Objective of this study was to investigate the residual levels of heavy metals in rice contract farming complex for exporting to China. Paddy soil, irrigation water and rice grain were taken from 20 fie1ds located in Icheon city, Cheorwon-gun, Cheongju city, Seocheon-gun, Gunsan city and Haenamgun. The elements of samples were analyzed using ion chromatography, ICP-OES, and ICP-MS after acid digestion. The arsenic (As) contents of paddy soil were ranged from 2.9 to 18.2 mg/kg, which were lower than 25 mg/kg as concern level of environmental pollution in Korea. Cadmium (Cd) was below the limit of quantitation (0.006 mg/kg) in all samples. The highest contents of copper (Cu) was detected to be 25.6 mg/kg in Seocheon-gun sample, but it was below 1/10 fold of the threshold levels 250 mg/kg for soil pollution. Also, the average contents of nikel (Ni), lead (Pb), zinc (Zn), and hexavalent chrome (Cr6+) were found to be lower than the criterion of soil pollution concern, and it was considered to be safe. The residual levels of arsenic in agricultural waters were relatively high, up to 24.3 ug/L in river water, but was detected as 1~2 ug/L level in the ground water. These levels are lower than the water quality standard, 0.05 mg/kg of agricultural water. The concentrations of mercury (Hg) and total chromium (Cr) in the white rice and brown rice were less than the limit of quantitation, and the levels of cadmium in the range of 0.004 to 0.068 mg/kg were less than safety criteria 0.2 mg/kg in Korea and China. In addition, the contents of lead (Pb) in white rice ranged from 0.002 to 0.136 mg/kg, which was safe to be 0.2 mg/kg for Korean white rice and 0.2 mg/kg for China brown rice. As a whole, the residual levels of heavy metals such as arsenic in rice was safely maintained as 1/10 to 1/20 of the residual limits of Korea and China. In conclusion, the heavy metals levels should not be worried in rice contract farming complex for exporting to China.

Iron is an essential mineral found in every cell of the human body to make the oxygen-carrying proteins hemoglobin and myoglobin. More than 2 billion people face Fe deficiency. Rice can be a potentially valuable source to supplement that mineral since it is staple food for two-thirds of the world’s population. To bring the nutritional level of the milled product up to that of the whole grain (brown), rice should be enriched with thiamin, niacin and iron. Also iron has important role that absorption from the photosynthetic cells proceeds, chlorophyll synthesis and the growth process of the plant. Orthologous genes, which are homologous genes that diverged after a speciation event, generally maintain a similar function in different species. We applied a McDonald-Kreitman Test (MKT) to examine more than 10,000 orthologous genes between rice (Oryza sativa) and Brachypodium (outgroup) based on different phenotypic groups. This analysis was undertaken to find fast evolutionary genes in rice iron uptake. Three groups were separated based on the phenotype and each group was examined with the outgroup for MKT. Fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were detected at each groups. Annotation of these genes were conducted and the predicted functions were also discussed here. And also, the association study between the candidate gene related to iron uptake phenotype was performed. These results support that using this orthologous based method, we may find some important candidate genes underlying the ion uptake in rice.

Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

Zinc (Zn) deficiency is one of the important abiotic factors limiting rice productivity world-wide and also a widespread nutritional disorder affecting human health. Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. We analyzed the transcriptome profiles for rice grain from high zinc content and low zinc content lines at the early milky stage using the Illumina Sequencing method. The analysis results for the sequencing data indicated that many transcripts showed different expressions between high zinc content and low zinc content in early milky stage of rice and RT-qPCR analyses confirmed the expression patterns of selected transcripts. Functional analysis of the differentially expressed transcripts indicated that genes have functional annotation and their functions are mainly involved in oxidation-reduction, metabolic, transport , transcript regulation, defense response and photosynthetic processes. Based on the functional annotation of the differentially expressed genes, the possible process that regulates these differentially expressed transcripts in rice grain responding to Zinc at the early milky stage was further analyzed. The functional classification of those genes indicated their connection with various metabolic pathways, Zinc transport, signal transduction, transcriptional regulation, and other processes related to growth and development in early milky stage of rice. Using Illumina sequencing technology, the differences between the transcriptomes of high zinc content and low zinc content lines the early milky stage was described here for the first time. The candidate transcripts may provide genetic resources that may be useful in the improvement of Zinc concentration of rice. The model proposed here is based on differences in expression and transcription between two rice lines. In addition, the model may support future studies on the molecular mechanisms underlying plant responses to Zinc.

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remain as a great challenge, it is important to establish piratical ways to manage them. A core collection, by definition, refers to a subset of entire population but preserves most of the possible genetic diversity, enhancing the efficiency for germplasm utilizations. Here we reports the whole genome resequencing of the 137 Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in Korean genebank of Rural Development Administration (RDA). We implemented the Illumna HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8x depth using Nipponbare as a reference. Comparisons of the sequences with the reference genome yield more than 15 million(M) single nucleotide polymorphisms (SNPs) and 1.3M insertion/deletion (INDELs). Phylogenetic and population analyses using 2,046,529 high quality SNPs successfully assigned each rice accessions to the relevant subgroups, suggesting those SNPs comprehensively capture evolutionary signatures accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for 4 exemplary agronomic traits from the KRIC_CORE manifest the utility of KRICE_CORE, identifying previously defined gene or novel genetic polymorphisms that potentially regulate the important phenotypes. This study provides strong evidences that the size of KRICE_CORE is small but contains such a high genetic and functional diversity across the genome. Thus those resequencing results will be useful for future breeding, functional and evolutionary studies in the post-genomic era.