QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.).

Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from a cross of the cold-tolerant japonica cultivar Jinbu and the cold-susceptible indica cultivar BR29 for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8 °C (day/night) cold stress regime revealed continuous variation for cold tolerance. Six QTLs including two on chromosome 1 and one each on chromosomes 2, 4, 10, and 11 for seedling cold tolerance were identified with phenotypic variation (R(2)) ranging from 6.1 to 16.5 %. The QTL combinations (qSCT1 and qSCT11) were detected in all stable cold-tolerant RIL groups, which explained the critical threshold of 27.1 % for the R(2) value determining cold tolerance at the seedling stage. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11, respectively, were fine mapped. The markers In1-c3, derived from the open reading frame (ORF) LOC_Os01g69910 encoding calmodulin-binding transcription activator (CAMTA), and In11-d1, derived from ORF LOC_Os11g37720 (Duf6 gene), co-segregated with seedling cold tolerance. The result may provide useful information on seedling cold tolerance mechanism and provide DNA markers for a marker-assisted breeding program to improve seedling cold tolerance in indica rice varieties.

Effect of Microwave Treatment on Adzuki Beans (Vigna angularis L.) under Dry State-Analyzing Microstructure, Water Absorption, and Antioxidant Properties.

In this study, a microwave was used on adzuki beans (Arari and Geomguseul) without water, in order to investigate their changes in microstructure, water absorption, and antioxidative properties. As the microwave treatment time increased (2450 MHz, 0 to 60 s), the lightness, redness, and yellowness were reduced, and moisture content significantly decreased in both varieties. The microstructure space between the seed coat, cotyledon, and pores within the cotyledon were observed, due to the loss of moisture. Regardless of microwave treatment, the water absorption behavior of the adzuki beans was sigmoidal. However, the water absorption kinetics of Arari increased after microwave treatment, whereas with microwave-treated Geomguseul, the water absorption rate decreased, compared to the control, except for the sample treated for 30 s. During soaking, the water absorption and softening rates in the microwave-treated adzuki bean were twice as fast as the untreated beans. Antioxidant activity, total phenolic compounds, and total flavonoid compounds were greatly improved by microwave treatment. These results indicate that microwave treatment affects the color, hydration, and bioactive compounds, and it can be used as a pretreatment method before processing adzuki beans.

Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars.

Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1, the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4-65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1. While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs.

Morphological and starch characteristics of the Japonica rice mutant variety Seolgaeng for dry-milled flour.

Producing good-quality, fine rice flour is more difficult than wheat flour because the rice grain is harder. The non-glutinous Japonica-type variety Seolgaeng, derived from N-methyl-N-nitrosourea (MNU) mutagenesis, and four other varieties, representing a range of amylose contents, were evaluated in this study. Dry-milled Seolgaeng rice flour exhibited an average particle size that is <70 µm, a more uniform particle-size proportion than other varieties. Moreover, we noted significant differences in the damaged starch content in flour from Seolgaeng compared to the other varieties (p<0.05). Seolgaeng flour showed a round starch structure, which would lead to better friability, finer particle size, and less damage to the endosperm during dry milling. Indeed, among all varieties evaluated in this study, dry-milled Seolgaeng flour had the finest particle size (averaging <70 µm) and exhibited less damaged starch. With its round starch granules, Seolgaeng is a suitable candidate for drymilled rice flour.

Identification of quantitative trait loci associated with rice eating quality traits using a population of recombinant inbred lines derived from a cross between two temperate japonica cultivars.

Improved eating quality is a major breeding target in japonica rice due to market demand. In this study, we performed genetic analysis to identify quantitative trait loci (QTLs) that control rice eating quality traits using 192 recombinant inbred lines (RILs) derived from a cross between two japonica cultivars, 'Suweon365' and 'Chucheongbyeo'. We evaluated the stickiness (ST) and overall evaluation (OE) of cooked rice using a sensory test, the glossiness of cooked rice (GCR) using a Toyo-taste meter, and measured the amylose content (AC), protein content (PC), alkali digestion value (ADV), and days to heading (DH) of the RILs in the years 2006 and 2007. Our analysis revealed 21 QTLs on chromosomes 1, 4, 6, 7, 8, and 11. QTLs on chromosomes 6, 7, and 8 were detected for three traits related to eating quality in both years. QTLs for ST and OE were identified by a sensory test in the same region of the QTLs for AC, PC, ADV, GCR and DH on chromosome 8. QTL effects on the GCR were verified using QTL-NILs (near-isogenic lines) of BC(3)F(4-6) in the Suweon365 background, a low eating quality variety, and some BC(1)F(3) lines. Chucheongbyeo alleles at QTLs on chromosomes 7 and 8 increased the GCR in the NILs and backcrossed lines. The QTLs identified by our analysis will be applicable to future marker-assisted selection (MAS) strategies for improving the eating quality of japonica rice.

PCR marker-based evaluation of the eating quality of japonica rice ( Oryza sativa L.).

Evaluation of eating quality in early breeding generations of rice is critical to developing varieties with better palatability. This paper reports DNA markers associated with eating quality of temperate japonica rice and an evaluation method aided by multiple regression analysis. A total of 30 markers comprising STSs, SNPs, and SSRs were tested for their association with palatability using 22 temperate japonica varieties with different palatability values. Eating quality-related traits of the 22 varieties were also measured. Of the 30 markers, 18 were found to be significantly associated with palatability and, consequently, a model regression equation with an R(2) value of 0.99 was formulated to estimate the palatability by the marker data set. Validation of the model equation using selected breeding lines indicated that the marker set and the equation are highly applicable to evaluation of the palatability of cooked rice in temperate japonica varieties.