BackgroundImproved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality.ResultsIn this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar ‘Hwaseong’ and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs.ConclusionThe qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map-based cloning of genes underlying this trait. To our knowledge, this is the first report to map a beneficial QTL for glossiness of cooked rice from a wild rice, O. rufipogon.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0135-0) contains supplementary material, which is available to authorized users.

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

: This study was conducted to know the variation and relationship of rice grain quality and starch pasting properties by transplanting times. Two early maturing rice cultivars which accounted for the most area of early maturing rice cultivar in Chungnam province were used. The experiment was laid out in a split-plot design with 3 replications. The main plot consisted of three transplanting times viz. early (April 25), ordinary (May 25) and late (June 25) with sub-plots containing two cultivars. According to the transplanting times, most of rice grain quality and starch pasting properties showed significant difference and Joami showed higher grain quality than Unkwang in all transplanting times. Especially, rice grain quality was improved when transplanted late, showing high head rice and glossiness of cooked rice due to the lower mean temperature during grain filling stage. Glossiness of cooked rice was positively correlated with head rice ratio, amylose content and setback value, and negatively correlated with chalky rice ratio and protein content. The highest positive and negative correlation were observed between breakdown value and peak viscosity (r = 0.98**), and breakdown and setback (r = -0.94**), respectively. These results provide some information for rice researchers and producers producing cultivars with an improved quality, suggesting that rice quality is highly influenced by temperature at grain filling stage, and transplanting times is crucial in improving rice quality. In addition, starch pasting properties are useful for determining rice quality because rice grain quality and starch pasting properties are dependent on each other.

Global sea-level rise, the effect of climate change, poses a serious threat to rice production owing to saltwater intrusion and the accompanying increase in salt concentration. The reclaimed lands, comprising 22.1% of rice production in Korea, now face the crisis of global sea-level rise and a continuous increase in salt concentration. Here, we investigated the relationship between the decrease in seed quality and the transcriptional changes that occur in the developing rice seeds under salt stress. Compared to cultivation on normal land, the japonica rice cultivar, Samgwang, grown on reclaimed land showed a greatly increased accumulation of minerals, including sodium, magnesium, potassium, and sulfur, in seeds and a reduced yield, delayed heading, decreased thousand grain weight, and decreased palatability and amylose content. Samgwang showed phenotypical sensitivity to salt stress in the developing seeds. Using RNA-seq technology, we therefore carried out a comparative transcriptome analysis of the developing seeds grown on reclaimed and normal lands. In the biological process category, gene ontology enrichment analysis revealed that the upregulated genes were closely associated with the metabolism of biomolecules, including amino acids, carboxylic acid, lignin, trehalose, polysaccharide, and chitin, and to stress responses. MapMan analysis revealed the involvement of upregulated genes in the biosynthetic pathways of abscisic acid and melatonin and the relationship of trehalose, raffinose, and maltose with osmotic stress. Interestingly, many seed storage protein genes encoding glutelins and prolamins were upregulated in the developing seeds under salt stress, indicating the negative effect of the increase of storage proteins on palatability. Transcription factors upregulated in the developing seeds under salt stress included, in particular, bHLH, MYB, zinc finger, and heat shock factor, which could act as potential targets for the manipulation of seed quality under salt stress. Our study aims to develop a useful reference for elucidating the relationship between seed response mechanisms and decreased seed quality under salt stress, providing potential strategies for the improvement of seed quality under salt stress.

Bbareumi' is an extremely early maturing rice cultivar with the fastest harvesting time in Korea. To develop 'Bbareumi', 'Joami' with good quality in Chungnam plain area and 'Hokuto' originating from Japan with the fastest heading date among genetic resources were used as breeding materials. After crossing them in 2010, the 'Bbareumi' cultivar was developed using the pedigree method. A yield trial was conducted from 2015 to 2016, and a local adaptability test was conducted from 2016 to 2018. The heading date of 'Bbareumi' was seven days earlier than 'Jinbuolbyeo', showing an average of June 23 rd , and it could be harvested from the end of July to the beginning of August when transplanted early in Chungnam plain area. 'Bbareumi' had a short culm length of 63.3 cm and panicle length of 19.3 cm. Milled rice yield was approximately 4.87 MT/ha and the percentage of head rice was 89.2% under normal fertilizer condition. 'Bbareumi' will be used as a premium rice brand with newly harvested rice before 'Chooseok', Korean Thanksgiving Day and is expected to contribute to the revitalization of double-cropping in the Chungnam plain area (Registration No. 8130).