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 R2 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.

Brown planthopper (BPH) is one of the most destructive insect pests of rice. Wild species of rice are a valuable source of resistance genes for developing resistant cultivars. A molecular marker-based genetic analysis of BPH resistance was conducted using an F(2) population derived from a cross between an introgression line, 'IR71033-121-15', from Oryza minuta (Accession number 101141) and a susceptible Korean japonica variety, 'Junambyeo'. Resistance to BPH (biotype 1) was evaluated using 190 F(3) families. Two major quantitative trait loci (QTLs) and two significant digenic epistatic interactions between marker intervals were identified for BPH resistance. One QTL was mapped to 193.4-kb region located on the short arm of chromosome 4, and the other QTL was mapped to a 194.0-kb region on the long arm of chromosome 12. The two QTLs additively increased the resistance to BPH. Markers co-segregating with the two resistance QTLs were developed at each locus. Comparing the physical map positions of the two QTLs with previously reported BPH resistance genes, we conclude that these major QTLs are new BPH resistance loci and have designated them as Bph20(t) on chromosome 4 and Bph21(t) on chromosome 12. This is the first report of BPH resistance genes from the wild species O. minuta. These two new genes and markers reported here will be useful to rice breeding programs interested in new sources of BPH resistance.

Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.

Tillering is an important trait of cereal crops that optimizes plant architecture for maximum yield. Teosinte Branched 1 (TB1) is a negative regulator of lateral branching and an inducer of female inflorescence formation in Zea mays (maize). Recent studies indicate that TB1 homologs in Oryza sativa (rice), Sorghum bicolor and Arabidopsis thaliana act downstream of the auxin and MORE AUXILIARY GROWTH (MAX) pathways. However, the molecular mechanism by which rice produces tillers remains unknown. In this study, transgenic rice plants were produced that overexpress the maize TB1 (mTB1) or rice TB1 (OsTB1) genes and silence the OsTB1 gene through RNAi-mediated knockdown. Because lateral branching in rice is affected by the environmental conditions, the phenotypes of transgenic plants were observed in both the greenhouse and the paddy field. Compared to wild-type plants, the number of tillers and panicles was reduced and increased in overexpressed and RNAi-mediated knockdown OsTB1 rice plants, respectively, under both environmental conditions. However, the effect was small for plants grown in paddy fields. These results demonstrate that both mTB1 and OsTB1 moderately regulate the tiller development in rice.

In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.

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Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3' downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5' NTR, transcript, and 3' NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT This study examined the genetic variation of cyanidin 3-glucoside (C3G) contents in blackish-purple rice. F2 populations were established from crosses between blackish purple rice and normal white rice. The blackish rice cultivars used were Jilinheimi, Heidao38, LK1A-2-12-1-1, Heugjinju, and No2, and the common white rice cultivars used were Hwachung super giant embryo and Heugbal. The purple pericarp color is known to be controlled by a set of dominant alleles, Pb (Prp-b) and Pp (Prp-a). In this study, the segregation of the black purple:brown:white pericarp in the F2 population was 9:3:4, demonstrating that the purple pericarp color was controlled by two dominant complementary genes. The F2 distribution of C3G showed continuous variation, with a tendency toward a lower level in all the crosses. However, some F2 crosses, such as Jilinheimi/Heidao38 and Jilinheimi/LK1A-2-12-1-1, showed transgressive segregation of the C3G content. C3G content of Jilinheimi linked on 84% level in C3G content of F2 population between Jilinheimi/Heidao38, and 41.3% level in Jilinheimi/LK1A-2-12-1-1. The results of the color difference meter and C3G content analysed by HPLC revealed highly significant correlations between the seed coat color of the colored rice germplasm and that of the segregated populations. There was a significant positive correlation between the C3G content with L* (lightness) and b* (yellowness). The a* (redness) was different in each cross, but there was a significant positive correlation between the C3G content with L* and b*.