4 7UH, United Kingdom
| | | | | | | | - Susan J Rosser
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom; and
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171
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Kemen AC, Honkanen S, Melton RE, Findlay KC, Mugford ST, Hayashi K, Haralampidis K, Rosser SJ, Osbourn A. Investigation of triterpene synthesis and regulation in oats reveals a role for β-amyrin in determining root epidermal cell patterning. Proc Natl Acad Sci U S A 2014; 111:8679-8684. [PMID: 24912185 DOI: 10.1073/pnas.1401553111s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
Sterols have important functions in membranes and signaling. Plant sterols are synthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene to cycloartenol. Plants also convert 2,3-oxidosqualene to other sterol-like cyclization products, including the simple triterpene β-amyrin. The function of β-amyrin per se is unknown, but this molecule can serve as an intermediate in the synthesis of more complex triterpene glycosides associated with plant defense. β-Amyrin is present at low levels in the roots of diploid oat (Avena strigosa). Oat roots also synthesize the β-amyrin-derived triterpene glycoside avenacin A-1, which provides protection against soil-borne diseases. The genes for the early steps in avenacin A-1 synthesis [saponin-deficient 1 and 2 (Sad1 and Sad2)] have been recruited from the sterol pathway by gene duplication and neofunctionalization. Here we show that Sad1 and Sad2 are regulated by an ancient root developmental process that is conserved across diverse species. Sad1 promoter activity is dependent on an L1 box motif, implicating sterol/lipid-binding class IV homeodomain leucine zipper transcription factors as potential regulators. The metabolism of β-amyrin is blocked in sad2 mutants, which therefore accumulate abnormally high levels of this triterpene. The accumulation of elevated levels of β-amyrin in these mutants triggers a "superhairy" root phenotype. Importantly, this effect is manifested very early in the establishment of the root epidermis, causing a greater proportion of epidermal cells to be specified as root hair cells rather than nonhair cells. Together these findings suggest that simple triterpenes may have widespread and as yet largely unrecognized functions in plant growth and development.
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Affiliation(s)
| | - Suvi Honkanen
- Departments of Metabolic Biology andInstitute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom; and
| | | | - Kim C Findlay
- Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk NR4 7UH, United Kingdom
| | | | | | | | - Susan J Rosser
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom; and
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172
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Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N, Varshney RK. Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1263-91. [PMID: 24710822 PMCID: PMC4035543 DOI: 10.1007/s00122-014-2301-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/17/2014] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops. The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Uday C. Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012 India
| | - Indra P. Singh
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Dibendu Datta
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | | | - N. Nadarajan
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
- The University of Western Australia (UWA), Crawley, 6009 Australia
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173
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Chen L, Hao L, Parry MAJ, Phillips AL, Hu YG. Progress in TILLING as a tool for functional genomics and improvement of crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:425-43. [PMID: 24618006 DOI: 10.1111/jipb.12192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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174
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Lafiandra D, Riccardi G, Shewry PR. Improving cereal grain carbohydrates for diet and health. J Cereal Sci 2014; 59:312-326. [PMID: 24966450 PMCID: PMC4064937 DOI: 10.1016/j.jcs.2014.01.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/20/2013] [Accepted: 01/01/2014] [Indexed: 12/20/2022]
Abstract
Starch and cell wall polysaccharides (dietary fibre) of cereal grains contribute to the health benefits associated with the consumption of whole grain cereal products, including reduced risk of obesity, type 2 diabetes, cardiovascular disease and colorectal cancer. The physiological bases for these effects are reviewed in relation to the structures and physical properties of the polysaccharides and their behaviour (including digestion and fermentation) in the gastro-intestinal tract. Strategies for modifying the content and composition of grain polysaccharides to increase their health benefits are discussed, including exploiting natural variation and using mutagenesis and transgenesis to generate further variation. These studies will facilitate the development of new types of cereals and cereal products to face the major health challenges of the 21st century.
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Affiliation(s)
- Domenico Lafiandra
- Università degli Studi della Tuscia, Department of Agriculture, Forestry, Nature and Energy, Via S.C. De Lellis, Viterbo 01100, Italy
| | - Gabriele Riccardi
- Università degli Studi di Napoli Federico II, Department of Clinical Medicine and Surgery, Via Pansini 5, Napoli 80131, Italy
| | - Peter R. Shewry
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Whiteknights Road, Reading RG6 6AR, UK
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175
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Tamiru M, Abe A, Utsushi H, Yoshida K, Takagi H, Fujisaki K, Undan JR, Rakshit S, Takaichi S, Jikumaru Y, Yokota T, Terry MJ, Terauchi R. The tillering phenotype of the rice plastid terminal oxidase (PTOX) loss-of-function mutant is associated with strigolactone deficiency. THE NEW PHYTOLOGIST 2014; 202:116-131. [PMID: 24350905 DOI: 10.1111/nph.12630] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
The significance of plastid terminal oxidase (PTOX) in phytoene desaturation and chloroplast function has been demonstrated using PTOX-deficient mutants, particularly in Arabidopsis. However, studies on its role in monocots are lacking. Here, we report cloning and characterization of the rice (Oryza sativa) PTOX1 gene. Using Ecotype Targeting Induced Local Lesions IN Genomes (EcoTILLING) and TILLING as forward genetic tools, we identified the causative mutation of an EMS mutant characterized by excessive tillering, semi-dwarfism and leaf variegation that corresponded to the PTOX1 gene. The tillering and semi-dwarf phenotypes of the ptox1 mutant are similar to phenotypes of known strigolactone (SL)-related rice mutants, and both phenotypic traits could be rescued by application of the synthetic SL GR24. The ptox1 mutant accumulated phytoene in white leaf sectors with a corresponding deficiency in β-carotene, consistent with the expected function of PTOX1 in promoting phytoene desaturase activity. There was also no accumulation of the carotenoid-derived SL ent-2'-epi-5-deoxystrigol in root exudates. Elevated concentrations of auxin were detected in the mutant, supporting previous observations that SL interaction with auxin is important in shoot branching control. Our results demonstrate that PTOX1 is required for both carotenoid and SL synthesis resulting in SL-deficient phenotypes in rice.
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Affiliation(s)
- Muluneh Tamiru
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- Iwate Agricultural Research Center, Narita 20-1, Kitakami, Iwate, 024-0003, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Kakoto Yoshida
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Koki Fujisaki
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Jerwin R Undan
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Sujay Rakshit
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
| | - Shinichi Takaichi
- Department of Biology, Nippon Medical School, Kawasaki, Kanagawa, 211-0063, Japan
| | - Yusuke Jikumaru
- Department of Biosciences, Faculty of Science and Technology, Teikyo University, Utsunomiya, Tochigi, 320-8851, Japan
| | - Takao Yokota
- Department of Biosciences, Faculty of Science and Technology, Teikyo University, Utsunomiya, Tochigi, 320-8851, Japan
| | - Matthew J Terry
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
- Centre for Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate, 024-0003, Japan
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176
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Patel JD, Wright RJ, Auld D, Chandnani R, Goff VH, Ingles J, Pierce GJ, Torres MJ, Paterson AH. Alleles conferring improved fiber quality from EMS mutagenesis of elite cotton genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:821-830. [PMID: 24374351 DOI: 10.1007/s00122-013-2259-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
Genetic improvements for many fiber traits are obtained by mutagenesis of elite cottons, mitigating genetic uniformity in this inbred polyploid by contributing novel alleles important to ongoing crop improvement. The elite gene pool of cotton (Gossypium spp.) has less diversity than those of most other major crops, making identification of novel alleles important to ongoing crop improvement. A total of 3,164 M5 lines resulting from ethyl methanesulfonate (EMS) mutagenesis of two G. hirsutum breeding lines, TAM 94L-25 and Acala 1517-99, were characterized for basic components of fiber quality and selected yield components. Across all measured traits, the ranges of phenotypic values among the mutant lines were consistently larger than could be explained by chance (5.27-10.1 for TAM 94 L-25 and 5.29-7.94 standard deviations for Acala 1517-99-derived lines). Multi-year replicated studies confirmed a genetic basis for these differences, showing significant correlations between lines across years and environments. A subset of 157 lines selected for superior fiber qualities, including fiber elongation (22 lines), length (22), lint percent (17), fineness (23), Rd value (21), strength (19), uniformity (21) and multiple attributes in a selection index (26) were compared to 55 control lines in replicated trials in both Texas and Georgia. For all traits, mutant lines showing substantial and statistically significant improvements over control lines were found, in most cases from each of the two genetic backgrounds. This indicates that genetic improvements for a wide range of fiber traits may be obtained from mutagenesis of elite cottons. Indeed, lines selected for one fiber trait sometimes conferred additional attributes, suggesting pleiotropic effects of some mutations and offering multiple benefits for the incorporation of some alleles into mainstream breeding programs.
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Affiliation(s)
- Jinesh D Patel
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
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177
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Gholami A, De Geyter N, Pollier J, Goormachtig S, Goossens A. Natural product biosynthesis in Medicago species. Nat Prod Rep 2014; 31:356-80. [PMID: 24481477 DOI: 10.1039/c3np70104b] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The genus Medicago, a member of the legume (Fabaceae) family, comprises 87 species of flowering plants, including the forage crop M. sativa (alfalfa) and the model legume M. truncatula (barrel medic). Medicago species synthesize a variety of bioactive natural products that are used to engage into symbiotic interactions but also serve to deter pathogens and herbivores. For humans, these bioactive natural products often possess promising pharmaceutical properties. In this review, we focus on the two most interesting and well characterized secondary metabolite classes found in Medicago species, the triterpene saponins and the flavonoids, with a detailed overview of their biosynthesis, regulation, and profiling methods. Furthermore, their biological role within the plant as well as their potential utility for human health or other applications is discussed. Finally, we give an overview of the advances made in metabolic engineering in Medicago species and how the development of novel molecular and omics toolkits can influence a better understanding of this genus in terms of specialized metabolism and chemistry. Throughout, we critically analyze the current bottlenecks and speculate on future directions and opportunities for research and exploitation of Medicago metabolism.
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Affiliation(s)
- Azra Gholami
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
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178
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Acanda Y, Martínez Ó, Prado MJ, González MV, Rey M. EMS mutagenesis and qPCR-HRM prescreening for point mutations in an embryogenic cell suspension of grapevine. PLANT CELL REPORTS 2014; 33:471-481. [PMID: 24362838 DOI: 10.1007/s00299-013-1547-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/12/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
KEY MESSAGE Embryogenic suspension cultures are suitable for EMS mutagenesis in grapevine, and HRM prescreening of EMS-treated somatic embryo clusters allows rapid detection of point mutations before plant regeneration. ABSTRACT Somatic embryogenesis is an excellent system for induced mutagenesis and clonal propagation in woody plants. Our work was focused on establishing a procedure for inducing ethyl methanesulfonate (EMS) mutagenesis in grapevine. Embryogenic cell aggregates (ECAs) growing in liquid medium were treated with increasing concentrations of EMS. We found that EMS dramatically affects the viability of ECAs at concentrations above 20 mM (25.5 ± 2.9 % survival), whereas concentrations above 10 mM affect embryogenic potential (22.1 ± 1.7 % of ECAs gave rise to embryos). Embryo masses generated from EMS-treated embryogenic cell aggregates were prescreened by quantitative PCR-High Resolution Melting (qPCR-HRM) to detect single nucleotide polymorphisms (SNPs) in a 1,000-bp VvNCED1-encoding DNA fragment, which served as the target gene. Detected mutations were verified in regenerated plants by PCR and sequencing. qPCR-HRM analysis of the difference plots for the fluorescence signals allowed detection of a mutation in a sample from an embryogenic aggregate treated with 10 mM EMS. To confirm the nature of the mutation, embryos from this aggregate were recovered and germinated, and leaves were collected for PCR and sequencing analysis. The alignment of sequences from regenerated plants with the wild-type sequence revealed a transitional mutation (G/C to A/T) in the 1,000-bp VvNCED1-encoding region. To our knowledge, this is the first time that EMS mutagenesis has been performed using an embryogenic cell suspension of grapevine.
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Affiliation(s)
- Yosvanis Acanda
- Departamento de Biología Vegetal y Ciencia del Suelo, Universidad de Vigo, Campus Universitario, 36310, Vigo, Spain
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179
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Serrat X, Esteban R, Guibourt N, Moysset L, Nogués S, Lalanne E. EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining TILLING mutant populations. PLANT METHODS 2014; 10:5. [PMID: 24475756 PMCID: PMC3923009 DOI: 10.1186/1746-4811-10-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/24/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetic method that combines chemical mutagenesis with high-throughput genome-wide screening for point mutation detection in genes of interest. However, this mutation discovery approach faces a particular problem which is how to obtain a mutant population with a sufficiently high mutation density. Furthermore, plant mutagenesis protocols require two successive generations (M1, M2) for mutation fixation to occur before the analysis of the genotype can begin. RESULTS Here, we describe a new TILLING approach for rice based on ethyl methanesulfonate (EMS) mutagenesis of mature seed-derived calli and direct screening of in vitro regenerated plants. A high mutagenesis rate was obtained (i.e. one mutation in every 451 Kb) when plants were screened for two senescence-related genes. Screening was carried out in 2400 individuals from a mutant population of 6912. Seven sense change mutations out of 15 point mutations were identified. CONCLUSIONS This new strategy represents a significant advantage in terms of time-savings (i.e. more than eight months), greenhouse space and work during the generation of mutant plant populations. Furthermore, this effective chemical mutagenesis protocol ensures high mutagenesis rates thereby saving in waste removal costs and the total amount of mutagen needed thanks to the mutagenesis volume reduction.
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Affiliation(s)
- Xavier Serrat
- Oryzon Genomics, S.A., Cornellà de Llobregat, Spain
- Departament de Biologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Luisa Moysset
- Departament de Biologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Nogués
- Departament de Biologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Eric Lalanne
- Oryzon Genomics, S.A., Cornellà de Llobregat, Spain
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180
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Induced Genetic Variation, TILLING and NGS-Based Cloning. BIOTECHNOLOGICAL APPROACHES TO BARLEY IMPROVEMENT 2014. [DOI: 10.1007/978-3-662-44406-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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181
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Wells R, Trick M, Soumpourou E, Clissold L, Morgan C, Werner P, Gibbard C, Clarke M, Jennaway R, Bancroft I. The control of seed oil polyunsaturate content in the polyploid crop species Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:349-362. [PMID: 24489479 PMCID: PMC3901927 DOI: 10.1007/s11032-013-9954-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/05/2013] [Indexed: 05/18/2023]
Abstract
Many important plant species have polyploidy in their recent ancestry, complicating inferences about the genetic basis of trait variation. Although the principal locus controlling the proportion of polyunsaturated fatty acids (PUFAs) in seeds of Arabidopsis thaliana is known (fatty acid desaturase 2; FAD2), commercial cultivars of a related crop, oilseed rape (Brassica napus), with very low PUFA content have yet to be developed. We showed that a cultivar of oilseed rape with lower than usual PUFA content has non-functional alleles at three of the four orthologous FAD2 loci. To explore the genetic basis further, we developed an ethyl methanesulphonate mutagenised population, JBnaCAB_E, and used it to identify lines that also carried mutations in the remaining functional copy. This confirmed the hypothesised basis of variation, resulting in an allelic series of mutant lines showing a spectrum of PUFA contents of seed oil. Several lines had PUFA content of ~6 % and oleic acid content of ~84 %, achieving a long-standing industry objective: very high oleic, very low PUFA rapeseed without the use of genetic modification technology. The population contains a high rate of mutations and represents an important resource for research in B. napus.
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Affiliation(s)
- Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Leah Clissold
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Peter Werner
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | - Carl Gibbard
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | | | - Richard Jennaway
- Saaten-Union UK Ltd., Rosalie Field Station, Bradley Road, Cowlinge, Newmarket, Suffolk, CB8 9HU UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Biology, University of York, Heslington, York, YO41 5DD UK
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182
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Berenschot AS, Quecini V. A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:1-13. [PMID: 24554834 PMCID: PMC3925473 DOI: 10.1007/s12298-013-0212-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/22/2013] [Accepted: 10/18/2013] [Indexed: 05/03/2023]
Abstract
Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.
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Affiliation(s)
- Amanda S. Berenschot
- />Centro de Pesquisa e Desenvolvimento de Recursos Genéticos, Instituto Agronômico, Caixa Postal 28, 13001-970 Campinas, SP Brazil
| | - Vera Quecini
- />Embrapa Uva e Vinho, Rua Livramento, 515, 95700-000 Bento Gonçalves, RS Brazil
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183
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Abstract
TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure.
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Affiliation(s)
- Peter Sharp
- Plant Breeding Institute, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
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184
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Shapter FM, Cross M, Ablett G, Malory S, Chivers IH, King GJ, Henry RJ. High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop. PLoS One 2013; 8:e82641. [PMID: 24367532 PMCID: PMC3867367 DOI: 10.1371/journal.pone.0082641] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/26/2013] [Indexed: 12/21/2022] Open
Abstract
Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD₉₇) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops.
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Affiliation(s)
- Frances M. Shapter
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
- * E-mail:
| | - Michael Cross
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Gary Ablett
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Sylvia Malory
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Ian H. Chivers
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
- Native Seeds Pty Ltd, Sandringham, Victoria, Australia
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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185
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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186
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Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X, Kahl G, Edwards D, Varshney RK. Functional genomics to study stress responses in crop legumes: progress and prospects. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1221-1233. [PMID: 32481190 DOI: 10.1071/fp13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/22/2013] [Indexed: 06/11/2023]
Abstract
Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Abirami Ramalingam
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Swapna Nayakoti
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei-Jian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guenter Kahl
- Goethe University Frankfurt am Main, Institute for Molecular BioSciences, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, St Lucia, Qld 4072, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
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187
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Lee LS, Till BJ, Hill H, Huynh OA, Jankowicz-Cieslak J. Mutation and mutation screening. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1099:77-95. [PMID: 24243197 DOI: 10.1007/978-1-62703-715-0_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular techniques have created the opportunity for great advances in plant mutation genetics and the science of mutation breeding. The powerful targeted induced local lesions in genomes (TILLING) technique has introduced the possibility of reverse genetics-the ability to screen for mutations at the DNA level prior to assessing phenotype. Fundamental to TILLING is the induction of mutant populations (or alternatively, the identification of mutants in the environment); and mutation induction requires an understanding and assessment of the appropriate mutagen dose required. The techniques of mutation induction, dose optimization, and TILLING are explained.
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Affiliation(s)
- L Slade Lee
- Cooperative Research Centre for Remote Economic Participation, Division of Research, Southern Cross University, Lismore, NSW, Australia
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188
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Bashalkhanov S, Eckert AJ, Rajora OP. Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae). Mol Ecol 2013; 22:5877-89. [PMID: 24118331 DOI: 10.1111/mec.12546] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/17/2013] [Indexed: 02/01/2023]
Abstract
One of the most important drivers of local adaptation for forest trees is climate. Coupled to these patterns, however, are human-induced disturbances through habitat modification and pollution. The confounded effects of climate and disturbance have rarely been investigated with regard to selective pressure on forest trees. Here, we have developed and used a population genetic approach to search for signals of selection within a set of 36 candidate genes chosen for their putative effects on adaptation to climate and human-induced air pollution within five populations of red spruce (Picea rubens Sarg.), distributed across its natural range and air pollution gradient in eastern North America. Specifically, we used FST outlier and environmental correlation analyses to highlight a set of seven single nucleotide polymorphisms (SNPs) that were overly correlated with climate and levels of sulphate pollution after correcting for the confounding effects of population history. Use of three age cohorts within each population allowed the effects of climate and pollution to be separated temporally, as climate-related SNPs (n = 7) showed the strongest signals in the oldest cohort, while pollution-related SNPs (n = 3) showed the strongest signals in the youngest cohorts. These results highlight the usefulness of population genetic scans for the identification of putatively nonneutral evolution within genomes of nonmodel forest tree species, but also highlight the need for the development and application of robust methodologies to deal with the inherent multivariate nature of the genetic and ecological data used in these types of analyses.
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Affiliation(s)
- Stanislav Bashalkhanov
- Faculty of Forestry and Environmental Management, University of New Brunswick, PO Box 44000, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada
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189
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Sun Z, Li N, Huang G, Xu J, Pan Y, Wang Z, Tang Q, Song M, Wang X. Site-specific gene targeting using transcription activator-like effector (TALE)-based nuclease in Brassica oleracea. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:1092-103. [PMID: 23870552 DOI: 10.1111/jipb.12091] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 07/13/2012] [Indexed: 05/22/2023]
Abstract
Site-specific recognition modules with DNA nuclease have tremendous potential as molecular tools for genome targeting. The type III transcription activator-like effectors (TALEs) contain a DNA binding domain consisting of tandem repeats that can be engineered to bind user-defined specific DNA sequences. We demonstrated that customized TALE-based nucleases (TALENs), constructed using a method called "unit assembly", specifically target the endogenous FRIGIDA gene in Brassica oleracea L. var. capitata L. The results indicate that the TALENs bound to the target site and cleaved double-strand DNA in vitro and in vivo, whereas the effector binding elements have a 23 bp spacer. The T7 endonuclease I assay and sequencing data show that TALENs made double-strand breaks, which were repaired by a non-homologous end-joining pathway within the target sequence. These data show the feasibility of applying customized TALENs to target and modify the genome with deletions in those organisms that are still in lacking gene target methods to provide germplasms in breeding improvement.
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Affiliation(s)
- Zijian Sun
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Southwest University, Chongqing, 400715, China
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190
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Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3-GENES GENOMES GENETICS 2013; 3:1707-15. [PMID: 23979943 PMCID: PMC3789795 DOI: 10.1534/g3.113.006270] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tandemly arrayed genes (TAGs) or gene clusters are prevalent in higher eukaryotic genomes. For example, approximately 17% of genes are organized in tandem in the model plant Arabidopsis thaliana. The genetic redundancy created by TAGs presents a challenge for reverse genetics. As molecular scissors, engineered zinc finger nucleases (ZFNs) make DNA double-strand breaks in a sequence-specific manner. ZFNs thus provide a means to delete TAGs by creating two double-strand breaks in the gene cluster. Using engineered ZFNs, we successfully targeted seven genes from three TAGs on two Arabidopsis chromosomes, including the well-known RPP4 gene cluster, which contains eight resistance (R) genes. The resulting gene cluster deletions ranged from a few kb to 55 kb with frequencies approximating 1% in somatic cells. We also obtained large chromosomal deletions of ~9 Mb at approximately one tenth the frequency, and gene cluster inversions and duplications also were achieved. This study demonstrates the ability to use sequence-specific nucleases in plants to make targeted chromosome rearrangements and create novel chimeric genes for reverse genetics and biotechnology.
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191
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Krothapalli K, Buescher EM, Li X, Brown E, Chapple C, Dilkes BP, Tuinstra MR. Forward genetics by genome sequencing reveals that rapid cyanide release deters insect herbivory of Sorghum bicolor. Genetics 2013; 195:309-18. [PMID: 23893483 PMCID: PMC3781961 DOI: 10.1534/genetics.113.149567] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing has allowed rapid progress in the application of forward genetics in model species. In this study, we demonstrated an application of next-generation sequencing for forward genetics in a complex crop genome. We sequenced an ethyl methanesulfonate-induced mutant of Sorghum bicolor defective in hydrogen cyanide release and identified the causal mutation. A workflow identified the causal polymorphism relative to the reference BTx623 genome by integrating data from single nucleotide polymorphism identification, prior information about candidate gene(s) implicated in cyanogenesis, mutation spectra, and polymorphisms likely to affect phenotypic changes. A point mutation resulting in a premature stop codon in the coding sequence of dhurrinase2, which encodes a protein involved in the dhurrin catabolic pathway, was responsible for the acyanogenic phenotype. Cyanogenic glucosides are not cyanogenic compounds but their cyanohydrins derivatives do release cyanide. The mutant accumulated the glucoside, dhurrin, but failed to efficiently release cyanide upon tissue disruption. Thus, we tested the effects of cyanide release on insect herbivory in a genetic background in which accumulation of cyanogenic glucoside is unchanged. Insect preference choice experiments and herbivory measurements demonstrate a deterrent effect of cyanide release capacity, even in the presence of wild-type levels of cyanogenic glucoside accumulation. Our gene cloning method substantiates the value of (1) a sequenced genome, (2) a strongly penetrant and easily measurable phenotype, and (3) a workflow to pinpoint a causal mutation in crop genomes and accelerate in the discovery of gene function in the postgenomic era.
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Affiliation(s)
| | - Elizabeth M. Buescher
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Xu Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Elliot Brown
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brian P. Dilkes
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
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192
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Dorn KM, Fankhauser JD, Wyse DL, Marks MD. De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:1028-38. [PMID: 23786378 PMCID: PMC3824206 DOI: 10.1111/tpj.12267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 06/01/2013] [Accepted: 06/10/2013] [Indexed: 05/22/2023]
Abstract
Field pennycress (Thlaspi arvense L.) has potential as an oilseed crop that may be grown during fall (autumn) and winter months in the Midwestern United States and harvested in the early spring as a biodiesel feedstock. There has been little agronomic improvement in pennycress through traditional breeding. Recent advances in genomic technologies allow for the development of genomic tools to enable rapid improvements to be made through genomic assisted breeding. Here we report an annotated transcriptome assembly for pennycress. RNA was isolated from representative plant tissues, and 203 million unique Illumina RNA-seq reads were produced and used in the transcriptome assembly. The draft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp. A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family. The final assembly was functionally annotated, allowing for the identification of putative genes controlling important agronomic traits such as flowering and glucosinolate metabolism. Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress. Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.
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Affiliation(s)
- Kevin M Dorn
- Department of Plant Biology, University of Minnesota1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN, 55108, USA
| | - Johnathon D Fankhauser
- Department of Plant Biology, University of Minnesota1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN, 55108, USA
| | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - M David Marks
- Department of Plant Biology, University of Minnesota1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN, 55108, USA
- *For correspondence (e-mail )
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193
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Monfared MM, Carles CC, Rossignol P, Pires HR, Fletcher JC. The ULT1 and ULT2 trxG genes play overlapping roles in Arabidopsis development and gene regulation. MOLECULAR PLANT 2013; 6:1564-79. [PMID: 23446032 DOI: 10.1093/mp/sst041] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The epigenetic regulation of gene expression is critical for ensuring the proper deployment and stability of defined genome transcription programs at specific developmental stages. The cellular memory of stable gene expression states during animal and plant development is mediated by the opposing activities of Polycomb group (PcG) factors and trithorax group (trxG) factors. Yet, despite their importance, only a few trxG factors have been characterized in plants and their roles in regulating plant development are poorly defined. In this work, we report that the closely related Arabidopsis trxG genes ULTRAPETALA1 (ULT1) and ULT2 have overlapping functions in regulating shoot and floral stem cell accumulation, with ULT1 playing a major role but ULT2 also making a minor contribution. The two genes also have a novel, redundant activity in establishing the apical–basal polarity axis of the gynoecium, indicating that they function in differentiating tissues. Like ULT1 proteins, ULT2 proteins have a dual nuclear and cytoplasmic localization, and the two proteins physically associate in planta. Finally, we demonstrate that ULT1 and ULT2 have very similar overexpression phenotypes and regulate a common set of key development target genes, including floral MADS-box genes and class I KNOX genes. Our results reveal that chromatin remodeling mediated by the ULT1 and ULT2 proteins is necessary to control the development of meristems and reproductive organs. They also suggest that, like their animal counterparts, plant trxG proteins may function in multi-protein complexes to up-regulate the expression of key stage- and tissue-specific developmental regulatory genes.
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Affiliation(s)
- Mona M Monfared
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, 800 Buchanan Street, Albany, CA 94710, USA
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194
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Wells R, Trick M, Fraser F, Soumpourou E, Clissold L, Morgan C, Pauquet J, Bancroft I. Sequencing-based variant detection in the polyploid crop oilseed rape. BMC PLANT BIOLOGY 2013; 13:111. [PMID: 23915099 PMCID: PMC3750413 DOI: 10.1186/1471-2229-13-111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products. RESULTS A protocol was developed to tag PCR products with 5' 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2.b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively. CONCLUSIONS The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs.
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Affiliation(s)
- Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fiona Fraser
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Leah Clissold
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jérôme Pauquet
- BIOGEMMA S.A.S., Chemin de Panedautes, Domaine de Sandreau, 31700, Mondonville, France
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
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195
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Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudhry I, Fernando L, Hutter H, Kieffer A, Lau J, Lee N, Miller A, Raymant G, Shen B, Shendure J, Taylor J, Turner EH, Hillier LW, Moerman DG, Waterston RH. The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Res 2013; 23:1749-62. [PMID: 23800452 PMCID: PMC3787271 DOI: 10.1101/gr.157651.113] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide variants (SNVs) with an average of eight nonsynonymous changes per gene and more than 16,000 insertion/deletion (indel) and copy number changes, providing an unprecedented genetic resource for this multicellular organism. To supplement this collection, we also sequenced 40 wild isolates, identifying more than 630,000 unique SNVs and 220,000 indels. Comparison of the two sets demonstrates that the mutant collection has a much richer array of both nonsense and missense mutations than the wild isolate set. We also find a wide range of rDNA and telomere repeat copy number in both sets. Scanning the mutant collection for molecular phenotypes reveals a nonsense suppressor as well as strains with higher levels of indels that harbor mutations in DNA repair genes and strains with abundant males associated with him mutations. All the strains are available through the Caenorhabditis Genetics Center and all the sequence changes have been deposited in WormBase and are available through an interactive website.
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Affiliation(s)
- Owen Thompson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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196
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Genomics approaches for crop improvement against abiotic stress. ScientificWorldJournal 2013; 2013:361921. [PMID: 23844392 PMCID: PMC3690750 DOI: 10.1155/2013/361921] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/22/2013] [Indexed: 12/13/2022] Open
Abstract
As sessile organisms, plants are inevitably exposed to one or a combination of stress factors every now and then throughout their growth and development. Stress responses vary considerably even in the same plant species; stress-susceptible genotypes are at one extreme, and stress-tolerant ones are at the other. Elucidation of the stress responses of crop plants is of extreme relevance, considering the central role of crops in food and biofuel production. Crop improvement has been a traditional issue to increase yields and enhance stress tolerance; however, crop improvement against abiotic stresses has been particularly compelling, given the complex nature of these stresses. As traditional strategies for crop improvement approach their limits, the era of genomics research has arisen with new and promising perspectives in breeding improved varieties against abiotic stresses.
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197
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Di Matteo A, Ruggieri V, Sacco A, Rigano MM, Carriero F, Bolger A, Fernie AR, Frusciante L, Barone A. Identification of candidate genes for phenolics accumulation in tomato fruit. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 205-206:87-96. [PMID: 23498866 DOI: 10.1016/j.plantsci.2013.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 01/31/2013] [Accepted: 02/03/2013] [Indexed: 05/02/2023]
Abstract
Phenolics are antioxidants present in tomato fruit that confer healthy benefits and exhibit crucial roles for plant metabolism and response to environmental stimuli. An approach based on two genomics platforms was undertaken to identify candidate genes associated to higher phenolics content in tomato fruit. A comparative transcriptomic analysis between the S. pennellii Introgression Line 7-3, which produced an average higher level of fruit phenolics, and the cultivated variety M82, revealed that their differences are attributed to genes involved in phenolics accumulation into the vacuole. The up-regulation of genes coding for one MATE-transporter, one vacuolar sorting protein and three GSTs supported this hypothesis. The observed balancing effect between two ethylene responsive factors (ERF1 and ERF4) was also hypothesized to drive the transcriptional regulation of these transport genes. In order to confirm such model a TILLING platform was explored. A mutant was isolated harbouring a point mutation in the ERF1 cds that affects the protein sequence and its expected function. Fruits of the mutant exhibited a significant reduced level of phenolics than the control variety. Changes in the expression of genes involved in sequestration of phenolics in vacuole also supported the hypothesized key-role of ERF1 in orchestrating these genes.
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Affiliation(s)
- Antonio Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy.
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198
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Townsend T, Segura V, Chigeza G, Penfield T, Rae A, Harvey D, Bowles D, Graham IA. The use of combining ability analysis to identify elite parents for Artemisia annua F1 hybrid production. PLoS One 2013; 8:e61989. [PMID: 23626762 PMCID: PMC3633910 DOI: 10.1371/journal.pone.0061989] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022] Open
Abstract
Artemisia annua is an important medicinal crop used for the production of the anti-malarial compound artemisinin. In order to assist in the production of affordable high quality artemisinin we have carried out an A. annua breeding programme aimed at improving artemisinin concentration and biomass. Here we report on a combining ability analysis of a diallel cross to identify robust parental lines for hybrid breeding. The parental lines were selected based on a range of phenotypic traits to encourage heterosis. The general combining ability (GCA) values for the diallel parental lines correlated to the positive alleles of quantitative trait loci (QTL) in the same parents indicating the presence of beneficial alleles that contribute to parental performance. Hybrids generated from crossing specific parental lines with good GCA were identified as having an increase in both artemisinin concentration and biomass when grown either in glasshouse or experimental field trials and compared to controls. This study demonstrates that combining ability as determined by a diallel cross can be used to identify elite parents for the production of improved A. annua hybrids. Furthermore, the selection of material for breeding using this approach was found to be consistent with our QTL-based molecular breeding approach.
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Affiliation(s)
- Theresa Townsend
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Vincent Segura
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Institut National de la Recherche Agronomique, UR0588, Orléans, France
| | - Godfree Chigeza
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Agricultural Research Council: Grain Crops Institute, Potchefstroom, South Africa
| | - Teresa Penfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Research and Knowledge Transfer, University of Exeter, Exeter, United Kingdom
| | - Anne Rae
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Genetics Department, Cherry Valley Farms Ltd., Caistor, United Kingdom
| | - David Harvey
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Dianna Bowles
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Ian A. Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- * E-mail:
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199
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Frerichmann SLM, Kirchhoff M, Müller AE, Scheidig AJ, Jung C, Kopisch-Obuch FJ. EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1 that are associated with annuality and winter hardiness. BMC PLANT BIOLOGY 2013; 13:52. [PMID: 23531083 PMCID: PMC3636108 DOI: 10.1186/1471-2229-13-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 02/21/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sugar beet (Beta vulgaris ssp. vulgaris L.) is an important crop for sugar and biomass production in temperate climate regions. Currently sugar beets are sown in spring and harvested in autumn. Autumn-sown sugar beets that are grown for a full year have been regarded as a cropping system to increase the productivity of sugar beet cultivation. However, for the development of these "winter beets" sufficient winter hardiness and a system for bolting control is needed. Both require a thorough understanding of the underlying genetics and its natural variation. RESULTS We screened a diversity panel of 268 B. vulgaris accessions for three flowering time genes via EcoTILLING. This panel had been tested in the field for bolting behaviour and winter hardiness. EcoTILLING identified 20 silent SNPs and one non-synonymous SNP within the genes BTC1, BvFL1 and BvFT1, resulting in 55 haplotypes. Further, we detected associations of nucleotide polymorphisms in BvFL1 with bolting before winter as well as winter hardiness. CONCLUSIONS These data provide the first genetic indication for the function of the FLC homolog BvFL1 in beet. Further, it demonstrates for the first time that EcoTILLING is a powerful method for exploring genetic diversity and allele mining in B. vulgaris.
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Affiliation(s)
- Sebastian LM Frerichmann
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
| | - Martin Kirchhoff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
- Nordsaat Saatzucht GmbH, Böhnshauser Straße, Langenstein, 38895, Germany
| | - Andreas E Müller
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
- Strube Research GmbH & Co. KG, Hauptstr. 1, Söllingen, 38387, Germany
| | - Axel J Scheidig
- Zoological Institute, Department of Structural Biology, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
| | - Friedrich J Kopisch-Obuch
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, Kiel, 24098, Germany
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200
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Induced Mutations Unleash the Potentials of Plant Genetic Resources for Food and Agriculture. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3010200] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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