Photosynthesis,Metabolite Composition and Anatomical Structure of Oryza sativa and Two Wild Relatives,O.grandiglumis and O.alta

Photosynthesis, enzyme activities and metabolite pools associated with primary carbon metabolism in leaves were studied in O. grandiglumis and O. alta （wild relatives of rice which produce high biomass） versus O. sativa （a japonica cultivar and a indica-japonica hybrid） to assess their potential for identifying traits which might be utilized to enhance rice productivity. The wild relatives had higher rates of photosynthesis on a fresh weight basis, and higher water use efficiency than the O. sativa lines. There were no striking differences in activities of a number of key enzymes in carbon and nitrogen metabolism between the wild relatives and cultivated rice lines. Along with higher rates of photosynthesis on a fresh weight basis, the leaves of the two wild species had higher nitrate content, higher levels of starch, glucose and fructose, and higher levels of organic acids （malate, succinate and acetate）, compared to the O. sativa lines. The results suggested that O. grandiglumis and O. alta have differences in physiology and primary metabolism which might be exploited to improve growth and productivity of cultivated rice.

Association Analysis of the Amino Acid Contents in Rice

The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.

Development of a Core Set from a Large Rice Collection using a Modified Heuristic Algorithm to Retain Maximum Diversity

A new heuristic approach was undertaken for the establishment of a core set for the diversity research of rice. As a result, 107 entries were selected from the 10 368 characterized accessions. The core set derived using this new approach provided a good representation of the characterized accessions present in the entire collection. No significant differences for the mean, range, standard deviation and coefficient of variation of each trait were observed between the core and existing collections. We also compared the diversity of core sets established using this Heuristic Core Collection （HCC） approach with those of core sets established using the conventional clustering methods. This modified heuristic algorithm can also be used to select genotype data with allelic richness and reduced redundancy, and to facilitate management and use of large collections of plant genetic resources in a more efficient way.

Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.