Madan K. Bhattacharyya

Genome sequence of the palaeopolyploid soybean

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme

We describe the cloning of the r (rugosus) locus of pea (Pisum sativum L.), which determines whether the seed is round or wrinkled. Wrinkled (rr) seeds lack one isoform of starch-branching enzyme (SBEI), present in round (RR or Rr) seeds. A major polymorphism in the SBEI gene between near-isogenic RR and rr lines shows 100% cosegregation with the r locus, establishing that the SBEI gene is at the r locus. An aberrant transcript for SBEI is produced in rr embryos. In rr lines the SBEI gene is interrupted by a 0.8 kb insertion that is very similar to the Ac/Ds family of transposable elements from maize. Failure to produce SBEI has complex metabolic consequences on starch, lipid, and protein biosynthesis in the seed.

One fungus, one name

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.

One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use.

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.

Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana

Phosphoinositide-specific phospholipase C cleaves the substrate phosphatidylinositol 4,5-bisphosphate and generates inositol 1,4,5-trisphosphate and 1,2-diacylglycerol, both of which are second messengers in the phosphoinositide signal transduction pathways operative in animal cells. Five PI-PLC isoforms, beta, gamma, delta, epsilon and zeta, have been identified in mammals. Plant PI-PLCs are structurally close to the mammalian PI-PLC-zeta isoform. The Arabidopsis genome contains nine AtPLC genes. Expression patterns of all nine genes in different organs and in response to various environmental stimuli were studied by applying a quantitative RT-PCR approach. Multiple members of the gene family were differentially expressed in Arabidopsis organs, suggesting putative roles for this enzyme in plant development, including tissue and organ differentiation. This study also shows that a majority of the AtPLC genes are induced in response to various environmental stimuli, including cold, salt, nutrients Murashige-Skoog salts, dehydration, and the plant hormone abscisic acid. Results of this and previous studies strongly suggest that transcriptional activation of the PI-PLC gene family is important for adapting plants to stress environments. Expression patterns and phylogenetic relationships indicates that AtPLC gene members probably evolved through multiple rounds of gene duplication events, with AtPLC4 and AtPLC5 and AtPLC8 and AtPLC9 being duplicated in tandem in recent times.

The soybean-Phytophthora resistance locus Rps1 -k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

BackgroundA series of Rps (resistance to Pytophthorasojae) genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean.ResultsHere the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region [1] was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus.ConclusionThese data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a heterochromatic region. Poor recombination frequencies combined with presence of two functional Rps genes at this locus has been providing stable Phytophthora resistance in soybean.

Systemic acquired resistance in soybean is regulated by two proteins, orthologous to Arabidopsis NPR1.

BackgroundSystemic acquired resistance (SAR) is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA) is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR) genes. Arabidopsis non-expressor of PR1 (NPR1) is a regulatory gene of the SA signal pathway [1–3]. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis.ResultsPathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA) or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i) PR-1 was induced following INA treatment and (ii) BGL2 following infection with Pseudomonas syringae pv. tomato (Pst), and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively.ConclusionComplementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential for oligomer-monomer transition of Arabidopsis NPR1, with Ser and Leu residues in GmNPR1-1 and GmNPR1-2, respectively, suggested that there may be differences between the regulatory mechanisms of GmNPR1 and Arabidopsis NPR proteins.

High Resolution Genetic and Physical Mapping of Molecular Markers Linked to the Phytophthora Resistance Gene Rps1-k in Soybean

The resistance of soybean to Phytophthora root and stem rot caused by Phytophthora sojae is conferred by a series of single-dominant Rps genes. We have applied random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analyses to isolate molecular markers linked to Rps1-k. Five RAPD markers were identified and mapped closely to one side of Rps1-k. AFLP analysis was carried out with near isogenic lines and bulks obtained from F3 families. Twenty-seven markers were identified. Nineteen of these were specific to the resistant parent. Five AFLP markers were amplified from the susceptible parent. One of these markers, TC1, mapped at 0.07 centimorgans (cM) from the Rps1 locus. Three AFLP markers were co-dominant, and one of these, CG1, mapped at a distance of 0.06 cM from the Rps1 locus on the opposite side of the rest of the markers. Two RAPD, 17 AFLP, and 14 restriction fragment length polymorphism (RFLP) markers originating from duplicated sequences were mapped within a 3-cM m...

HMG-CoA reductase gene families that differentially accumulate transcripts in potato tubers are developmentally expressed in floral tissues

We isolated two full-length cDNA clones encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) from potato (Solanum tuberosum) L. tubers. The clones, designated hmg2.2 and hmg3.3, are members of previously described gene subfamilies. In addition to being induced by arachidonic acid in tubers, hmg2.2 transcript accumulates developmentally in young flowers, and in mature sepals and ovaries, whereas transcript for hmg3.3 accumulates in mature petals and anthers. Our data suggest that members of specific HMGR-encoding gene sub-families might be involved in both defense responses and flower development. Accumulation of different HMGR transcripts could provide some control of isoprenoid biosynthesis by producing isoforms specific for classes of end-products produced in particular tissues.

The Fusarium virguliforme Toxin FvTox1 Causes Foliar Sudden Death Syndrome-Like Symptoms in Soybean

Fusarium virguliforme causes sudden death syndrome (SDS) in soybean. The pathogen has never been isolated from diseased foliar tissues; therefore, one or more toxins have been considered to cause foliar SDS development. Cell-free F. virguliforme culture filtrates containing a toxin causes foliar SDS in soybean. A low-molecular-weight protein of approximately 13.5 kDa (FvTox1), purified from F. virguliforme culture filtrates, produces foliar SDS-like symptoms in cut soybean seedlings. Anti-FvTox1 monoclonal antibodies raised against the purified FvTox1 were used in isolating the FvTox1 gene. In the presence of light, recombinant FvTox1 protein expressed in an insect cell line resulted in chlorosis and necrosis in soybean leaf disks that are typical foliar SDS symptoms. SDS-susceptible but not the SDS-resistant soybean lines were sensitive to the baculovirus-expressed toxin. The requirement of light for foliar SDS-like symptom development indicates that FvTox1 induces foliar SDS in soybean, most likely through production of free radicals by interrupting photosynthesis.