The genetic locus controlling supernodulation in soybean (Glycine max L.) co-segregates tightly with a cloned molecular marker

Evolutionary duplication of lipo-oligochitin-like receptor genes in soybean differentiates their function in cell division and cell invasion

Gene duplication in evolution has long been viewed as a mechanism for functional divergence. We recently cloned two related lipo-oligo-chitin receptor genes (GmNFR1α and GmNFR1β) in Glycine max(soybean) that allowed the distinction of two nodulation factor (NF) responses during early legume nodule ontogeny, namely invasion of the root hair and concomitant cortical cell divisions. Root-controlled GmNFR1αmutants nod49 and rj1 failed to form curled root hairs, infection threads and nodules but develop subepidermal cortical cell divisions (CCD) and mycorrhizal associations. In contrast GmNFR1β mutant PI437.654 had full symbiotic abilities. However, GmNFR1α mutants formed normal nodules at reduced frequency when inoculated with high Bradyrhizobium titers. The mutation was complemented in Agrobacterium rhizogenes K599 transformed roots using both CaMV 35S and the native GmNFR1promoters. GmNFR1α may encode a high affinity NF receptor responsible for the entire nodulation cascade while GmNFR1β with lower affinity to NF suffices to induce cell divisions but not early infection events.

Live-cell imaging reveals periarbuscular membrane domains and organelle location in Medicago truncatula roots during arbuscular mycorrhizal symbiosis

In the arbuscular mycorrhizal symbiosis, the fungal symbiont colonizes root cortical cells, where it establishes differentiated hyphae called arbuscules. As each arbuscule develops, the cortical cell undergoes a transient reorganization and envelops the arbuscule in a novel symbiosis-specific membrane, called the periarbuscular membrane. The periarbuscular membrane, which is continuous with the plant plasma membrane of the cortical cell, is a key interface in the symbiosis; however, relatively little is known of its composition or the mechanisms of its development. Here, we used fluorescent protein fusions to obtain both spatial and temporal information about the protein composition of the periarbuscular membrane. The data indicate that the periarbuscular membrane is composed of at least two distinct domains, an "arbuscule branch domain" that contains the symbiosis-specific phosphate transporter, MtPT4, and an "arbuscule trunk domain" that contains MtBcp1. This suggests a developmental transition from plasma membrane to periarbuscular membrane, with biogenesis of a novel membrane domain associated with the repeated dichotomous branching of the hyphae. Additionally, we took advantage of available organelle-specific fluorescent marker proteins to further evaluate cells during arbuscule development and degeneration. The three-dimensional data provide new insights into relocation of Golgi and peroxisomes and also illustrate that cells with arbuscules can retain a large continuous vacuolar system throughout development.

SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean

Supernodulation in soybean (Glycine max L. Merr.) is an important source of nitrogen supply to subterranean ecological systems. Single nucleotide-amplified polymorphism (SNAP) markers for supernodulation should allow rapid screening of the trait in early growth stages, without the need for inoculation and phenotyping. The gene GmNARK (Glycine max nodule autoregulation receptor kinase), controlling autoregulation of nodulation, was found to have a single nucleotide polymorphism (SNP) between the wild-type cultivar Sinpaldalkong 2 and its supernodulating mutant, SS2-2. Transversion of A to T at the 959-bp position of the GmNARK sequence results in a change of lysine (AAG) to a stop codon (TAG), thus terminating its translation in SS2-2. Based on the identified SNP in GmNARK, five primer pairs specific to each allele were designed using the WebSnaper program to develop a SNAP marker for supernodulation. One A-specific primer pair produced a band present in only Sinpaldalkong 2, while two T-specific pairs showed a band in only SS2-2. Both complementary PCRs, using each allele-specific primer pair were performed to genotype supernodulation against F2 progeny of Sinpaldalkong 2 x SS2-2. Among 28 individuals with the normal phenotype, eight individuals having only the A-allele-specific band were homozygous and normal, while 20 individuals were found to be heterozygous at the SNP having both A and T bands. Twelve supernodulating individuals showed only the band specific to the T allele. This SNAP marker for supernodulation could easily be analyzed through simple PCR and agarose gel electrophoresis. Therefore, use of this SNAP marker might be faster, cheaper, and more reproducible than using other genotyping methods, such as a cleaved amplified polymorphic sequence marker, which demand of restriction enzymes.

Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase

Proliferation of legume nodule primordia is controlled by shoot-root signaling known as autoregulation of nodulation (AON). Mutants defective in AON show supernodulation and increased numbers of lateral roots. Here, we demonstrate that AON in soybean is controlled by the receptor-like protein kinase GmNARK (Glycine max nodule autoregulation receptor kinase), similar to Arabidopsis CLAVATA1 (CLV1). Whereas CLV1 functions in a protein complex controlling stem cell proliferation by short-distance signaling in shoot apices, GmNARK expression in the leaf has a major role in long-distance communication with nodule and lateral root primordia.

Genomics and plant breeding

Much of our most basic understanding of genetics has its roots in plant genetics and crop breeding. The study of plants has led to important insights into highly conserved biological process and a wealth of knowledge about development. Agriculture is now well positioned to take its share benefit from genomics. The primary sequences of most plant genes will be determined over the next few years. Informatics and functional genomics will help identify those genes that can be best utilized to crop production and quality through genetic engineering and plant breeding. Recent developments in plant genomics are reviewed.

Classical and molecular genetics of the model legume Lotus japonicus

The model legume Lotus japonicus was demonstrated to be amenable to classical and molecular genetic analysis, providing the basis for the genetic dissection of the plant processes underlying nodulation and nitrogen fixation. We have developed an efficient method for the sexual hybridization of L. japonicus and obtained F1 progeny derived from a cross of L. japonicus B-129-S9 Gifu x B-581 Funakura. Over half of the cross-pollinations resulted in fertile hybrid seed, which were confirmed morphologically and by single arbitrary primer DNA amplification polymorphisms using the DAF technique. Molecular and morphological markers segregated in true Mendelian fashion in a F2 population of 100 plants. Several DAF loci were linked using the MAPMAKER software to create the first molecular linkage groups of this model legume. The mapping population was advanced to generate a set of immortal recombinant inbred lines (F6; RILs), useful for sharing plant material fixed genetically at most genomic regions. Morphological loci for waved stem shape (Ssh), dark leaf color (Lco), and short flowering period (Fpe) were inherited as single dominant Mendelian loci. DAF markers were dominant and were detected between Gifu and Funakura at about one per primer, suggesting that the parents are closely related. One polymorphism (270G generated by single octomer primer 8.6m) was linked to a morphological locus controlling leaf coloration. The results demonstrate that (i) Lotus japonicus is amenable to diploid genetic analysis, (ii) morphological and molecular markers segregate in true diploid fashion, (iii) molecular polymorphisms can be obtained at a reasonable frequency between the related Gifu and Funakura lines, and iv) the possibility exists for map-based cloning, marker assisted selection and mapping of symbiotic mutations through a genetic and molecular map.

Inheritance of polymorphic markers generated by DNA amplification fingerprinting and their use as genetic markers in soybean

DNA amplification fingerprinting (DAF) using a high primer-to-template ratio and single, very short arbitrary primers, was used to generate amplified fragment length polymorphic markers (AFLP) in soybean (Glycine max (L.) Merr.). The inheritance of AFLPs was studied using a cross between the ancestral Glycine soja PI468.397 and Glycine max (L.) Merr. line nts382, F1 and F2 progeny. The amplification reaction was carried out with soybean genomic DNA and 8 base long oligonucleotide primers. Silver-stained 5% polyacrylamide gels containing 7 M urea detected from 11 to 28 DAF products with primers of varying GC content (ranging from 50 to 100% GC). Depending on their intensity, AFLPs were classified into three classes. DAF profiles were reproducible for different DNA extractions and gels. Forty AFLPs were detected by 26 primers when comparing G. soja and G. max. Most AFLPs were inherited as dominant Mendelian markers in F1 and F2 populations. However, abnormal inheritance occurred with about 25% of polymorphisms. One marker was inherited as a maternal marker, presumably originating from organelle DNA while another showed apparent paternal inheritance. To confirm the nuclear origin and utility of dominant Mendelian markers, three DAF polymorphisms were mapped using a F11 mapping population of recombinant inbred lines from soybean cultivars Minsoy x Noir 1. The study showed that DAF-generated polymorphic markers occur frequently and reliably, that they are inherited as Mendelian dominant loci and that they can be used in genome mapping.

DNA amplification fingerprinting using arbitrary mini-hairpin oligonucleotide primers

The enzymatic amplification of DNA directed by very short oligonucleotides of arbitrary sequence produces complex DNA profiles useful for genome analysis and identity testing. Mini-hairpins harboring a "core" arbitrary sequence at the 3' terminus primed the amplification of a wide range of templates ranging from plasmid DNA to plant and animal genomes. Primer core regions of only 3 nucleotides produced complex fingerprints, but the hairpin sequence also influenced the amplification reaction. Oligonucleotide substitution with degenerate bases tailored the complexity of fingerprint patterns. Simulation studies of the amplification of plasmids pUC18 and pBR322 using primers with short arbitrary cores allowed assignment of amplification products to expected regions and revealed physical interaction between annealing sites during amplification of first-round products. Mini-hairpin primers can increase detection of polymorphic DNA, and be used to study subgenomic fragments like yeast artificial chromosomes (YACs), cloned DNA and PCR products.

Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean

Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2-3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.

Physical mapping of a region in the soybean (Glycine max) genome containing duplicated sequences

Pulsed-field gel electrophoresis (PFGE) was used to study a cluster of molecular markers in the soybean genome. There were 550 kb per centimorgan (cM) in the cluster, which is close to the calculated average for the whole genome. The analysis was complicated by the presence of duplicated sequences, and some ambiguities arising from this were resolved by using second-dimension conventional electrophoresis to relate physical maps to the RFLP map of soybean. The results show that there is a high degree of conservation of 'rare cutter' sites between homoeologous regions. Finally, PFGE can confirm physical linkage of monomorphic copies of markers, which can aid in the study and comparison of homoeologous regions that are invisible to RFLP analysis.