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Abstract: To facilitate the wider use of genetic resources including newly collected cultivated and wild azuki bean germplasm, the genetic diversity of the azuki bean complex, based on 13 simple [...]

We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of ~50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.

Rhizobia can infect roots of host legume plants and induce new organs called nodules, in which they fix atmospheric nitrogen. Infection generally starts with root hair curling, then proceeds inside newly formed, intracellular tubular structures called infection threads. A successful symbiotic interaction relies on infection threads advancing rapidly at their tips by polar growth through successive cell layers of the root toward developing nodule primordia. To identify a plant component that controls this tip growth process, we characterized a symbiotic mutant of Medicago truncatula, called rpg for rhizobium-directed polar growth. In this mutant, nitrogen-fixing nodules were rarely formed due to abnormally thick and slowly progressing infection threads. Root hair curling was also abnormal, indicating that the RPG gene fulfils an essential function in the process whereby rhizobia manage to dominate the process of induced tip growth for root hair infection. Map-based cloning of RPG revealed a member of a previously unknown plant-specific gene family encoding putative Iong coiled-coil proteins we have called RRPs (RPG-related proteins) and characterized by an 'RRP domain' specific to this family. RPG expression was strongly associated with rhizobial infection, and the RPG protein showed a nuclear localization, indicating that this symbiotic gene constitutes an important component of symbiotic signaling. genetics | symbiosis | coiled-coil

Abstract: Convicilins, a set of seed storage proteins, differ from vicilins, a related group of seed storage proteins, mainly because of the presence of the N-terminal extension, an additional sequence [...]

Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is considered a major constraint in the production of common bean (Phaseolus vulgaris L.). This study aimed to evaluate, in a backcross plant-breeding program, the efficiency of selecting plants resistant to anthracnose using marker-assisted selection (MAS) for two resistance genes, Co-5 and Co-42 derived from the resistance source G2333 based on the linked PCR based markers SAB3 and SAS13. The amplification of both markers was compared using DNAs extracted with two techniques, alkaline extraction, which is a fast, and inexpensive method for high throughput screening; versus a proteinase K based miniprep extraction, which is more time consuming but provides more DNA. To further evaluate the effectiveness of the markers in selecting for resistance, we compared the marker genotypes and observed phenotypes for 266 plants from eight backcross families inoculated with a field isolate of anthracnose. The Co-5 gene and SAB3 proved to be useful and the markers associated with Co-5 and Co-42 could be pyramided to give added levels of anthracnose resistance.

Genetic differences between azuki bean (Vigna angularis var. angularis) and its presumed wild ancestor (V. angularis var. nipponensis) were resolved into QTL for traits associated with adaptation to their respective distinct habits. A genetic linkage map constructed using progenies from a cross between Japanese cultivated and wild azuki beans covers 92.8% of the standard azuki bean linkage map. A reciprocal translocation between cultivated and wild azuki bean parents was identified on the basis of the linkage map having a pseudolinkage group and clustering of seed productivity-related QTL with large effect near the presumed breakpoints. In total, 162 QTL were identified for 46 domestication-related traits. Domestication of azuki bean has involved a trade-off between seed number and seed size: fewer but longer pods and fewer but larger seeds on plants with shorter stature in cultivated azuki bean being at the expense of overall seed yield. Genes found related to germination and flowering rime in cultivated azuki bean may confer a selective advantage to the hybrid derivatives under some ecological conditions and may explain why azuki bean has evolved as a crop complex in Japan.

Sinorhizobium meliloti forms symbiotic, nitrogen-fixing nodules on the roots of Medicago truncatula. The bacteria invade and colonize the roots through structures called infection threads. S. meliloti unable to produce the exopolysaccharide succinoglycan are unable to establish a symbiosis because they are defective in initiating the production of infection threads and in invading the plant. Here, we use microarrays representing 16,000 M. truncatula genes to compare the differential transcriptional responses of this host plant to wild-type and succinoglycan-deficient S. meliloti at the early time point of 3 days postinoculation. This report describes an early divergence in global plant gene expression responses caused by a rhizobial defect in succinoglycan production, rather than in Nod factor production. The microarray data show that M. truncatula inoculated with wild-type, succinoglycan-producing S. meliloti more strongly express genes encoding translation components, protein degradation machinery, and some nodulins than plants inoculated with succinoglycan-deficient bacteria. This finding is consistent with wild-type-inoculated plants having received a signal, distinct from the well characterized Nod factor, to alter their metabolic activity and prepare for invasion. In contrast, M. truncatula inoculated with succinoglycan-deficient S. meliloti more strongly express an unexpectedly large number of genes in two categories: plant defense responses and unknown functions. One model consistent with our results is that appropriate symbiotically active exopolysaccharides act as signals to plant hosts to initiate infection thread formation and that, in the absence of this signal, plants terminate the infection process, perhaps via a defense response. nitrogen fixation | nodule | succinoglycan | rnicroarray | legume

The tribe Genisteae includes genera of great ecological importance in Mediterranean countries because they are dominant elements of many plant communities. Genetic variation and diversification patterns in Stauracanthus (Genisteae) provide information relevant for the study of the processes of diversification in relation to the environmental history of the western Mediterranean. Nineteen populations of S. boivinii and S. genistoides were assessed by 11 chloroplast microsatellite markers, revealing 44 haplotypes. Both species had different haplotypes and contrasting patterns of karyological, morphological, and genetic variation. In the minimum spanning tree of the haplotypes, AMOVA analysis, and nested clade analysis, S. boivinii had high levels of differentiation and restricted gene flow among populations. Allopatric differentiation occurred between the Moroccan and Iberian populations of S. genistoides, although S. genistoides subsp, spectabilis and subsp. vicentinus had high levels of differentiation among populations ([F.sub.ST]), whereas S. genistoides subsp. genistoides had a low FST. Genetic patterns are discussed in relation to the Messinian salinity crisis (MSC): hard conditions drove plants to refuge habitats along the Atlantic coast and higher altitude areas in the Moroccan mountains (S. genistoides subsp. spectabilis and S. boivinii). After the MSC, S. boivinii underwent polyploidization and expansion, whereas S. genistoides expanded and continued diversifying into S. genistoides subspp. genistoides and vicentinus. Key words: chloroplast microsatellites; cpSSRs; Leguminosae; Messinian salinity crisis; northern Morocco; phylogeography; southern Spain; Stauracanthus.

Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling early Nod factor perception and signaling in the Fabaceae Medicago truncatula to understand the selective forces shaping the evolution of these genes. We used 30 M. truncatula genotypes sampled in a genetically homogeneous region of the species distribution range. We first sequenced 24 independent loci and detected a genomewide departure from the hypothesis of neutrality and demographic equilibrium that suggests a population expansion. These data were used to estimate parameters of a simple demographic model incorporating population expansion. The selective neutrality of genes controlling Nod factor perception was then examined using a combination of two complementary neutrality tests, Tajima's D and Fay and Wu's standardized H. The joint distribution of D and H expected under neutrality was obtained under the fitted population expansion model. Only the gene DMI1, which is expected to regulate the downstream signal, shows a pattern consistent with a putative selective event. In contrast, the receptor-encoding genes NFP and NORK show no significant signatures of selection. Among the genes that we analyzed, only DMI1 should be viewed as a candidate for adaptation in the recent history of M. truncatula.

Cell suspensions of the model legume Medicago truncatula accumulated the isoflavonoid phytoalexin medicarpin in response to yeast elicitor or methyl jasmonate (MJ), accompanied by decreased levels of isoflavone glycosides in MJ-treated cells. DNA microarray analysis revealed rapid, massive induction of early (iso)flavonoid pathway gene transcripts in response to yeast elicitor, but not MJ, and differential induction by the two elicitors of sets of genes encoding transcription factors, ABC transporters, and [beta]-glucosidases. In contrast, both elicitors induced genes encoding enzymes for conversion of the isoflavone formononetin to medicarpin. Four MJ-induced [beta]-glucosidases were expressed as recombinant enzymes in yeast, and three were active with isoflavone glucosides. The most highly induced [beta]-glucosidase was nuclear localized and preferred flavones to isoflavones. The results indicate that the genetic and biochemical mechanisms underlying accumulation of medicarpin differ depending on the nature of the stimulus and suggest a role for MJ as a signal for rapid hydrolysis of preformed, conjugated intermediates for antimicrobial biosynthesis during wound responses. glucosidase | methyl jasmonate | phytoanticipin | cell culture | elicitation

Backyard gardens, dump heaps, and kitchen middens are thought to have provided important venues for early crop domestication via generation of hybrids between otherwise isolated plant species. However, this process has rarely been demonstrated empirically. For the majority of polyploid crops, it remains uncertain to what extent hybridization and polyploidization preceded domestication or were precipitated by human activities. Using archaeological, ethnobotanical, geographical, and genetic data, we investigate the extent and significance of predomestication cultivation, backyard sympatry, and spontaneous hybridization for the Mimosoid legume tree Leucaena, which is used as a food crop throughout south-central Mexico. We show that predomestication cultivation was widespread, involved numerous independent transitions from the wild to cultivation, and resulted in extensive artificial sympatry of 2-6 species locally and 13 species in total. Using chloroplast and rapidly evolving nuclear-encoded DNA sequences, we demonstrate that hybridization in Leucaena has been extensive and complex, spawning a diverse set of novel hybrids as a result of juxtaposition of species in cultivation. The scale and complexity of hybridization in Leucaena is significantly greater than that documented for any other Mexican plant domesticates so far. However, there are striking parallels between Leucaena and the other major Mexican perennial domesticates Agave and Opuntia, which show very similar domestication via backyard hybridization pathways. Our results suggest that backyard hybridization has played a central role in Mesoamerican crop domestication and demonstrate that the simple step of bringing species together in cultivation can provide a potent trigger for domestication. domestication | Leguminosae | Leucaena | Mesoamerica

Abstract: Legumes are members of the family Fabaceae or Leguminosae and include economically important grain legumes, oilseed crops, forage crops, shrubs, and tropical or subtropical trees. Legumes are a rich [...]

Hedysarum boreale Nutt. is a perennial legume native to western North America, with robust foliage in the late spring season. Due to its wide native range, forage value, and [N.sub.2] fixation, H. boreale is of interest for rangeland revegetation and production. Seed cost is a major obstacle for utilization of H. boreale, primarily due to seed shattering and unreliable seed production, such that a need for improved germplasm exists. This study characterized the genetic relationships of H. boreale accessions, so plant breeders and geneticists will have the information necessary to maintain a broad genetic base within selected germplasm populations. Amplified fragment length polymorphism markers were used on 17 available accessions from Utah, Idaho, Colorado, and Alaska. Seventy percent of the total genetic variation was found within all 17 accessions, yet each accession showed significant isolation by distance. Genetic diversity within accessions was greatest in sites located in eastern Utah. The sole cultivar, Timp, had slightly greater genetic diversity than a collection made from the same site approximately 20 yr later. Two groups of metapopulations were identified in Utah, separated longitudinally approximately along the Wasatch mountain range.

Abstract: Sequence data for 2 non-coding regions of the chalcone isomerase gene were analyzed to study the genetic architecture of common bean (Phaseolus vulgaris L.). One region corresponded to the [...]

Interseeding nontraditional, cool-season legumes into bermudagrass [Cynodon dactylon (L.) Pers.] paddocks was evaluated as an approach to increasing the quality and duration of forage production and replacing a portion of the N fertilizer required in the southern Great Plains. We compared the effects of interseeding either grass pea (Lathyrus sativa L. 'AC-Greenfix') or lentil (Lens culinaris Med. 'Indianhead') with N fertilizer rates of 0, 45, or 90 kg [ha.sup.-1] N. All plots received 60 kg [P.sub.2][O.sub.5] [ha.sup.-1] in early March. The legume and fertilizer treatments were imposed in mid-March during 2001, 2002, and 2003. Forage samples were clipped from 0.25 [m.sup.-2] quadrats on five sampling dates between I May and 15 July each year. Yield, N concentration, species composition, and in vitro digestible dry matter (IVDDM) were determined. Year, sampling date, and treatment showed significant (P < 0.05) effects, as did the two-way interactions between all three factors. Total end-of-season standing dry matter of bermudagrass and grass pea was 5550 [+ or -] 423 (SEM) kg [ha.sup.-1], which was similar to biomass production with 45 kg [ha.sup.-1] N (5305 [+ or -] 570 kg [ha.sup.-1]) and less than that produced with 90 kg [ha.sup.-1] N (7785 [+ or -] 725 kg [ha.sup.-1]). Forage N and IVDDM concentrations for the grass pea treatment were 34 and 6% higher than for bermudagrass, but N and IVDDM concentrations of the forage mixture were intermediate between the higher N rates. Although additional studies are needed to optimize management for the interseeded legumes, we conclude that this practice can improve the quality and duration of bermudagrass forage production in this region.

The common bean (Phaseolus vulgaris L.) was introduced from the Americas into the Iberian Peninsula approximately 500 yr ago. Considerable genetic variation for morphological traits, allozymes, phaseolin protein, and reaction to bacterial, fungal, and viral diseases exist in the germplasm. Our objective was to identify novel genetic variation in an collection from the Iberian Peninsula. Three hundred forty-seven accessions were characterized for seven morphological traits, phaseulin protein, and eight allozymes at the Mision Biologica de Galicia, Pontevedra, Spain, between 1998 and 2005. All 347 accessions were cultivated common bean of which 102 were typical Andean and 52 were Middle American, corresponding to the two major gene pools. Nine groups could be identified among the remaining 193 accessions. Twentyeight accessions with the Middle American phaseolin formed four groups: 13 large (41-55 g 100 seed [weight.sup.-1]), five very large (56-70 g 100 seed [weight.sup.-1]), two extra-large (>70 g 100 seed [weight.sup.-1]), and eight inter-gene pool recombinants. The latter had one or more morphological and allozyme traits of the Andean gene pool. Similarly, 165 accessions with the Andean phaseolin formed five groups: 19 extra-large, 30 very large, 80 medium (25-40 g 100 seed [weight.sup.-1]), 10 small (

Abstract: A PCR approach with degenerate primers designed from conserved NBS-LRR (nucleotide binding site--leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from [...]

Abstract: The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted [...]

Abstract: The genus Desmodium contains ca. 450 species, distributed in Eastern Asia, Mexico, and Brazil, with 40 endemic species in Mexico, including Desmodium sumichrastii (Schinder) Standley. Randomly amplified polymorphic DNA [...]

Most land plants can form a root symbiosis with arbuscular mycorrhizal (AM) fungi for assimilation of inorganic phosphate from the soil. In contrast, the nitrogen-fixing root nodule symbiosis is almost completely restricted to the legumes. The Finding that the two symbioses share common signaling components in legumes suggests that the evolutionarily younger nitrogen-fixing symbiosis has recruited functions from the more ancient AM symbiosis. The recent advances in cloning of the genes required for nodulation and AM symbioses from the two model legumes, Medicago truncatula and Lotus japonicus, provide a unique opportunity to address biological questions pertaining to the evolution of root symbioses in plants. Here, we report that nearly all cloned legume genes required for nodulation and AM symbioses have their putative orthologs in nonlegumes. The orthologous relationship can be clearly defined on the basis of both sequence similarity and microsyntenic relationship. The results presented here serve as a prelude to the comparative analysis of orthologous gene function between legumes and nonlegumes and facilitate our understanding of how gene functions and signaling pathways have evolved to generate species--or family-specific phenotypes.

Nuclear-cytoplasmic partitioning and traffic between cytoplasmic and nuclear compartments are fundamental processes in eukaryotic cells. Nuclear pore complexes mediate transport of proteins, RNAs and ribonucleoprotein particles in and out of the nucleus. Here we present positional cloning of a plant nucleoporin gene, Nup133, essential for a symbiotic signal transduction pathway shared by Rhizobium bacteria and mycorrhizal fungi. Mutation of Nup133 results in a temperature sensitive nodulation deficient phenotype and absence of mycorrhizal colonization. Root nodules developing with reduced frequency at permissive temperatures are ineffective and electron microscopy show that Rhizobium bacteria are not released from infection threads. Measurement of ion fluxes using a calcium-sensitive dye show that Nup133 is required for the [Ca.sup.2+] spiking normally detectable within minutes after application of purified rhizobial Nod-factor signal molecules to root hairs. Localization of NUP133 in the nuclear envelope of root cells and root hair cells shown with enhanced yellow fluorescent protein fusion proteins suggests a novel role for NUP133 nucleoporins in a rapid nuclear-cytoplasmic communication after host-plant recognition of symbiotic microbes. Our results identify a component of an intriguing signal process requiring interaction at the cell plasma membrane and at intracellular nuclear and plastid organelle-membranes to induce a second messenger. legume symbiosis | nucleoporin | nuclear pore | plant-microbe interaction

Genetic variation in 27 populations of Ulex species from southern Spain and northern Morocco (Betic-Rif arc) was assessed using 11 chloroplast microsatellite (cpSSR) markers, which revealed 47 different haplotypes. These nonrecombinant, haploid markers allow measurement of genetic variation in closely related species of Ulex where molecular phylogenetic analyses have not provided a clear view of interspecific relationships. Discriminant analysis indicates that the haplotypes are useful to differentiate among species, and analysis of molecular variance (AMOVA) shows high levels of differentiation among populations. The minimum spanning tree (MST), that represents the connections between the haplotypes, suggests that the eastern Rifean U. africanus haplotypes are more genetically related than those from southern Spain. The latter may have lost genetic diversity while colonizing new habitats, eventually differentiating entiating into U. baeticus and U. scaber. Hybridization between these populations, followed by polyploidization, may have originated the tetraploids (U. congestus and U. borgiae) that colonized new habitats associated with acidic rocks. Separate groupings of U. scaber populations may indicate multiple origins from different stocks. Diversification in this group of Ulex species could be related to the opening of the Alboran Sea by Middle Miocene, when the populations from Morocco and Spain became isolated ,torn each other. Key words: chloroplast microsatellitcs; cpSSRs; genetic variation; Leguminosae; northern Morocco; southern Spain; Ulex.