Introgression has been achieved from wild species Oryza grandiglumis (2n = 48, CCDD, Acc. No. 101154) into O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. An advanced introgression (backcross) line, HG101, produced from a single plant from BC5F3 families resembled Hwaseongbyeo, but it showed differences from Hwaseongbyeo in several traits, including days to heading and culm length. To detect the introgressions, 450 microsatellite markers of known chromosomal position were used for the parental survey. Of the 450 markers, 51 (11.3%) detected O. grandiglumis segments in HG101. To characterize the effects of alien genes introgressed into HG101, an F(2:3) population (150 families) from the cross Hwaseongbyeo/HG101 was developed and evaluated for 13 agronomic traits. Several lines outperformed Hwaseongbyeo in several traits, including days to heading. Genotypes were determined for 150 F2 plants using simple sequence repeat markers. Qualitative trait locus (QTL) analysis was carried out to determine the relationship between marker genotype and the traits evaluated. A total of 39 QTL and 1 gene conferring resistance to blast isolate were identified using single-point analysis. Phenotypic variation associated with each QTL ranged from 4.2 to 30.5%. For 18 (46.2%) of the QTL identified in this study, the O. grandiglumis-derived alleles contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favorable wild alleles were detected for days to heading, spikelets per panicle, and grain shape traits. Grain shape QTL for grain weight, thickness, and width identified in the F(2:3) lines were further confirmed based on the F4 progeny test. The confirmed locus, tgw2 for grain weight is of particular interest because of its independence from undesirable height and maturity. Several QTL controlling amylose content and grain traits have not been detected in the previous QTL studies between Oryza cultivars, indicating potentially novel alleles from O. grandiglumis. The QTL detected in this study could be a rich source of natural genetic variation underlying the evolution and breeding of rice.

A quantitative trait locus (QTL) analysis was carried out with a recombinant inbred line (RIL) population to identify the chromosomal regions responsible for cold tolerance of rice (Oryza sativa L.). The RIL population, consisting of 80 lines, was developed from a cross between the indica cultivar, Milyang 23 and the japonica weedy rice, Hapcheonaengmi 3. The population was genotyped with 2 morphological and 132 DNA markers, providing an average interval size of 11.3 cM, and was also evaluated for traits related to agricultural performance in cold water and in control plots. The RILs showed delayed heading and reduced culm length in the cold water plot and the differences in heading date and culm length between two plots were statistically significant. Cold tolerance was measured as days to heading, culm length, spikelet fertility, leaf discoloration, and panicle exsertion in the cold water plot, and difference in days to heading and the reduction ratio of culm length between two plots. A total of 14 QTLs for 7 traits were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to three. Phenotypic variation associated with each QTL ranged from 5.8 to 32.8 %. No digenic interaction was detected. Several QTLs associated with cold tolerance were clustered in a few chromosomal blocks. For 11 (78.6 %) of the QTLs identified in this study, the Hapcheonaengmi 3-derived alleles contributed desirable effects and favorable alleles were detected for difference in days to heading, spikelet fertility, panicle exsertion and leaf discoloration. From this study, it can be concluded that weedy rice is useful as a source of valuable alleles for breeding cold tolerance in rice.

In our previous study, we reported the grain weight (GW) QTL, tgw11 in isogenic lines derived from a cross between Oryza sativa ssp. Japonica cv. Hwaseong and O. grandiglumis. The O. grandiglumis allele at tgw11 decreased GW in the Hwaseong background. To fine-map tgw11, one F5 plant homozygous for the O. grandiglumis DNA in the target region on chromosome 11 was selected from F4 line, CR1242 segregating for tgw11 and crossed with Hwaseong to produce secondary F2 and F3 populations. QTL analysis using 760 F2 plants confirmed the existence of tgw11 with an R 2 value of 15.0%. This QTL explained 32.2% of the phenotypic variance for GW in 91 F3 lines. Substitution mapping with 65 F3 lines with informative recombination breakpoints in the target region was carried out to narrow down the position of the tgw11. The result indicated that tgw11 was located in the 900-kb interval between two SSR markers, RM224 and RM27358. QTLs for grain width and grain thickness were also located in the same interval suggesting that a single gene is involved in controlling these three traits. Analysis of F3 lines indicated that the variation in TGW is associated with variation in grain shape, specifically grain thickness and grain width. Genetic analysis indicated that the O. grandiglumis allele for small seed was dominant over the Hwaseong allele. SSR markers tightly linked to the GW QTL would be useful in marker-assisted selection for variation in GW in breeding program.

In a previous study, we reported the grain weight QTL, tgw2 in the 150 F2:3 lines derived from a cross between Oryza sativa subssp. Japonica cv. Hwaseongbyeo and HG101. This QTL was confirmed in F4 lines (CR1242) segregating for the target region. For fine mapping of tgw2, one F5 plant homozygous for the O. grandiglumis DNA in the target region was selected from CR1242 and crossed with Hwaseongbyeo to produce the F2 and F3 populations. QTL analysis using 490 F2 plants confirmed the existence of tgw2 with an R 2 value of 28.0%. This QTL explained 61.3% of the phenotypic variance for 1,000-grain weight in 64 F3 lines. Substitution mapping with 47 F3 lines and 74 F4 plants with informative recombination breakpoints in the target region was carried out to narrow down the position of the tgw2. The result indicated that tgw2 was located in the 384-kb interval between two SSR markers, RM12813 and RM12836. Annotation data of BACs in this 384-kb region revealed that forty-five putative genes exist in this interval including the GW2 gene responsible for grain weight and width. Considering the position of the QTL tgw2, it appears that tgw2 is functionally related to the gene GW2. However, the possibility that another unknown mechanism might be responsible for regulation of grain weight at tgw2 cannot be ruled out. Four QTLs for grain length, grain width, and grain thickness were also located in the same interval suggesting that a single gene is involved in controlling these four traits. Substitution mapping also indicated that two QTLs for grain weight and culm length, tgw2 and cl2, were tightly linked.