Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools that reliably access genes with orthology to the genomes of well-characterized reference species. Here we report an efficient platform for designing cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM designer is enhanced by graphical displays of query results, which we describe as “circular viewer” and “search-within-results” functions. CSGM platform provides a virtual PCR representation, called eHT-PCR, that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.

To tolerate environmentally adverse conditions such as cold, drought, and salinity, plants often synthesize and accumulate proline in cells as compatible osmolytes. δ1 -Pyrroline-5-carboxylate synthetase(P5CS) catalyzes the rate-limiting step of proline biosynthesis from glutamate. Two complete genes, MtP5CS1 and MtP5CS2, were isolated from the model legume Medicago truncatula by cDNA cloning and bacterial artificial chromosome library screening. Nucleotide sequence analysis showed that both genes consisted of 20 exons and 19 introns. Alignment of the predicted amino acid sequences revealed high similarities with P5CS proteins from other plant species. The two MtP5CS genes were expressed in response to high salt and low temperature treatments. Semi-quantitative reverse transcription-polymerase chain reaction showed that MtP5CS1 was expressed earlier than MtP5CS2, indicating differential regulation of the two genes. To evaluate the reverse genetic effects of nucleotide changes on MtP5CS function, a Targeting Induced Local Lesions in Genomes approach was taken. Three mutants each were isolated for MtP5CS1 and MtP5CS2, of which a P5CS2 nonsense mutant carrying a codon change from arginine to stop was expected to bring translation to premature termination. These provide a valuable genetic resource with which to determine the function of the P5CS genes in environmental stress responses of legume crops.

Soil moisture condition is an important limiting factor in growth and yield in rice culture. The purpose of this study was to compare the influence on the growth, yield and Quality of rice subjected to soil moisture stress (SMS) at different growth stages. Ajaponica rice cultivar, Dongjinbyeo, was cultured under flooded conditions in a plastic container filled with silty loam soil. The container was subjected to SMS until the initial wilting point (IWP) coincided with about 10% in soil moisture content and about-200 kPa in soil matric potential, and was then irrigated again, at 6 and 5 of main growth stage in 1996 and 1997, respectively. At maturity, the plant height, tiller number, leaf area and top dry weight were decreased more in SMS treatments at the early stage than the late stage. The averaged yield index of SMS to control in both years was lowest at meiosis (62.5%), which primarily resulted from lower percent ripened grain and 1,000 grain weight, and second＇ reduced the spikelet number per panicle and panicle number per hill, and followed at tillering stage (68.5%) which resulted from the lower production in tiller number and top dry matter during and after SMS treatment. The percent-age of read rice in SMS plants varied with the treatment stage as order of lower at meiosis (44.0%), heading (53.9%), panicle initiation (70.1%), tillering (72.1%), ripening (75.8%) and 5 days after transplanting (DAT) (79.0%). Protein content in brown rice was slightly larger in SMS at late growth stage than the control, while the contents of fat and ash differed very little between SMS and control. Contents of Mg and K and Mg/K in brown rice with SMS were lower at some treatment stages such as at ripening or panicle initiation.

Spikelet and vascular bundle development in rice panicles is considered to be the important elements in determining the genotype's yield capacity and translocation ability of assimilates into grains, respectively. This study was conducted to clarify the varietal differences of the spikelet and vascular bundle formations among three rice cultivars; Iksan 435 (japonica), Dongjinbyeo (japonica) and Namcheonbyeo (Tongl-type). Iksan 435 had more primary rachis branches (PRBs), secondary rachis branches (SRBs) and spikelets per panicle than Dongjinbyeo, but less than Namcheonbyeo. Among three cultivars, Namcheonbyeo showed the highest spikelet number per panicle which were differentiated SRBs mainly on PRBs of lower rachis nodes. And Namchenbyeo showed the highest number of large vascular bundle (LVB) as well as small vascular bundle (SVB) and it displayed the largest diameter of LVB. Between the two japonica cultivars, the numbers of LVBs end SVBs were significantly higher in Iksan 435 than those in Dongjinbyeo. The PRBs to LVBs ratio of Namcheonbyeo was twice as large as those of Dongjinbyeo and Iksan 435. These results indicate that the newly bred cultivar, Iksan 435, has improved yield capacity by increasing the number of especially rachis branches and spikelets formation as well as 1,000 grain weight, compared to other former japonicas