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 the cross of a cold-tolerant japonica and a cold-sensitive indica cultivars, for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8oC (day/night) cold-stress regime showed continuous variations for cold tolerance or sensitivity. Six QTLs for seedling cold tolerance were identified on chromosomes 1, 2, 4, 10, and 11 with percent phenotypic variation (R2) ranging from 6.1% to 16.5%. Three main-effect QTLs (qSCT1, qSCT4, and qSCT11) were detected in all cold-tolerant RILs which explained high sum of phenotypic variation (SPV) ranging from 27.1% to 50.6%. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11 were fine mapped. The marker In1-c3 from ORF LOC_Os01g69910 of the BAC clone B1455F06 encoding calmodulin-binding transcription activator (CAMTA) and another marker, In11-d1 from ORF LOC_Os11g37720 (Duf6 gene) of the BAC clone OSJNBa0029K08, co-segregated with seedling cold tolerance. These two InDel markers amplified 241-bp and 158-bp alleles, respectively, in cold-tolerant RILs, and in the cold-tolerant donor Jinbu, which were absent in cold-sensitive parent BR29 and cold-sensitive RILs.

Brown planthopper (BPH) is a major insect pest of tropical indica and temperate japonica rice in Asia and Africa. A major BPH resistance gene, Bph18 derived from IR65482-7-216-1-2 has been fine mapped on chromosome 12 and confers strong resistance to the Korean biotype of BPH. The Bph18 gene is tightly linked to the STS marker, 7312.T4A and is non-allelic to previously reported resistance genes present on chromosome 12. The Bph18 gene has been transferred into two elite japonica cultivars (Jinbubyeo and Junambyeo) background through marker-assisted backcross breeding (MAB) strategy. Foreground selection using STS markrs linked to the Bph18 gene in advanced backcross progenies confirmed homozygous marker alleles associated with BPH resistance. Background selection of the breeding lines with 260 simple repeat (SSR) markers revealed rapid conversion toward recurrent parent genotypes with less donor chromosomal segments (5.3-16.7%). Major agronomic traits of the progenies were analyzed and some breeding lines have agronomic traits comparable to the recurrent parent. One breeding line (S.523) with multiple-resistance to BPH and major diseases, desirable agronomic traits and grain quality has been recommended for regional testing in Korea. MAB is the suitable strategy to incorporate new genes into susceptible japonica to develop elite breeding lines.

This study was done to understand the G x E interaction of rice blast reaction for Japonica high quality rice varieties and to observe blast pattern for high quality varieties. Twenty one percent of the total sum of squares (SST) in blast reaction data of high quality Japonica varieties is attributed to genotype (G) by environment (E) interaction variation. This portion of blast response is higher than 8～12% of G x E effect in blast severity data obtained from various ecotypes of rice varieties. Blast response scores obtained from high quality Japonica varieties group were more severely affected by environment condition than mixed groups with Japonica and Indica varieties. Interaction Principal Component Analysis (IPCA) scores obtained from AMMI analysis for the leaf blast response implied variation of G x E interaction. Correlation analysis suggested that IPCA1 was associated with latitude, maximum mean temperature, precipitation and mean cloud amount. IPCA2 was associated with mean relative humidity, and IPCA3 was associated with precipitation and minimum relative humidity. Pattern analysis generated nine genotype clusters according to blast reaction over 11 regions. Collectively, the A, B, C, and D groups were susceptible to rice blast, where as the E, F, G, H, and I groups were relatively resistant to rice blast through multi-location blast nursery test. Relationship between the identified genes of high quality varieties and blast scores at each test site in the level of group could be analyzed based on the results from G x E Interaction analysis.