Leaf mold disease in tomato (Solanum lycopersicum) is caused by Cladosporium fulvum, a fungal leaf pathogen. One of effective ways to control leaf mold is to breed disease-resistant tomato cultivars. Cf-4 and Cf-9 resistance (R) genes encode proteins that carry a leucine rich repeat domain and are located in plasma membrane. They trigger hypersensitive response following recognition of corresponding Avr4 and Avr9 proteins of C. fulvum, respectively. Cf-4 and Cf-9 genes are originated from wild tomato species S. habrochaites and S. pimpinellifolium and have been introgressed into commercial tomato cultivars. These two highly homologous orthologs exist as a cluster with four highly homologous paralogs. Due to this reason, development of genetic markers to distinguish these two functional R genes from their orthologs and paralogs is difficult. In this study, we tried to develop single-nucleotide polymorphism (SNP) markers to select tomato cultivars carrying resistant Cf-9 genotype. The genomic sequences of resistant Cf-4 and Cf-9 alleles, susceptible cf-9 alleles, and their paralogs were obtained from the GenBank database, and two functional SNPs causing non-synonymous substitution were found among them. Based on two SNPs, the Cf-9_2-SNP-F/R primer set for high resolution melting (HRM) analysis was developed. HRM analysis with this primer set could successfully distinguish tomato cultivars carrying resistant Cf-9 allele among 30 commercial tomato cultivars, which were characterized with the gene-based marker. These indicate that the SNP marker developed in this study is useful to trace Cf-9 genotype efficiently in marker-assisted selection in tomato.

Tomato spotted wilt virus (TSWV) causes one of the most destructive viral diseases that threaten tomato (Solanum lycopersicum) worldwide. So far, eight TSWV resistance genes, Sw1a, Sw1b, sw2, sw3, sw4, Sw-5b, Sw-6, and Sw-7 have been identified and Sw-5b has been incorporated into tomato for prevention of TSWV. The objectives of this research are first to discover single nucleotide polymorphisms (SNPs) in Sw-5 alleles and then to develop SNP markers to distinguish resistant genotypes against TSWV for marker-assisted breeding in tomato. First, DNA sequences of Sw-5b alleles from both resistant and susceptible cultivars amplified using known Sw-5 gene-based marker was analyzed. The single functional SNP (G→A) was detected as non-synonymous substitution because this SNP causes change of arginine (Arg599) to glutamine (Gln599). Next, the primer pair for high resolution melting analysis (HRM) was designed around this SNP. To determine accuracy of this SNP marker to distinguish resistant Sw-5b genotypes against TSWV, genotypes of 32 commercial tomato cultivars were checked. The newly developed SNP marker could select six cultivars carrying resistant Sw-5b genotype, which was 100% correlated with genotypes based on the gene-based marker. These results indicate that the SNP maker developed in this study could be useful for better tracking resistance to TSWV in tomato breeding.

QTL analysis for cold tolerance-related traits was conducted using 75 introgression lines (IL) developed from a cross between a japonica weedy rice and Tongil-type rice. A molecular linkage map consisting of 136 SSR markers was constructed to identify QTLs associated with cold tolerance. 75 ILs and the parents were evaluated for three traits associated with cold tolerance: seedling height and SAPD values at the seedling stage. The plants were grown for 15 days in the low temperature condition (13/20℃ day/night) and the control condition (25/20℃ day/night) in the growth chamber. A total of six QTL were identified for two traits and phenotypic variance explained by each QTL ranged from 4.3% to 35.7%. Among two QTL for seedling height, one QTL, sh1 for seedling height was detected at both conditions. The other QTL on chromosome 6 was detected in the low temperature condition. Four QTL were identified for SPAD value and two were detected on chromosomes 2 and 5. At these loci, Milyang 23 alleles increased the SPAD value. The other two QTL on chromosomes 1 and 4 were detected at the low temperature plot. At these loci, Hapcheonaengmi 3 alleles increased the SPAD values. These results indicate that Hapcheonaengmi 3 alleles might increase tolerance to low temperature in the Milyang 23 background because SPAD value is positively correlated with chlorophyll content and N content in rice. The markers linked to low temperature tolerance at the seedling stage would be useful in selecting for lines with enhanced cold tolerance in a breeding program.

This study was carried out to identify the quantitative trait loci (QTLs) for traits related to cold tolerance using an introgression lines (ILs) derived from a cross between a japonica weedy rice and a Tongil-type rice. Among the 80 RILs, one line (CR1835) showing tolerance for cold tolerance related to traits such as panicle exsertion and discoloration in the cold water plot was selected and backcrossed to the recurrent parent, Milyang 23. This line possessed Hapcheonaengmi 3 segments on chromosomes 1, 5 and 11. By two backcrosses to Milyang 23 and selfing, a total of 88 BC3F5 progenies were developed. The 88 ILs were evaluated for traits related to agricultural performance in cold water and in control plots. Cold tolerance was measured as difference of the culm length, spikelet fertility between two plots and panicle exsertion in cold water plot. The 88 ILs showed decreased culm length and increased anthocyan content in cold water plot than in the control water plot.

In the previous study, 141 BC3F2 lines from a cross between the Oryza sativa cv. Milyang 23 and O. glaberrima were used to identify favorable wild QTL alleles for yield component traits. In this study, we carried out QTL analysis of four grain morphology as well as four yield component traits using 141 BC3F5 lines from the same cross and compared QTLs detected in two different generations. The mean number of O. glaberrima segments in the 141 BC3F5 lines ranged from 1 to 13 with 2.69 and 5.71 of the average means of homozygous and heterozygous segments, respectively. There was a three-fold difference in the number of QTLs detected for four traits commonly evaluated in two generations (seven QTLs in the BC3F5 vs 21 in the BC3F2 population). The percentages of the phenotypic variance explained by QTLs in the BC3F5 population were similar to or less than those in the BC3F2 population. This is probably due to the difference in the genetic composition of two populations and the environmental effects. The locations of the QTLs commonly detected in both generations were in good agreement except for one QTL for spikelets per panicle. The yield QTL, yd3 was colocalized with the spikelets per panicle, spp3. Yield increase at this locus is due to the increase in spikelets per panicle, because both traits were associated with increase in spikelets per panicle and yield due to the presence of an O. glaberrima allele. Clusters of QTLs for grain morphology traits were observed in two chromosome regions. One cluster harboring five QTLs near SSR markers RM106 and RM263 was detected on chromosome 2. This population would serve as a foundation for development of the introgression line population from a cross between Milyang 23 and O. glaberrima.

In this study, a 141 BC3F4 lines from across between the O. sativa cv. Milyang23 as there current parent, and O. glaberrima as the donor parent was used to identify favorable QTL alleles from O. glaberrima for yield and yield components. To detect the introgressions, 198 microsatellite markers of known chromosomal position were used for the parental survey. Of the 178 markers, 128 (64.6%) showed polymorphism. Among them, 115 SSR markers were used to construct a genetic linkage map with average interval length of 12.7 cM based on the previous rice molecular genetic map. The mean number of O. glaberrima segments in the population was 1.84 ranging from 0 to 7. The average length of the segments was 16.6 cM and ranged from 0.5 to 232.5 cM. This population consisting of 141 lines was used to evaluate for six traits of agronomic importance and genotypes were determined for 141 BC3F5 using SSR markers. A total of 22 QTLs for 6 traits were detected on chromosomes 1, 2, 3, 4, 5, 6, 7 and 9. Phenotypic variance associated with each QTL ranged 9.5% ~ 58.2%. For 26 of the QTLs identified in this study, the O. glaberrima alleles contributed a desirable agronomic effect despite the over all undesirable characteristics of the wild phenotype. Favorable wild alleles were detected for culm length, panicle length, yield, panicles per plant and 1000-grain weight. When compared with previous studies involving interspecific crosses, it can be concluded that O. glaberrima is useful asa source of valuable alleles for rice improvement. There sults will be discussed.