No abstract

Three human chromosome loci (1q43, 10p12.31, and 12q21.31) were recently associated with the susceptibility to primary open-angle glaucoma (POAG) in a Japanese population; however, this was not replicated in three subsequent studies using South Indian, Afro-Caribbean, and Chinese populations. To identify genetic markers that are robustly associated across ethnic populations, numerous markers in addition to the six in the three reported loci were examined in this study. A total of 31 single-nucleotide polymorphism (SNP) markers were genotyped for 1115 Korean participants, and many neighboring SNPs were imputed using the Korean HapMap Project genotype data. Each SNP was statistically tested for association with POAG susceptibility by comparisons among 211 POAG patients with 904 unaffected controls. A strong and statistically significant association was found with a previously unreported SNP, rs7098387 (odds ratio, OR ¼ 2.0 (1.4-3.0), P ¼ 0.00038) at the 10p12.31 locus (where 11 SNPs were typed and 38 imputed) in contrast to the reported rs7081455, which was too poorly correlated with newly associated rs7098387 (r 2 ¼ 0.003, D 0 ¼ 0.40) to show association. Additionally, a modest association was observed with the reported rs693421 (OR ¼ 1.4 (1.1-1.7), P ¼ 0.0082) and several other SNPs located within and around ZP4 at the 1q43 locus (10 SNPs typed and 14 imputed). However, no association was observed with the reported rs7961953 SNP or any other SNPs at the 12q21.31 locus, upstream of TMTC2 (10 SNPs typed and 29 imputed). Accordingly, POAG susceptibility association was replicated using rs7098387 (C) rather than rs7081455 (T) at the 10p12.31 locus and additionally with rs693421 (T) at the 1q43 locus.

BackgroundBehçet’s disease (BD) susceptibility had been associated with single-nucleotide polymorphisms (SNPs) in IL23R–IL12RB2, IL10, STAT4, or ERAP1 locus in Japanese, Turkish, Chinese, and other populations, but not in a Korean genome-wide association study (GWAS). We aimed to fine-map BD risk association of these four loci using extensive imputation and additional genotyping for replication.MethodsIn the discovery phase, 369 patients with BD enrolled in the previous Korean GWAS and 2000 controls retrieved from a population-based cohort of healthy Koreans were imputed for their genotypes of all SNPs in the four loci using the Asian data of the 1000 Genomes Project as reference. For genotype imputation of ERAP1 SNPs, the adjacent ERAP2 SNPs were also covered. For the 10 most significantly associated SNPs (8 imputed and 2 GWAS-genotyped), an additional 84 patients with BD and 283 healthy controls were genotyped for replication. The results from the discovery and replication phases were pooled for meta-analysis using the Mantel-Haenszel test to estimate the odds ratio (OR) and 95% confidence interval (CI).ResultsAn IL23R–IL12RB2 intergenic SNP rs1495965 was significantly associated with BD risk (OR (95% CI) = 1.5 (1.3, 1.7), P = 2.5 × 10−7) in the pooled meta-analysis of the discovery (1.4 (1.2, 1.7), P = 4.9 × 10−7) and replication (1.9 (1.3, 2.6), P = 6.0 × 10−4) phases. BD risk association was fine-mapped on the intergenic region rather than the two flanking genes, as rs1495966 and rs4655535, almost perfectly correlated with rs1495965 (r 2 = 0.99), were also located in the same intergenic region. Consistent with previous reports, the P values tended to be lower within IL23R than IL12RB2. On the other hand, several IL10 SNPs were suggested for association in the discovery phase but all failed in the replication phase. No SNP in ERAP1–ERAP2 and STAT4 was suggested even in the discovery phase.ConclusionsBD susceptibility association was fine-mapped on the intergenic region between IL23R and IL12RB2 as marked by three correlated SNPs, rs1495965, rs1495966, and rs4655535.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-017-1435-5) contains supplementary material, which is available to authorized users.

The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.

Salinity stress is one of the major factors in the reduction of plant growth and crop yield worldwide. To improve our ability to grow crops in high-salinity environments, plant responses to salinity stress must be tightly controlled. Here, in order to further understand the precise regulation of plant responses under high salinity conditions, the function of the MYB3 transcription factor was studied as a repressor to control excessive accumulation of lignin and anthocyanin under salt stress conditions. Nuclear-localized MYB3 forms a homodimer. It is ubiquitously expressed, especially in vascular tissues, and its expression is highly induced by NaCl in various tissues such as roots, leaves, stems, and flowers. myb3 mutant plants exhibited longer root growth in high NaCl conditions than wild-type plants. However, several NaCl responsive or signaling genes were not significantly altered in myb3 compared to wild-type. Interestingly, high accumulation of lignin and anthocyanin was displayed in myb3, and the expression of genes involved in lignin and anthocyanin biosynthesis, such as PAL1, C4H, COMT, 4CL3, DFR and LDOX, sharply increased in myb3 compared to those of wild-type plants under NaCl treatment. According to yeast-two hybrid screenings, various transcription factors, including anthocyanin regulators TT8 and EGL3, were isolated as MYB3 interacting proteins. MYB3 was characterized as a transcriptional repressor and its repressor domain is located in the C-terminus of MYB3. Overall, these results suggest that nuclear-localized MYB3 functions as a transcriptional repressor for the control of lignin and anthocyanin accumulation under salinity stress conditions.