As a first step of mapping genes conferring resistance to the brown planthopper, Nilaparvata lugens Stål, in Gayabyeo using a population derived from a cross between Gayabyeo and Taebaegbyeo, we performed the whole genome resequencing of these two Tongil-type rice varieties. The amount of raw sequence data was about 18.5X109 bp and 17.9X109 bp in Gayabyeo and Taebaegbyeo, respectively. After quality trimming and read mapping onto Nipponbare reference genome sequence, 9.3X109 bp was mapped in Gayabyeo with mapping depth of 25.0X, and 9.5X109 bp was mapped in Taebaegbyeo with mapping depth of 25.5X. Between Gayabyeo and Nipponbare, 1,585,880 SNPs were detected, while 1,416,898 SNPs were detected between Taebaegbyeo and Nipponbare. Between Gayabyeo and Taebaegbyeo, 284,501 SNPs were detected. Among the SNPs between Gayabyeo and Taebaegbyeo, 21.2% were in genic region and 78.8% were in intergenic region. In CDS region, 15,924 SNPs were detected, among which synonymous SNPs covered 47.3% and non-synonymous SNPs covered 52.7%. We designed Cleaved Amplified Polymorphic Sequences (CAPS) markers with SNPs in the restriction enzyme recognition sites, and 20 CAPS markers were tested. Of the 20 markers, 19 markers showed polymorphism and one marker showed monomorphism between Gayabyeo and Taebaegbyeo. It is expected that sufficient DNA markers for mapping genes with a population derived from a cross between Gayabyeo and Taebaegbyeo can be developed based on the results of the study.

Bacterial spot of tomato (Solanum lycopersicum L.) is caused by at least four species of Xanthomonas with multiple physiological races. In this study, we developed a mapping population for association analysis of bacterial spot resistance. For this population, six advanced breeding lines with distinct sources of resistance were first crossed in all combinations and their F1 hybrids were intercrossed. The 1,100 segregating progeny from these crosses were evaluated in the field against T1 strains. Based on this individual evaluation, we selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicate field trials inoculated with T1 and T3 strains. A total of 461 markers across 12 chromosomes were used for genotyping these selections. Of these markers, an optimized subset of 384 SNPs was derived from the 7,720 SNP Infinium array developed by the Solanaceae Coordinated Agricultural Project (SolCAP). For association analysis to detect known resistance loci and additional novel loci, we used the mixed models with correction for population structure, and found that accounting for kinship appeared to be sufficient. Detection of known loci was not improved by adding a correction for structure using either a Q matrix from model-based clustering or covariate matrix from Principal Component Analysis. Both single-point and haplotype analyses identified strong associations in the region of the genome known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Additional QTL associated with resistance were detected on chromosomes 1, 3, 4, 6 and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance. Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.