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First published online September 9, 2009; 10.1104/pp.109.144097 Plant Physiology 151:978-984 (2009) © 2009 American Society of Plant Biologists
Mutagenesis and Beyond! Tools for Understanding Legume Biology1Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (M.T., J.W., K.S.M.); Department of Metabolic Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (T.L.W.); and Institut des Sciences du Végétale, Unité Propre de Recherche 2355, CNRS, 91198 Gif sur Yvette, France (P.R.)
The family Leguminosae is one of the largest families of flowering plants and includes important crop legumes such as soybean (Glycine max) and lentil (Lens culinaris) and forage legumes like alfalfa (Medicago sativa). Legumes vary in habit from annual to perennial and in their genomes from simple diploids to large and complex polyploids. Two legume species, Medicago truncatula and Lotus japonicus, are being used as models to study legume genetics and genomics. Both of these species belong to the Galegoid clade that includes pea (Pisum sativum) and alfalfa but is also closely related to the other agriculturally important major clade, the Phaseoloid, that includes bean (Phaseolus vulgaris). M. truncatula and L. japonicus thus represent very useful model systems to study pertinent issues that are relevant to economically vital legumes. These two species were chosen as models because of their diploid, relatively small genomes (450–550 Mb), self-fertility, relative ease of genetic transformation, and short generation time. The success of any species as a molecular genetic model depends on the availability of versatile genetic and genomic resources. The genomes of both of these species are being sequenced by international consortiums and are approaching completion (Sato et al., 2008
Mutagenesis is a fundamental approach in biology to identify gene function, and in plants it may involve using chemicals, ionizing radiation, or specific DNA insertion sequences. All of these have been attempted in legumes including the models M. truncatula and L. japonicus, and comprehensive tools for M. truncatula have been described in a recent review (Ane et al., 2008
Alkylated agents such as ethylmethane sulfonate (EMS) have been widely used in the past for producing mutagenized populations, which can then be used for forward genetic screens. It is applicable readily to most plant species, inducing single base pair G/C-to-A/T substitutions in nucleotides. TILLING (McCallum et al., 2000
Fast-neutron bombardment (FNB) and
Insertions such as T-DNA, transposons, or retrotransposons that disrupt gene functions have been used in both model legumes. T-DNA tagging was successfully tested in M. truncatula (Scholte et al., 2002
The transposable element of tobacco (Nicotiana tabacum) cell type 1 (Tnt1) is a very active 5.3-kb copia-type retrotransposon isolated from tobacco cell cultures (Grandbastien et al., 1989
The advantages of Tnt1 as an insertional mutagen in M. truncatula are numerous: insertions are stable during seed-to-seed generation in greenhouses; transposition can be activated by tissue culture; new transpositions show preference toward transcribed regions without a strong preference for a unique target site sequence (d'Erfurth et al., 2003a
The Tnt1 retroelement was initially introduced into M. truncatula and shown to transpose in tissue culture by the group of P. Ratet (d'Erfurth et al., 2003a
The Tnt1 population at the Noble Foundation is generated from a single parental line, Tnk88-7-7, that contains five copies of the Tnt1 element. Tnk88-7-7 was obtained by introducing the Tnt1-containing construct into the R108 genotype and subsequent selfing. This parental line contains only transposed Tnt1 copies, not the original construct. Extensive PCR analysis using sequence-specific primers and sequence analysis of thermal asymmetric interlaced (TAIL)-PCR fragments found no antibiotic resistance markers, left and right T-DNA borders, or any other sequences of the transformation vector. The vector was detected in the progenitor of Tnk88-7-7 but not in Tnk88-7-7 itself, suggesting that the Tnt1 element had transposed during the transformation process. The vector and the transposed Tnt1 copies ended up in different plants by segregation during the selfing process in soil. The pipeline for generation of the population is schematically depicted in Figure 1
and has three components for community utilization: forward genetic screening of mutant phenotypes; reverse genetic screening of DNA pools; and a FST database. In brief, mutagenesis is accomplished by cultivating leaf explants from the parental line on auxin- and cytokinin-containing culture media and regenerating new plants via somatic embryogenesis (Tadege et al., 2005
At the Noble Foundation, an annual open and free Tnt1 screening workshop have been organized to catalogue mutant phenotypes and make them available to the scientific community. The first such screening was conducted in the summer of 2005 involving various groups from France, the United Kingdom, and the United States primarily interested in nodulation biology. To date, approximately 7,000 lines have been screened for phenotypes ranging from symbiotic and root development to leaf architecture and shoot meristem functions. Some representative root and nodule phenotypes are shown in Figure 2 . Tnt1 tagging provides more allelic series of mutants compared with other insertional mutagenesis due to the higher density of Tnt1 insertions. The highest frequencies of confirmed alleles found so far are for the nodulation gene NIN (nine), the lamina gene STENOFOLIA (eight), and the unifoliate gene SINGLE LEAFLET1 (six). Interestingly, no two alleles of the nine inserts in the NIN gene (C. Pislariu and M. Udvardi, personal communication) or the eight inserts in the STENOFOLIA gene (M. Tadege and K. Mysore, unpublished data) have been found to have insertions in the same physical location. The insertion site sequences within the gene or between these two genes also do not show any particular homology or specific pattern consistent with the absence of a strong sequence-specific target site for Tnt1 insertion.
To customize reverse screening, genomic DNA has been extracted from 13,500 lines and is being pooled in one dimension with superpools of 500 lines, smaller pools, and mini pools that are convenient for PCR-based screening. Two pairs of one Tnt1-specific and one gene-specific primer combination are used in a standard PCR screening to look for Tnt1 insertion in a gene of interest. The screening starts by running the PCR with the superpools. Once a positive signal is identified in the superpool(s), the screening continues down to the smallest pool until the individual line(s) containing the insert is identified. So far, 20 superpools from 10,000 lines have been optimized for the community service. FST sequencing is in progress to recover most of the plant sequences flanking the Tnt1 insert. Tnt1-flanking plant sequences are obtained by TAIL-PCR using a combination of two or three nested Tnt1-specific primers and one arbitrary primer. PCR products are then cloned and sequenced. Sequences are deposited in a Tnt1 FST database (currently 15,476 FST sequences) that is equipped with GBrowser and BLAST search functions and is publicly available (http://bioinfo4.noble.org/mutant/database.php). Protocols for an efficient 454 sequencing platform are being optimized to significantly increase the number of FSTs available to the community. Seeds corresponding to the FSTs of interest can be ordered online for a small handling charge per line. Nondestructive phenotype screening of the Tnt1 lines and reverse genetic screening of DNA pools can be arranged by contacting K. Mysore (ksmysore{at}noble.org) until an online service is established.
The first plant TILLING service was developed for Arabidopsis using LICOR sequencers (Till et al., 2006a
Lotus TILLING established tools for both forward and reverse genetic analyses. Arguably, it is the most extensively used platform and has generated much data. A structured population of M2 progeny of 4,904 EMS-mutagenized M1 embryos was generated in the ecotype Gifu, but thematic populations were also assembled (Perry et al., 2009 Since TILLING is readily applicable to most plant species, it is especially suited to species where there are few genomic resources and where insertion mutagenesis to create knockout mutants is difficult either through a lack of appropriate elements or an inefficient transformation system. Moreover, since it is a non-genetically modified (GM) technology, it is also especially desirable in those crops/countries where application of GM technology is restricted. These advantages have facilitated its swift move from models to legume crops and have meant that some crops have been used in depth already. Pea was used as a pan-European platform under the European Union Grain Legumes Integrative Program (http://www.eugrainlegumes.org/), and this has a direct link to the breeders and other stakeholders under its Technology Transfer Platform (http://www.gl-ttp.com/products_services/technical_services/genomic_resources_from_glip/functional_genomics). Soybean TILLING, established with support from the U.S. Department of Agriculture (USDA), has now targeted almost 130 amplicons across 4,600 lines (divided between Forrest and Williams82 plants), one mutation on average occurring every 130 or 190 kb, respectively. The soybean platform has extensive agronomic targets (K. Meksem, personal communication), including low phytate, higher seed yield and improved seed oil quality, improved nodulation (based on the NARK mutants, in collaboration with P. Gresshoff and colleagues at the University of Queensland), and improved resistance to cyst nematode.
Phaseolus, chickpea (Cicer arietinum), and lupin (Lupinus albus) TILLING are in different degrees of development. A population of Phaseolus BAT93 has been established jointly by two groups (Porch et al., 2009
The prediction of Henikoff and Comai (2003)
We thank all those researchers who provided us with unpublished and prepublication data. We also thank Hee-Kyung Lee, Erin Hartwell, Janie Gallaway, and Colleen Elles for their excellent technical assistance in regenerating and maintaining the M. truncatula Tnt1 lines and Jillian Perry for reading the manuscript. Received July 1, 2009; accepted September 3, 2009; published September 9, 2009.
1 This work was supported by the Samuel Roberts Noble Foundation, the National Science Foundation (Plant Genome grant no. DBI 0703285), the European Union (Grain Legumes Integrated Project grant no. FOOD–CT–2004–506223), and the Biotechnology and Biological Sciences Research Council.
2 These authors contributed equally to the article. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Kirankumar S. Mysore (ksmysore{at}noble.org). www.plantphysiol.org/cgi/doi/10.1104/pp.109.144097 * Corresponding author; e-mail ksmysore{at}noble.org.
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