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Medicago truncatula Functional Genomics - An Invaluable Resource for Studies on Agriculture Sustainability

Written By

Francesco Panara, Ornella Calderini and Andrea Porceddu

Submitted: November 16th, 2011 Published: September 12th, 2012

DOI: 10.5772/51016

From the Edited Volume

Functional Genomics

Edited by Germana Meroni and Francesca Petrera

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1. Introduction

Legume functional genomics has moved many steps forward in the last two decades thanks to the improvement of genomics technologies and to the efforts of the research community. Tools for functional genomics studies are now available in Lotus japonicus, Medicago truncatula and soybean. In this chapter we focus on M.truncatula, as a model species for forage legumes, on the main achievements obtained due to the reported resources and on the future perspectives for the study of gene function in this species.


2. Why do we need a functional genomics tool for forage legumes?

Legumes are widely grown for grain and forage production, their world economic importance being second only to grasses. Legume species are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as nodule. Moreover legumes are able to establish other types of interactions such as arbuscular mycorrhyzal symbiosis with several fungi. For these outstanding biological properties legumes are considered among the most promising species for improving the sustainability of agricultural systems. In fact for farming system to remain productive and to be environmentally and economically sustainable on the long term it is necessary to replenish the reserves of nutrients which are removed or lost from the soil. Nodulating legumes have the potential to provide all nitrogen required for their growth and in this way to influence its balance in the soil and thus its availability for subsequent crops. In addition by reducing the inputs of fertilizers, legumes reduce the risk of nitrogen contamination of water resources. Furthermore, probably due to the wealth of interactions with other organisms, legumes have evolved an intricate network of secondary metabolites that, as the recent advances in the knowledge of their nutraceutical properties are proving, can be considered of great importance for livestock welfare and for the quality of their products.

Two legume species, Medicago truncatula and Lotus japonicus, are being used as model to study legume genetics and genomics. Medicago truncatula is closely related to alfalfa, the most important forage legume in the world. It has a small, diploid genome, it is self fertile and amenable to genetic transformation. In the present review we summarize the state of the art of M. truncatula genomics with particular emphasis on the available resources for functional genomics studies such as mutant collections.


3. Medicago truncatula genome sequencing

Functional genomics is greatly aided by knowledge on genome sequence and transcriptome of the target species. A concerted effort was carried out in M. truncatula which made genome data available to the community.

Legumes are the plant family with the greatest amount of genomic data available. Three legume species, Medicago truncatula, Lotus japonicus, and Glycine max, have been sequenced [1]. The assembly of Medicago truncatula genome is close to completion [2].

M. truncatula sequencing was initially carried out on Bacterial Artificial Chromosome (BAC) libraries following a BAC-by-BAC approach focused on gene-rich BACs. To date the available sequence data consist of three main batches: i) 246Mb of non redundant sequences that could be organized in large scaffolds separated by gaps and anchored to the eight M.truncatula physical chromosomes, ii) 17.3Mb of unanchored scaffolds and iii) 104.2Mb of additional unique sequence obtained by next generation sequencing (NGS) with Illumina sequencing. In total, 367.5Mb of M.truncatula genome representing 73,5% of the ~500Mb of the predicted genome size and about 94% of the expressed genes is available.

Taken together BAC sequences and non-redundant Illumina assemblies contain 62,388 gene loci with 14,322 gene prediction annotated as transposons. The average M. truncatula gene is 2,211 bp in length, contains 4.0 exons and has a coding sequence of 1,001 bp. Genome analysis and comparisons to other sequenced genomes allowed the identification of a 58-Myr-ago whole genome duplication (WGD) that has been associated with the evolution of rhizobial nodulation in M. truncatula and its relatives. Some nodulation-specific signalling components might have evolved through duplication and neo-functionalization from more ancient genes involved in host-mycorrhyzal signalling [2].

Another interesting feature is the presence of many amplified and somehow specialized gene families like nine leghaemoglobines, 563 Nodule Cystein-Rich Peptides (NCRs), 764 nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes, genes in the flavonoid pathway such as chalcone synthases (CHS), chalcone reductases, chalcone isomerases. Many gene duplications occurred with the creation of large gene clusters [2].

The availability of a first draft of the Medicago truncatula genome sequence has promoted several initiatives aimed at identifying molecular markers suitable for both evolutionary and genetic mapping studies.

384 inbred lines of M.truncatula with a 5x coverage and a subset of 30 with deep coverage (20x) will be resequenced through an Illumina-Solexa sequencing pipeline by the Medicago HapMap Project. In the first report on the analysis of sequence data from 26 M.truncatula accessions with ~15x average genome coverage, 3,063,923 mapped single nucleotide polymorphisms (SNPs) were described and first estimates of nucleotide diversity (θw =0.0063 and θπ =0.0043 bp−1), population scaled recombination rate and rate of decay of linkage disequilibrium have been published [3]. More recently the same material was used to estimate population recombination rates at 1 kb scale and very interestingly in the three chromosomes analysed recombination was higher near centromeric regions in stark contrast to what observed in every non-plant system and in the majority of plants that show a negative gradient of recombination from telomeric to centromeric regions [4].

In parallel, plant phenotyping is ongoing in greenhouse experiments for the Medicago lines. The combination of genetic and phenotypic data will be organized in a platform for genome-wide association mapping (GWAS) studies.


4. Functional genomics in Medicago truncatula

The discovery of gene function in model species is accomplished by exploiting resources such as mutant collections, using the ability to implement plant genetic transformation and analyzing gene transcription. In M. truncatula all the three approaches can be performed.

Several strategies were pursued in M. truncatula to produce mutant collections (Tab. 1) and they will be analysed in the following section.

ReferenceMutagenesis techniqueBackgroundNotes
(5)EMSJemalong population 28281,500 seeds treated for 24h with 0.2%EMS. 400 M1 plants obtained. 250,000 M2 seeds harvested as a single batch.
(6)γ-rayJemalong line J5462 M1 plants, screened as M2 families.
(8)EMSJemalong A173-7,000 M1 plants in 10-20 lots. M2 seeds bulked from each lot.
(9)T-DNAR108-1 (c3)Test populations with 3 different T-DNAs
(10)Tnt1R108-1 (c3)First test population with Tnt1 (~200 R0 plants)
(11)FNBJemalong A1780.000 M1, 460.000 M2
(12;13)Tnt1R108-1 (c3)7,000 Tnt1 mutants, presently extended to 19,000 as reported in
(14)Tnt1R108-1 (c3)~1000 R0
(14)EMSJemalong 2HA2500 M2 plants
(14)Activation taggingR108-1 (c3)~100 mutant lines
(15)EMSMedicago littoralis ‘Angel’Development of new annual medics varieties (i.e. resistant to herbicides)
(16)Tnt1Jemalong 2HAMutants produced in the frame of the european Grain Legumes Integrated Project (GLIP). The total number of mutants produced by 10 labs all around Europe should be several thousands (~6000). 2000 of them will integrate the Tnt1 collection at Noble.
(17)FNBJemalong A1731,200 M1 plants, 156,000 M2 plants
(18)EMSJemalong A17http://
2 populations. The first (not using single seed descent, SSD) 500 M1 produced 4500 M2. In the second (using SSD) 4350 M1 and 4350 M2.

Table 1.

Mutant collections in Medicago spp. EMS = ethyl methanesulphonate.


5. Chemical-physical mutagenesis

5.1. Target Induced Local Lesion IN Genomes (TILLING)

Alkylating agents such as ethyl methanesulphonate (EMS) have been used to develop mutant collections of Medicago truncatula. EMS induces single base pair C/G to A/T substitution in nucleotides. The mutagenized seeds are germinated and the resulting plants are selfed to produce M1 progenies. The M1 plants are then grown and a TILLING M2 collection is established by growing few seeds from each M1 plant. Total genomic DNA is purified from each M1 plant and pooled. The mutant collections are usually screened with reverse genetics approaches. TILLING involves the identification of mismatches in heteroduplexes formed by single stranded DNA from the wild type and mutant alleles of the target locus. The target sequences are generated by PCR amplification from bulked DNA isolated from single M1 plants using labelled primers appropriate for the detection strategy employed. The amplicons are then heated, causing strand separation, re-annealed in order to form heteroduplexes, cleaved by an endonuclease active on single stranded DNA (i.e. CelI from celery) at the mismatch point and the products separated by electrophoresis. Several EMS mutant collections of Medicago truncatula are available. Within the framework of the European Grain Legume Integrated Project two mutant collections were established. The two collections showed the same number of M2 lines that however were obtained from M1 populations with different size. Genetic analysis of the two collections allowed to define that the number of meristematic cells that contribute to seed (germ-line) in Medicago truncatula is 3. The number of mutations detected in the two EMS populations was 1 every 485 kb. A pilot reverse genetic experiment with 56 target genes revealed an efficiency of 13 independent alleles per exon screened, 67% of which were missense and 5% nonsense mutations. An Italian functional genomics initiative produced a small collection of TILLING mutants with about 2500 M2 lines and a reported efficiency of about 4 independent alleles for target sequence. Catalogue of mutant phenotypes were developed and services for reverse screening with target sequence are available ( A list of M.truncatula mutants is reported in Table 2.

ReferenceMutagenesis techniqueNew mutantsPhenotypeGene/Mutant line
(6)γ-ray2Nod-, Myc-TR25, TR26
(6)γ-ray4Nod±, Myc+TR34, TR79, TR89, TRV9
(6)γ-ray9Nod+Fix-, Myc+TR3, TR9, TR13, TR36, TR62, TR69, TR74, TR183, TRV15
(6)γ-ray3Nod++Nts, Myc+TR122, TRV3, TRV8
(8)EMS1EIN, Nod++sickle = skl1
(8)EMS1Nod-C71 = Domi
(20)EMS3developmentalmtapetala (tap), palmyra (plm), speckle (spk)
(21)EMS5Nod-B85, B129, C54, P1, Y6 Individuation of 4 complementation groups (DMI1, DMI2, DMI3, NSP):
dmi1-1 = C71 = domi
dmi1-2 = B129
dmi1-3 = Y6
dmi2-1 = TR25
dmi2-2 = TR26
dmi2-3 = P1
dmi3-1 = TRV25
nsp1-1 = B85
nsp1-2 = C54
(22)EMS7Calcium oxalate defectivecod1, cod2, cod3, cod4, cod5, cod6, cod7
(23)EMS1Nod-, root hair deformationhcl = B56
(24)EMS1Blocked in the formation of nodule primordialpdl1
(24)EMS1Blocked in the formation and/or maintenance of epidermal cell infectionlin1
(first citation)
(21)EMS3Nod-, root hair deformationshcl-1 = B56
hcl-2 = W1
hcl-3 = AF3
(25)EMS6Oxalate crystal morphology defectivecmd1, cmd2, cmd3, cmd4, cmd5, cmd6
(26)Fast Neutron2Nod-, cortical cell divisionnsp2-1
(27)EMS1Nod-, does not respond to Nod Factors by induction of root hair deformationnfp = C31
(29)EMS1Blocked in the formation and/or maintenance of epidermal cell infectionlin1
(first description)
(30)EMS1Numerous infections and polyphenolicsNip
(31)EMS1Nod-, defective in lateral root developmentLatd
(32)γ-ray2Nod+,Fix-,Myc+Mtsym20 = TRV43, TRV54
Mtsym21 = TRV49
(32)γ-ray1Nod-/+,Myc+Mtsym15 = TRV48;
(32)γ-ray1Nod-,Myc-/+Mtsym16 = TRV58
(33)Fast Neutron6Fix-dnf1-1 = 1D-1; dnf1-2 = 4A-17; dnf2 = 1B-5; dnf3 = 2C-2; dnf4 = 2E-1; dnf5 = 2F-16; dnf6 = 2H-8; dnf7 = 4D-5
(34)Fast Neutron1Nod-bit1
(35)Tnt11Single leafletsgl1
(36)Fast Neutron1Increased nodule numberEfd
(37)EMS1Impaired in nodule primordium invasionApi
(38)EMS1Aberrant root hair curling and infection thread formationRpg
(39)EMS1Myc++, Nod-/+B9
(40)Fast neutron1Leaf dissectionpalm1
(41)T-DNA1Compact rootscra1 (not tagged)
(42)Tnt1variousLeaf epidermal morphologyVarious
(43)Tnt11Lack of lignin in the interfascicular regionnst1
(44)Tnt11Secondary cell wall thickening in pithmtstp1
(45)Fast neutron1Compund leaf developmentfcl1
(46)Fast neutron1Root determined noudulationrdn1
(47;48)Fast neutron1Myc-, Nod-Vpy
(49)Activation tagging1Lack of hemolytic saponinsLha
(50)(1)Tnt11Stay greenMtSGR
(51)Tnt11Smooth leaf marginslm1
(52)Tnt11Reduced leaf blade expansionStf
(53)Tnt11Inhibition of rust germ tube differentiationirg1

Table 2.

Medicago truncatula mutants. Nodulation phenotypes: Nod++ = hypernodulator, Nod+ = wild type nodulator, Nod± = reduced nodulation, Nod- = lack of nodules, Nod-/+ = late nodulation. Nitrogen fixation phenotypes: Fix+ = wild type, Fix- = no fixation. Mychorrhization phenotypes: Myc+ = wild type, Myc- = absent or reduced mychorrhizas, Myc-/+ = mix of normal colonization and events of formation only of appressoria with no intercellular hyphae developing from them, Myc++ = hyper responsive to mychorrhization. Nts = nitrate tolerant nodulation. EIN = ethylene insensitive.

5.2. “Delete a gene” collections

Irradiation of plant seeds to appropriate dose of fast neutrons and γ-rays results in deletion of DNA fragments of variable lengths with an average modest reduction of seed viability.

Large mutant collections by seed irradiation have been created for Medicago truncatula functional genomics studies. Although the first experiments were based on γ-ray irradiation of the Jemalong J5 seeds [6] the main body of the collection was obtained by Fast Neutron Bombardment (FNB) of the genotype A17. Globally the two larger collections, stored at the John Innes Center and at the Noble Foundation, consist of about 616,000 M2 FNB families.

Both reverse and forward genetic approaches have been successfully applied to study mutants from these collections.

Reverse screening of FNB populations have been carried out by the DeTILLING strategy described by Rogers C et al. [17]. This strategy allows detection of mutants by PCR on bulks of DNAs of FNB mutants. The wild type target amplification is avoided by a strategy that combines restriction enzyme digestion of the template and the use of poison primers. With this strategy a mutant recovery rate of 29% has been obtained from a population of 156.000 M2 plants (4 genes out of 14 screened).

Nevertheless deletion size can hamper reverse genetics screening (Chen R., personal communication) leaving forward genetics as the main choice in case of FNB populations. However map-based cloning required to discover the mutation of interest is helped by strategies such as transcriptional cloning, originally devised by Mitra R M et al. [54], which has allowed the identification of FNB induced mutations (see Table 3). This approach relies on the identification of mutated genes through detailed genome-wide transcriptomic analyses. Also genome-wide analyses of FNB mutant are expected to benefit of the recent development of a Medicago truncatula genome-wide tiling array by Nimblegen. A list of Medicago truncatula FNB mutants characterized by forward genetics approaches is reported in Table 2.


6. Insertional mutagenesis with DNA mobile elements

6.1. Tnt1

T-DNA tagging has been the strategy of choice for many mutant collections in Arabidopsis and it has allowed fundamental discoveries in gene functions and advances in both basic and applied plant research [55]. Unfortunately only Arabidopsis can be transformed easily by the floral-dip method which allows the generation of large numbers of mutants in a cost-effective manner. Up to now transformation for the other plant species including M. truncatula can only be achieved by tissue culture-based protocols requiring great efforts to produce the number of mutants that would allow a significant genome coverage. An interesting strategy has been recently published in the legume Lotus japonicus based on the endogenous retrotransposon LORE1 [56;57]. LORE1, originally activated via tissue culture, retained its activity for some regenerated plants in the subsequent generations. Based on such discovered germline activity, tagged M1 mutant collections were produced by seed propagation from activated starter lines (M0) [57;58].

In M.truncatula large scale collections of mutants have been constructed using the tobacco Tnt1 retrotransposon. d'Erfurth and colleagues have demonstrated that in the Medicago truncatula R108 genotype, this element has the ability to transpose during the early steps of in vitro regeneration [10] with a high rate of insertion in transcribed genomic regions. Sequence analyses of insertion sites has showed the virtual absence of insertion site preference. The average amount of new insertions per regenerated line was calculated in the order of ~25. Based on these data it was shown that a collection of 14-16.000 Tnt1 lines will store tagging events for about 90% of M.truncatula genes [13]. Such an ambitious objective has been pursued by working on two Medicago truncatula lines.

The collection maintained at the Noble Foundation ( which includes also the first mutants generated by CNRS in France, is based on the genotype R108-c3. Another collection of about 1000 lines from the same R-108 line was produced by CNR-IGV in Italy.

In the framework of the GLIP project 8000 Tnt1 mutants were produced from the Jemalong 2HA (2HA3-9-10-3) line. The GLIP collection is maintained by the various labs that participated to the project and a subset of plants were merged with the collection at the Noble Foundation.

Iantcheva and colleagues reported that Tnt1 transposition efficiency in Jemalong 2HA has a lower efficiency with only 10-15 new insertions per line and a variable percentage of regenerated plants without transposition [16]. The adoption of 2HA line for mutagenesis instead of R108, was motivated by the highest DNA homology to the line used for genome sequencing (Jemalong A17), and for the presence of active and characterized endogenous retroelements [59].

Tnt1 mutant collections have been screened with both forward and reverse genetic approaches. Forward approaches have been based on cloning of host sequence flanking the insertion sites and subsequent identification of events linked to the studied mutation. Based on the duplicated Tnt1 long terminal repeats (LTR) sequences several molecular approaches including thermal asymmetric interlaced (TAIL)-PCR, Inverse-PCR have been used to recover the host sequences flanking the insertion sites [60]. Segregation analysis of each cloned insertion site can then be used to select the event linked to the mutation. In alternative the insertion sites associated with the mutations can be selected by segregation analysis prior to host sequence cloning by employing a sequence specific amplification polymorphism (S-SAP) based protocol.

Confirmation of the identity of the mutation can be obtained by means of complementation tests based on the reintroduction of the wild type gene sequence in the mutated background. In alternative one could obtain independent alleles of the target gene and compare their similarity to the original mutant phenotype. This can be done using TILLING and Tnt1 mutant populations as demonstrated by many publications that report successful recovery of alleles by reverse screening [61] and Table 3. The power of the Tnt1 mutagenesis approach is also witnessed by the prevalence of publications reporting successful gene cloning based on such strategy compared to the others since 2008 (Table 2 and 3).

(62)dmi2NORKPhysical mapping
(63)dmi1AY497771, possible membrane receptorPhysical mapping
(64)dmi3Ca2 and Calmodulin dependent protein kinasePhysical mapping/Transcriptional based cloning
(65)nsp2GRAS Transcriptional regulatorPhysical mapping
(66)nsp1GRAS Transcriptional regulatorPhysical mapping
(46)sunnCLV1-like LRR receptor kinasePhysical mapping and gene homology
(67)mtpimMADS-boxReverse screening on Tnt1 collection
(68)mtpt4Phosphate transporterRNAi and TILLING (reverse)
(34)bit1ERF transcription factor required for nodulation (ERN)Transcriptional based cloning
(35)sgl1MtUNI (transcription factor)Tnt1 forward
(36)efdEthilene responsive factor required for nodule differentiationFast neutron reverse
(38)rpgPutative long coiled-coil proteinMap based cloning
(28)sickleMtEIN2, ethylene signaling geneMap based cloning and gene homology
(69)linE3 ubiquitin ligase containing a U-box and WD40 repeat domainsPositional cloning
(70)srlkLRR kinase TILLING reverse and RNAi
(71)mate1MATETnt1 reverse
(72)ugt78g1Glucosyl transferaseTnt1 reverse
(73)mtapetalaMtPI, MADS Box transcription factorRNAi and mutation segregation analisys
(40)palm1Cys(2)His(2)zinc finger transcription factorFast neutron forward and Tnt1 reverse
(74)MtSYMREM1, remorinTnt1 reverse
(44)dnf1Signal peptidase complex subunitFast neutron microarray based cloning
(43)nst1NAC transcription factorForward screening and Tnt1 flanking region cloning
(44)mtstp1WRKY transcription factorForward screening and Tnt1 flanking region cloning
(75)ccr1, ccr2Cinnamoyl CoA ReductaseTnt1 reverse
(76)ugt73f3Glucosyl transferaseTnt1 reverse
(45)fcl1Class M KNOXFast neutron forward, map based cloning and Tnt1 reverse
(77)rdn1Uncharacterized plant familyMapping
(78)fta, ftcMtFTa, MtFTc, protein ligandsTnt1 reverse
(48)vpyVapyrinMicroarray based cloning, Tnt1 reverse
(49)lhaCYP716A12, Cytochrome P450Flanking sequence tagging and TILLING
(50)MtSGRStay green geneTnt1 forward and flanking sequence cloning
(51)slm1Auxin efflux carrier proteinTnt1 forward and flanking sequence cloning
(52)stfStenofolia, WUSCHEL-like homeobox transcription factorTnt1 forward and flanking sequence cloning
(71)mate2MATETnt1 reverse
(53)irg1Cys(2)His(2) zinc finger transcription factorTnt1 forward and flanking sequence cloning
(79)mtparMYB transcription factorTnt1 reverse

Table 3.

Medicago genes characterized using mutants.


7. RNAi and VIGS

Reverse genetics studies in Medicago truncatula did not only take advantage of the many mutant populations available but also of techniques based on post-transcriptional gene silencing (PTGS). In this case plants are transformed with a construct that will produce double-stranded RNAs that will guide sequence-specific mRNA degradation of the target gene. The phenotype of the transformed plants can gradually vary from wild type to knock-out thus many transformants are needed to obtain the desired effect. Mild effects can be beneficial in case of essential genes whose complete loss-of-function may cause lethal phenotypes. RNAi in M.truncatula has been extensively used to study gene function but it has not been a matter of a functional genomics approach as for Arabidopsis and the AGRIKOLA collection [80]. Nevertheless many gene functions have been characterized exploiting RNAi. A list of gene function and Medicago truncatula physiology studies that used RNAi approaches is reported in Table 4.

ReferenceSilenced genePhenotype
(75)Lyk3Marked reduction of nodulation when inoculated with Sm 2011ΔNodFE-GFP
(75)Lyk4Effect on infection thread morphology
(81)CDPK1Reduced root hair and root cell lengths. Diminution of both rhizobial and mycorrhizal symbiotic colonization.
(82)DMI2Reduction of organelle-like symbiosomes in nodules
(76)MtHAP2-1Alteration of nodule development
(84)MtCPK3Increased average nodule number
(85)MtCRE1Cytokinin-insensitive roots, increate number of lateral roots, strong reduction in nodulation.
(86)MtPIN2, MtPIN3, MtPIN4Reduced number of nodules
(87)CHSReduced levels of flavonoids and subsequent inability to nodulate
(88)PR10-1 (pathogenesis related)Reduced colonization by the root pathogen A.euteiches.
(89)HMGR1Dramatic decrease in nodulation.
(90)IPD3No obvious phenotype observed
(63)MtPT4Premature death of mycorrhizal arbuscules.
(91)MtSNF4bReduced seed longevity, alteration in non reducing sugar content.
(92)ENOD40-1, ENOD40-2Reduced nodule number and altered symbiosome development.
(93)MtFNSII-1, MtFNSII-2Reduced nodulation
(94)MtCDD1Alteration of the Arbuscular Mycorrhizal – mediated accumulation of apocarotenoids
(95)MtDXS2Reduction of AM-induced apocarotenoid accumulation.
(78)MtSERF1Strong inhibition of somatic embryogenesis
(73)MtPI, MtNGL9Altered flower development
(96)MtWUSStrong inhibition of somatic embryogenesis
(65)SrlkTransgenic root growth less inibited by salt stress.
(97)FLOT2, FLOT4Reduced nodulation and root development.
(98)MtMSBP1Aberrant mycorrhizal phenotype with thik and septated appressoria, decrease number of arbuscules and distorted arbuscule morphology.
(99)MtCDC16Decreased number of lateral roots and increased number of nodules. Reduced sensivity to auxin.
(100)NPR1Acceleration of root hair curling at the beginning of symbiosis estabilishment
(101)MtSNARP2Aberrant early senescent nodules where differentiated bacteroids degenerate rapidly.
(74)MtSYMREM1Reduced nodulation and abnormal nodule development
(102)MtN5Reduced nodulation
(103)VapyrinImpaired passage across epidermis by AM fungi. Abolition of arbuscule formation.
(104)MtAOC1No nodulation phenotype observed
(105)γECSLower homoglutathione content. Lower biological nitrogen fixation associated with a reduction in the expression of the leghemoglobin and thioredoxin S1 genes. Reduction in nodule size.
(106)MtSAP1Lower level of storage globulin proteins, vicilin and legumin in seeds and germination deficiency.
(107)MtNR1, MtNR2Reduced nitrate or nitrite reductase activity and NO level.
(108)MtNoa/Rif1Decrease in NO production in roots but not in nodules. Reduction of nodule number and nitrogen fixation capacity.
(109)MtROPGEF2Effect on cytosolic Ca2+ gradient and subcellular structure of root hairs. Reduced root hair growth.
(110)MtROP9Reduced growth , no ROS generation after microbial infection. Promoted mycorrhizal and A.euteiches early hyphal root colonization. Impaired rhizobial colonization.
(111)MtNAC969Improved growth under salt stress.

Table 4.

Use of RNAi approaches in Medicago truncatula.

Virus-induced gene silencing (VIGS) is a PTGS technique that can be used transiently by scrubbing leaves or introducing the viral vector in the plant by agro-infiltration. VIGS is being used for large scale forward genetics screening by inoculation of cDNA library and subsequent identification of the gene involved in the process of interest [112]. Viral vectors working on Medicago truncatula have been recently described. Grønlund et al. used successfully a Pea Early Browning Virus (PEBV) based vector for both transient expression of reporter genes and for silencing of the Phytoene Desaturase (PDS) gene that causes a bleaching phenotype [113]. Várallyay and colleagues constructed two VIGS vectors based on the Sunnhemp Mosaic Virus (SHMV) that can systemically infect M.truncatula without causing severe symptoms and reported a successful silencing of the Chlorata 42 gene [114]. Large scale screenings based on VIGS analysis have not been reported for M. truncatula as far.


8. Perspectives

Functional genomics of forage legumes started with the aim of determining the molecular and genetic bases of nitrogen fixation and since the beginning mutant collections have been thoroughly screened also for mycorrhyzal symbiosis. These aspects are still being investigated and we expect that many more results will be published in the next years. A better understanding of nitrogen fixation and symbiosis is fundamental for the development of a sustainable agriculture aiming at a reduction of inputs and at maintaining soil fertility. Nitrogen (N) is one of the crucial nutrients for all organisms including plants. The doubling of world food production in the past four decades was contributed by a sevenfold increase of N fertilization [115]. The anthropogenic N which is mostly lost to air, water and land affects climate, the chemistry of the atmosphere, and the composition and function of terrestrial and aquatic ecosystems [116]. Improving the ability of plants to exploit environmental nitrogen would decrease N fertilization and its negative consequences; therefore a deep understanding of legume symbiosis with nitrogen fixing bacteria could help the long term goal of transferring the associative ability of legume species to non-symbiotic crops of agronomic relevance. As a consequence functional genomics of nodulation will have an impact on reduction of intensive agriculture practices with benefits for the preservation of environment and quality of human activities.

Another positive role for legumes in an environmental perspective is addressed by species such as Lotus spp. that have strong adaptive characteristics making them good candidates for restoration and phytoremediation of degraded environments [117]. This happens in the Flooding Pampa (Argentina) where the presence of proteinaceous forages was re-established by the introduction of L. tenuis, being the other legume species reduced by the harsh environmental condition.

Pastures and feedstuff including forage legumes have a higher quality compared to those based only on grasses and provide an important input of protein in animal nutrition. More recently public and scientific debate has reassessed forage legumes importance for the quality of livestock nutrition and welfare has having relevant consequences on the quality of final products (meat, milk etc.) and ultimately on human health. This happened because of the occurrence of bovine spongiform encephalopathy (BSE) related to the traditional use of offal in animal feed lots as a source of protein.

Functional genomics in M.truncatula proved useful in the study and comprehension of many aspects of plant development and plant secondary metabolism that could not be discovered in earlier models such as Arabidopsis. The availability of genomics tools in an increasing number of species has the effect of widening the possibility of new discoveries in the field of plant biology. Worth mentioning the recent advances in understanding compound leaf development and zygomorphic flower ontogeny based on the analysis of several mutants in M.truncatula.

Living organisms, and among them plants, can be considered as an abundant and diverse set of biofactories with the ability to synthesize an enormous variety of chemical compounds. Legumes contain chemicals that can prove useful for their anti-oxidant, anti-viral, anti-microbial, anti-diabetic, anti-allergenic and anti-inflammatory properties [118]. These properties are related to secondary molecules such as flavonoids and saponins.

Modest levels of protoanthocyanidins (PAs) in forages reduce the occurrence of bloat and at the same time promote increased dietary protein nitrogen utilization in ruminant animals [119]. The lack of PAs in the leaves of the major forage legume such as alfalfa has prompted studies for the understanding of the molecular and cellular biology of PA polymerization, transport, and storage helped by the functional genomics tools available for M.truncatula. Recent positive achievements were obtained by biotechnological strategies based on the overexpression of MYB transcription factors that induced PAs accumulation in both alfalfa and clover leaves [79].

In addition to well-known beneficial properties of flavonoids (cit) recent evidence suggests that flavonoids themselves, particularly fractions rich in PAs, can significantly reduce cognitive deterioration in animal model systems [120-122], and may more generally promote improvements in memory acquisition, consolidation, storage, and retrieval under nondegenerative conditions.

In Chinese medicine one of the oldest herbal medicine was obtained by the roots of the legume plant licorice (Glychyrriza glabra).containing the triterpenoid saponin glychyrrizin exhibiting a wide range of pharmacological activities. Cytochrome P450 monooxygenases were proved to be responsible for synthesis of glychyrrizin via oxidative steps based on biochemical experiments [123].

In forage legumes saponins can be toxic to monogastric animals and reduce forage palatability for ruminants. Mutant analysis in M.truncatula has unveiled the genetic control of key biosynthetic steps for saponins related to oxidation and glycosilation [49;124], opening possibilities of biotechnological manipulation of saponins in alfalfa.

Both human and animal nutritional science are bound to profit from plant genetic analysis and nutritional genomics, opening possibilities to more personalized approaches to medicine and improvement of the quality of life.


  1. 1. Sato S, Sachiko I,T Satoshi . Structural analyses of the genomes in legumes. Curr Opin Plant Biol 2010;13 (2):146-52.
  2. 2. Young ND, Debellé Fdr, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011;480 (7378):520-4.
  3. 3. Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, et al. Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A 2011;108 (42):E864-E870.
  4. 4. Paape T, Zhou P, Branca A, Briskine R, Young N and Tiffin P. Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome. Genome Biol Evol 2012;4 (5):726-37.
  5. 5. Benaben V, Duc G, Lefebvre V. TE7, An Inefficient Symbiotic Mutant of Medicago truncatula Gaertn. cv Jemalong. Plant Physiol 1995;107 (1):53-62.
  6. 6. Sagan M, Morandi D, Tarenghi E and Duc G.. Selection of nodulation and mycorrhizal mutants in the modelplantMedicagotruncatula (Gaertn.) after γ-raymutagenesis. Plant Science 1995;111 :63-71.
  7. 7. Cook DR, VandenBosch K, de Bruijn FJ. Model legumes get the nod. The Plant Cell 1997;3 :275.
  8. 8. Penmetsa R and Cook DR. A Legume Ethylene-Insensitive Mutant Hyperinfected by Its Rhizobial Symbiont. Science 1997;275 (5299):527-30.
  9. 9. Scholte M, d'Erfurth I, Rippa S, Mondy S, Cosson V, Durand P, et al. T-DNA tagging in the model legume Medicago truncatula allows efficient gene discovery. Molecular Breeding 2002;10 (4) :203-15.
  10. 10. d'Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A and Ratet P. Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 2003;34 (1):95-106.
  11. 11. Wang H. Fast neutron bombardment (FNB) mutagenesis for forward and reverse genetic studies in plants. ed. Global Science Books, Isleworth, UK, pp 629-639; 2006.
  12. 12. Tadege M, Ratet P and Mysore K. Insertional mutagenesis: a Swiss Army knife for functional genomics of Medicago truncatula. Trends Plant Sci 2005;10 (5):229-35.
  13. 13. Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, et al. Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 2008;54 (2):335-47.
  14. 14. Porceddu A, Panara F, Calderini O, Molinari L, Taviani P, Lanfaloni L, et al. An Italian functional genomic resource for Medicago truncatula. BMC Res Notes 2008;1 :129.
  15. 15. Oldach KH, Peck DM, Cheon JUDY, Williams KJ and Nair R. Identification of a Chemically Induced Point Mutation Mediating Herbicide Tolerance in Annual Medics (Medicago spp.). Annals of Botany 2008;101 :997-1005.
  16. 16. Iantcheva A, Chabaud M, Cosson V, Barascud M, Schutz B, Primard-Brisset C, et al. Osmotic shock improves Tnt1 transposition frequency in Medicago truncatula cv Jemalong during in vitro regeneration. Plant Cell Rep 2009;28 (10):1563-72.
  17. 17. Rogers C, Wen J, Chen R and Oldroyd G. Deletion-Based Reverse Genetics in Medicago truncatula. Plant Physiology 2009;151(3) :1077-86.
  18. 18. Signor CL, Savois V, Aubert Gg, Verdier J, Nicolas M, Pagny G, et al. Optimizing TILLING populations for reverse genetics in Medicago truncatula. Plant Biotechnol J 2009;7 (5):430-41.
  19. 19. Sagan M, deLarambergue H. Genetic analysis of symbiosis mutants in Medicago truncatula. ed. Kluwer Academic Publishers, Dordrecht, The Netherlands; 1998.
  20. 20. Penmetsa RV. Production and characterization of diverse developmental mutants of Medicago truncatula. Plant Physiol 2000;123 (4):1387-98.
  21. 21. Catoira R, Timmers AC, Maillet F, Galera C, Penmetsa RV, Cook D, et al. The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling. Development 2001;128 (9):1507-18.
  22. 22. Nakata PA. Isolation of Medicago truncatula mutants defective in calcium oxalate crystal formation. Plant Physiol 2000;124 (3):1097-104.
  23. 23. Wais RJ, Galera C, Oldroyd G, Catoira R, Penmetsa RV, Cook D, et al. Genetic analysis of calcium spiking responses in nodulation mutants of Medicago truncatula. Proc Natl Acad Sci U S A 2000;97 (24):13407-12.
  24. 24. Cohn JR, Uhm T, Ramu S, Nam YW, Kim DJ, Penmetsa RV, et al. Differential regulation of a family of apyrase genes from Medicago truncatula. Plant Physiol 2001;125 (4):2104-19.
  25. 25. McConn MM. Oxalate reduces calcium availability in the pads of the prickly pear cactus through formation of calcium oxalate crystals. J Agric Food Chem 2004;52 (5):1371-4.
  26. 26. Oldroyd G. Identification and Characterization of Nodulation-Signaling Pathway 2, a Gene of Medicago truncatula Involved in Nod Factor Signaling. Plant Physiology 2003;131(3) :1027-32.
  27. 27. Amor BB, Shaw SL, Oldroyd GED, Maillet F, Penmetsa RV, Cook D, et al. The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. Plant J 2003;34 (4):495-506.
  28. 28. Penmetsa RV, Uribe P, Anderson J, Lichtenzveig J, Gish JC, Nam YW, et al. The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations. Plant J 2008;55 (4):580-95.
  29. 29. Kuppusamy KT, Endre G, Prabhu R, Penmetsa RV, Veereshlingam H, Cook DR, et al. LIN, a Medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections. Plant Physiol 2004;136 (3):3682-91.
  30. 30. Veereshlingam H, Haynes JG, Penmetsa RV, Cook DR, Sherrier DJ. nip, a symbiotic Medicago truncatula mutant that forms root nodules with aberrant infection threads and plant defense-like response. Plant Physiol 2004;136 (3):3692-702.
  31. 31. Bright LJ, Liang Y, David, .Mitchell and Harris J. The LATD Gene of Medicago truncatula Is Required for Both Nodule and Root Development. MolecularPlant Microbe Interaction 2005;18(6) :521-432.
  32. 32. Morandi D, Prado E, Sagan M&DGr. Characterisation of new symbiotic Medicago truncatula (Gaertn.) mutants, and phenotypic or genotypic complementary information on previously described mutants. Mycorrhiza 2005;15 (4):283-9.
  33. 33. Starker CG, Parra-Colmenares AL, Smith L, Mitra RM. Nitrogen fixation mutants of Medicago truncatula fail to support plant and bacterial symbiotic gene expression. Plant Physiol 2006;140 (2):671-80.
  34. 34. Middleton PH, Jakab J, Penmetsa RV, Starker CG, Doll J, Kalò P, et al. An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction. Plant Cell 2007;19 (4):1221-34.
  35. 35. Wang H, Chen J, Wen J, Tadege M, Li G, Liu Y, et al. Control of compound leaf development by FLORICAULA/LEAFY ortholog SINGLE LEAFLET1 in Medicago truncatula. Plant Physiol 2008;146 (4):1759-72.
  36. 36. Vernié T, Moreau S, de Billy Fo, Plet J, Combier JP, Rogers C, et al. EFD Is an ERF transcription factor involved in the control of nodule number and differentiation in Medicago truncatula. Plant Cell 2008;20 (10):2696-713.
  37. 37. Teillet A, Garcia J, de Billy Fo, Gherardi Ml, Huguet T, Barker DG, et al. api, A novel Medicago truncatula symbiotic mutant impaired in nodule primordium invasion. Mol Plant Microbe Interact 2008;21 (5):535-46.
  38. 38. Arrighi JFo, Godfroy O, de Billy Fo, Saurat O, Jauneau A&GC. The RPG gene of Medicago truncatula controls Rhizobium-directed polar growth during infection. Proc Natl Acad Sci U S A 2008;105 (28):9817-22.
  39. 39. Morandi D, le Signor C, Gianinazzi-Pearson V and Duc G. A Medicago truncatula mutant hyper-responsive to mycorrhiza and defective for nodulation. Mycorrhiza 2009;19 :4635-441.
  40. 40. Chen J, Yu J, Ge L, Wang H, Berbel A, Liu Y, et al. Control of dissected leaf morphology by a Cys(2)His(2) zinc finger transcription factor in the model legume Medicago truncatula. Proc Natl Acad Sci U S A 2010;107 (23):10754-9.
  41. 41. Laffont C, Blanchet S, Lapierre C, Brocard L, Ratet P, Crespi M, et al. The compact root architecture1 gene regulates lignification, flavonoid production, and polar auxin transport in Medicago truncatula. Plant Physiol 2010;153 (4):1597-607.
  42. 42. Vassileva V, Zehirov G, Ugrinova M. Variable leaf epidermal leaf morphology in Tnt1 insertional mutants of the model legume Medicago truncatula LEGUME MEDICAGO TRUNCATULA. Biotechnol\&Biotechnol Eq 2010;24(4) :2060-5.
  43. 43. Zhao Q, Gallego-Giraldo L, Wang H, Zeng Y, Ding SY, Chen F&DR. An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula. Plant J 2010;63 (1):100-14.
  44. 44. Wang D, Griffitts J, Starker C, Fedorova E, Limpens E, Ivanov S, et al. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science 2010;327 (5969):1126-9.
  45. 45. Peng J, Yu J, ans Yingqing Guo ans Guangming Li HW, Bai G and and Chen R. Regulation of Compound Leaf Development in Medicago truncatula by Fused Compound Leaf1, a Class M KNOX Gene. The Plant Cell 2011;23 :3929-43.
  46. 46. Schnabel E, Journet EP, de Carvalho-Niebel F, Duc G. and Frugoli J. The Medicago truncatula SUNN gene encodes a CLV1-like leucine-rich repeat receptor kinase that regulates nodule number and root length. Plant Mol Biol 2005;58 (6):809-22.
  47. 47. Murray JD. Invasion by invitation: rhizobial infection in legumes. Mol Plant Microbe Interact 2011;24 (6):631-9.
  48. 48. Murray JD, Muni RRD, Torres-Jerez I, Tang Y, Allen S, Andriankaja M, et al. Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula. Plant J 2011;65 (2):244-52.
  49. 49. Carelli M, Biazzi E, Panara F, Tava A, Scaramelli L, Porceddu A, et al. Medicago truncatula CYP716A12 is a multifunctional oxidase involved in the biosynthesis of hemolytic saponins. Plant Cell 2011;23 (8):3070-81.
  50. 50. Zhou C, Han L, Pislariu C, Nakashima J, Fu C, Jiang Q, et al. From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement. Plant Physiol 2011;157 (3):1483-96.
  51. 51. Zhou C, Han L, Hou C, Metelli A, Qi L, Tadege M, et al. Developmental analysis of a Medicago truncatula smooth leaf margin1 mutant reveals context-dependent effects on compound leaf development. Plant Cell 2011;23 (6):2106-24.
  52. 52. Tadege M&Mysore K. Tnt1 retrotransposon tagging of STF in Medicago truncatula reveals tight coordination of metabolic, hormonal and developmental signals during leaf morphogenesis. Mob Genet Elements 2011;1 (4):301-3.
  53. 53. Uppalapati SR, Ishiga Y, Doraiswamy V, Bedair M, Mittal S, Chen J, et al. Loss of abaxial leaf epicuticular wax in Medicago truncatula irg1/palm1 mutants results in reduced spore differentiation of anthracnose and nonhost rust pathogens. Plant Cell 2012;24 (1):353-70.
  54. 54. Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, GED GO&SL. A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Science 2004;101(13 :4701.
  55. 55. O'Malley R and Ecker J. Linking genotype to phenotype using the Arabidopsis unimutant collection. The Plant Journal 2010;61 (6) :928-40.
  56. 56. Fukai E, Umehara Y, Sato S, Endo M, Kouchi H, Hayashi M, et al. Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants. PLoS Genet 2010;6 (3):e1000868.
  57. 57. Fukai E, Soyano T, Umehara Y, Nakayama S, Hirakawa H, Tabata S, et al. Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. Plant J 2012;69 (4):720-30.
  58. 58. Urbanski DF, Malolepszy A, Stougaard Jand S.Ugerrǿj. Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. Plant J 2012;69 (4):731-41.
  59. 59. Rakocevic A, Mondy S, Tirichine Ll, Cosson V, Brocard L, Iantcheva A, et al. MERE1, a low-copy-number copia-type retroelement in Medicago truncatula active during tissue culture. Plant Physiol 2009;151 (3):1250-63.
  60. 60. Ratet P. Medicago truncatula handbook. ed. Noble Foundation; 2006.
  61. 61. Cheng X, Wen J, Tadege M, Ratet P. Reverse genetics in medicago truncatula using Tnt1 insertion mutants. Methods in molecular biology 2011;678 :179-190.
  62. 62. Endre G, Kereszt A, Kevei Zn, Mihacea S, Kalò Pand Kiss G. A receptor kinase gene regulating symbiotic nodule development. Nature 2002;417 (6892):962-6.
  63. 63. Ané JM, Kiss GrB, Riely BK, Penmetsa RV, Oldroyd G, Ayax C, et al. Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 2004;303 (5662):1364-7.
  64. 64. Lèvy J, Bres C, Geurts R, Chalhoub B, Kulikova O, Duc G, et al. A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 2004;303 (5662):1361-4.
  65. 65. Kalò P, Gleason C, Edwards A, Marsh J, Mitra RM, Hirsch S, et al. Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators. Science 2005;308 (5729):1786-9.
  66. 66. Smit P, Raedts J, Portyanko V, Debellé Fdr, Gough C, Bisseling T and Geurts R. NSP1 of the GRAS protein family is essential for rhizobial Nod factor-induced transcription. Science 2005;308 (5729):1789-91.
  67. 67. Benlloch R, d'Erfurth I, Ferrandiz C, Cosson V, Beltràn JP, Canas LA, et al. Isolation of mtpim proves Tnt1 a useful reverse genetics tool in Medicago truncatula and uncovers new aspects of AP1-like functions in legumes. Plant Physiol 2006;142 (3):972-83.
  68. 68. Javot H, Penmetsa RV, Terzaghi N, Cook DR. A Medicago truncatula phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis. Proc Natl Acad Sci U S A 2007;104 (5):1720-5.
  69. 69. Kiss E, Olàh Br, Kalò P, Morales M, Heckmann AB, Borbola A, et al. LIN, a novel type of U-box/WD40 protein, controls early infection by rhizobia in legumes. Plant Physiol 2009;151 (3):1239-49.
  70. 70. de Lorenzo L, Merchan F, Laporte P, Thompson R, Clarke J, Sousa C and Crespi M. A novel plant leucine-rich repeat receptor kinase regulates the response of Medicago truncatula roots to salt stress. Plant Cell 2009;21 (2):668-80.
  71. 71. Zhao J and Dixon R. MATE transporters facilitate vacuolar uptake of epicatechin 3'-O-glucoside for proanthocyanidin biosynthesis in Medicago truncatula and Arabidopsis. Plant Cell 2009;21 (8):2323-40.
  72. 72. Peel GJ, Pang Y, Modolo LV. The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago. Plant J 2009;59 (1):136-49.
  73. 73. Benlloch R, Roque En, Ferràndiz C, Cosson V, Caballero T, Penmetsa RV, et al. Analysis of B function in legumes: PISTILLATA proteins do not require the PI motif for floral organ development in Medicago truncatula. Plant J 2009;60 (1):102-11.
  74. 74. Lefebvre B, Timmers T, Mbengue M, Moreau S, Hervé C, Tòth K, et al. A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proc Natl Acad Sci U S A 2010;107 (5):2343-8.
  75. 75. Zhou R, Jackson L, Shadle G, Nakashima J, Temple S, Chen F. Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula. Proceedings of the National Academy of Sciences National Acad Sciences; 2010;107(41) :17803-17808.
  76. 76. Naoumkina M and Dixon R. Characterization of the mannan synthase promoter from guar (Cyamopsis tetragonoloba). Plant Cell Rep 2011;30 (6):997-1006.
  77. 77. Schnabel EL, Kassaw TK, Smith LS, Marsh JF, Oldroyd GE, Long SR. The ROOT DETERMINED NODULATION1 gene regulates nodule number in roots of Medicago truncatula and defines a highly conserved, uncharacterized plant gene family. Plant Physiol 2011;157 (1):328-40.
  78. 78. Laurie ÌR, Diwadkar P, Jaudal M, Zhang L, Hecht V, Wen J, et al. The Medicago FLOWERING LOCUS T Homolog, MtFTa1, Is a Key Regulator of Flowering Time. Plant Physiology 2011;156 :2207-24.
  79. 79. Verdier J, Zhao J, Torres-Jerez I, Ge S, Liu C, He X, et al. MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. Proc Natl Acad Sci U S A 2012;109 (5):1766-71.
  80. 80. Hilson Pierre, Small Ian, Kuiper Martin. European consortia building reference resources for Arabidopsis functional genomics. Curr Opin Plant Biol 2012;6:426-9.
  81. 81. Ivashuta S, Liu J, Liu J, Lohar DP, Haridas S, Bucciarelli B, et al. RNA interference identifies a calcium-dependent protein kinase involved in Medicago truncatula root development. Plant Cell 2005;17 (11):2911-21.
  82. 82. Limpens E, Mirabella R, Fedorova E, Franken C, Franssen H, Bisseling T&GR. Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2. Proc Natl Acad Sci U S A 2005;102 (29):10375-80.
  83. 83. Arrighi JF, Barre A, Amor BB, Bersoult A, Soriano LC, Mirabella R, et al. The Medicago truncatula lysin [corrected] motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes. Plant Physiol 2006;142 (1):265-79.
  84. 84. Gargantini PR, Gonzalez-Rizzo S, Chinchilla D, Raices M, Giammaria V, Ulloa RM, et al. A CDPK isoform participates in the regulation of nodule number in Medicago truncatula. Plant J 2006;48 (6):843-56.
  85. 85. Gonzalez-Rizzo S, Crespi M and Frugier F. The Medicago truncatula CRE1 cytokinin receptor regulates lateral root development and early symbiotic interaction with Sinorhizobium meliloti. Plant Cell 2006;18 (10):2680-93.
  86. 86. Huo X, Schnabel E, Hughes K and Frugoli J. RNAi Phenotypes and the Localization of a Protein::GUS Fusion Imply a Role for Medicago truncatula PIN Genes in Nodulation. J Plant Growth Regul 2006;25 (2):156-65.
  87. 87. Wasson AP, Pellerone FI. Silencing the flavonoid pathway in Medicago truncatula inhibits root nodule formation and prevents auxin transport regulation by rhizobia. Plant Cell 2006;18 (7):1617-29.
  88. 88. Colditz F, Niehaus K and Krajinski F. Silencing of PR-10-like proteins in Medicago truncatula results in an antagonistic induction of other PR proteins and in an increased tolerance upon infection with the oomycete Aphanomyces euteiches. Planta 2007;226 (1):57-71.
  89. 89. Kevei Zn, Lougnon G, Mergaert P, Horvàth GbV, Kereszt A, Jayaraman D, et al. 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula. Plant Cell 2007;19 (12):3974-89.
  90. 90. Messinese E, Mun JH, Yeun LH, Jayaraman D, Rougé P, Barre A, et al. A novel nuclear protein interacts with the symbiotic DMI3 calcium- and calmodulin-dependent protein kinase of Medicago truncatula. Mol Plant Microbe Interact 2007;20 (8):912-21.
  91. 91. Rosnoblet C, Aubry C, Leprince O, Vu BL, Rogniaux H and Buitink J. The regulatory gamma subunit SNF4b of the sucrose non-fermenting-related kinase complex is involved in longevity and stachyose accumulation during maturation of Medicago truncatula seeds. Plant J 2007;51 (1):47-59.
  92. 92. Wan X, Hontelez J, Lillo A, Guarnerio C, van de Peut D, Fedorova E, et al. Medicago truncatula ENOD40-1 and ENOD40-2 are both involved in nodule initiation and bacteroid development. J Exp Bot 2007;58 (8):2033-41.
  93. 93. Zhang J, Subramanian S, Zhang Y&Yu O. Flavone synthases from Medicago truncatula are flavanone-2-hydroxylases and are important for nodulation. Plant Physiol 2007;144 (2):741-51.
  94. 94. Floss DS, Hause B, Lange PR, Kùster H, Strack D and Walter M. Knock-down of the MEP pathway isogene 1-deoxy-D-xylulose 5-phosphate synthase 2 inhibits formation of arbuscular mycorrhiza-induced apocarotenoids, and abolishes normal expression of mycorrhiza-specific plant marker genes. Plant J 2008;56 (1):86-100.
  95. 95. Floss DS, Schliemann W, Schmidt JÃ, Strack D and Walter M. RNA interference-mediated repression of MtCCD1 in mycorrhizal roots of Medicago truncatula causes accumulation of C27 apocarotenoids, shedding light on the functional role of CCD1. Plant Physiol 2008;148 (3):1267-82.
  96. 96. Chen SK, Kurdyukov S, Kereszt A, Wang XD, Gresshoff PM. The association of homeobox gene expression with stem cell formation and morphogenesis in cultured Medicago truncatula. Planta 2009;230 (4):827-40.
  97. 97. Haney CH. Plant flotillins are required for infection by nitrogen-fixing bacteria. Proc Natl Acad Sci U S A 2010;107 (1):478-83.
  98. 98. Kuhn H, Kùster H&RN. Membrane steroid-binding protein 1 induced by a diffusible fungal signal is critical for mycorrhization in Medicago truncatula. New Phytol 2010;185 (3):716-33.
  99. 99. Kuppusamy KT, Ivashuta S, Bucciarelli B, Vance CP, Gantt JS. Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula. Plant Physiol 2009;151 (3):1155-66.
  100. 100. Peleg-Grossman S, Golani Y, Kaye Y, Melamed-Book N and Levine A. NPR1 protein regulates pathogenic and symbiotic interactions between Rhizobium and legumes and non-legumes. PLoS One 2009;4 (12):e8399.
  101. 101. Laporte P, Satiat-Jeunemaìtre B, Velasco I, Csorba T, Van de Velde W, Campalans A, et al. A novel RNA-binding peptide regulates the establishment of the Medicago truncatula-Sinorhizobium meliloti nitrogen-fixing symbiosis. Plant J 2010;62 (1):24-38.
  102. 102. Pii Y, Astegno A, Peroni E, Zaccardelli M, Pandolfini T and Crimi M. The Medicago truncatula N5 gene encoding a root-specific lipid transfer protein is required for the symbiotic interaction with Sinorhizobium meliloti. Mol Plant Microbe Interact 2009;22 (12):1577-87.
  103. 103. Pumplin N, Mondo SJ, Topp S, Starker CG, Gantt JS. Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis. Plant J 2010;61 (3):482-94.
  104. 104. Zdyb A, Demchenko K, Heumann J, Mrosk C, Grzeganek P, Gòbel C, et al. Jasmonate biosynthesis in legume and actinorhizal nodules. New Phytol 2011;189 (2):568-79.
  105. 105. Msehli SE, Lambert A, Baldacci-Cresp F, Hopkins J, Boncompagni E, Smiti SA, et al. Crucial role of (homo)glutathione in nitrogen fixation in Medicago truncatula nodules. New Phytol 2011;192 (2):496-506.
  106. 106. Gimeno-Gilles C, Gervais ML, Planchet E, Satour P, Limami AM. A stress-associated protein containing A20/AN1 zing-finger domains expressed in Medicago truncatula seeds. Plant Physiol Biochem 2011;49 (3):303-10.
  107. 107. Horchani F, Prèvot M, Boscari A, Evangelisti E, Meilhoc E, Bruand C, et al. Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules. Plant Physiol 2011;155 (2):1023-36.
  108. 108. Pauly N, Ferrari C, Andrio E, Marino D, Piardi Sp, Brouquisse R, et al. MtNOA1/RIF1 modulates Medicago truncatula-Sinorhizobium meliloti nodule development without affecting its nitric oxide content. J Exp Bot 2011;62 (3):939-48.
  109. 109. Riely BK, He H, Venkateshwaran M, Sarma B, Schraiber J, Anè J-M&CD. Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs. Plant J 2011;65 (2):230-43.
  110. 110. Kiirika LM, Bergmann HF, Schikowsky C, Wimmer D, Korte J, Schmitz U, et al. Silencing of the Rac1 GTPase MtROP9 in Medicago truncatula Stimulates Early Mycorrhizal and Oomycete Root Colonizations But Negatively Affects Rhizobial Infection. Plant Physiol 2012;159 (1):501-16.
  111. 111. de Zélicourt A, Diet A, Marion J, Laffont C, Ariel F, Moison Ml, et al. Dual involvement of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence. Plant J 2012;70 (2):220-30.
  112. 112. Senthil-Kumar M and Mysore K. New dimensions for VIGS in plant functional genomics. Trends Plant Sci 2011;16 (12):656-65.
  113. 113. Grǿnlund M, Constantin G, Piednoir E, Kovacev J, Johansen IE. Virus-induced gene silencing in Medicago truncatula and Lathyrus odorata. Virus Res 2008;135 (2):345-9.
  114. 114. Vàrallyay E, Lichner Z, Sáfrány J, Havelda Z, Salamon P, Bisztray G&Bn. Development of a virus induced gene silencing vector from a legumes infecting tobamovirus. Acta Biol Hung 2010;61 (4):457-69.
  115. 115. Ollivier J, Töwe S, Bannert A, Hai B, Kastl EM, Meyer A, et al. Nitrogen turnover in soil and global change. FEMS Microbiol Ecol 2011;78 (1):3-16.
  116. 116. Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, et al. Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 2008;320 (5878):889-92.
  117. 117. Escaray FJ, Menendez AB, Gárriz A, Pieckenstain FL, Estrella MJ, Castagno LN, et al. Ecological and agronomic importance of the plant genus Lotus. Its application in grassland sustainability and the amelioration of constrained and contaminated soils. Plant Sci 2012;182 :121-33.
  118. 118. Howieson JG. Nitrogen-fixing leguminous symbioses. %P ed. Springer; 2008.
  119. 119. Dixon RA. Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiol 2010;154 (2):453-7.
  120. 120. Ho L, Chen LH, Wang J, Zhao W, Talcott ST, Ono K, et al. Heterogeneity in red wine polyphenolic contents differentially influences Alzheimer's disease-type neuropathology and cognitive deterioration. J Alzheimers Dis 2009;16 (1):59-72.
  121. 121. Pasinetti GM, Zhao Z, Qin W, Ho L, Shrishailam Y, Macgrogan D, et al. Caloric intake and Alzheimer's disease. Experimental approaches and therapeutic implications. Interdiscip Top Gerontol 2007;35 :159-75.
  122. 122. Wang J, Ferruzzi MG, Ho L, Blount J, Janle EM, Gong B, et al. Brain-targeted proanthocyanidin metabolites for Alzheimer's disease treatment. J Neurosci 2012;32 (15):5144-50.
  123. 123. Seki A, Satoru S; Kiyoshi O; Masaharu M; Toshiyuki O; Hiroshi M; et al.. Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin. Plant Cell 2011, 23(6) 4112-4123.
  124. 124. Naoumkina MA, Modolo LV, Huhman DV, Urbanczyk-Wochniak E, Tang Y, Sumner LW. Genomic and coexpression analyses predict multiple genes involved in triterpene saponin biosynthesis in Medicago truncatula. Plant Cell 2010;22 (3):850-66.

Written By

Francesco Panara, Ornella Calderini and Andrea Porceddu

Submitted: November 16th, 2011 Published: September 12th, 2012