Prunus persica “Mihong” cultivar is a domesticated white peach that was generated from the crossing between “Yumyeong” and “Chiyomaru” cultivars in the Republic of Korea in 1995. We launched “Mihong” genome sequencing in 2018 and “Mihong” reached to 200 scaffold and 241 Mb sequences using long-read sequencing and Hi-C technology. F₁ populations of ”Kawanakajima Hakuto,” “Mihong,” “Changhowon Hwangdo,” and “Yumi” were developed in NIHHS. These four cultivars were sequenced and assembled using the SOAPdenovo version 2.04. First, we surveyed the SSRs in “Mihong” assembly sequences and extracted the ±300 bp flanking sequences containing SSRs. Second, the assembly sequences of three cultivars were aligned and mapped against “Mihong” ±300 bp flanking sequences using BLASTn (version 2.2.29+). We anticipated the differential length in SSRs among the four cultivars. We sorted the primers with a standard deviation over 4.5 (STEV > 4.5) among the four cultivars. In addition, we surveyed the primers having difference in over 10 bp with “Kawanakajima Hakuto” and “Mihong” for polymorphic markers in the mapping population. All primer pairs were designed to generate amplicons of 150-200 bp in coating SSR regions using primer3 (version 3-2.2.3). We selected 260 SSR markers with a physical distance of average per 1 Mb. These SSR markers accounted for 74% polymorphism in the four genotypes. Finally, a F₁ population of “Kawanakajima Hakuto” and “Mihong” covered 884.5 cM with 465 SNPs and 86 SSRs and this genetic map matched correctly to the HI-C pseudomolecule of P. persica.

Flooding stress causes a significant reduction in soybean yield. The development of flood-tolerant cultivars is an effective way to minimize yield loss due to flooding. Information on candidate genes for flooding tolerance is useful for developing tolerant lines. The
objective
of this study was to identify potential candidate genes for flooding tolerance in soybean by integrating the results of a quantitative trait locus analysis and RNA sequencing. A total of 19 genes showed good amplification in capillary electrophoresis and were further analyzed through a reverse transcription quantitative polymerase chain reaction (qRT-PCR); two of these genes showed differential expression among tolerant and susceptible lines. The expression of Glyma.12g030900 and Glyma.10g050300 in leaf and root tissues, respectively, was higher in several tolerant lines than in the susceptible lines under flooding stress. The chlorophyll index of the tolerant lines was also consistently higher than that of the susceptible lines over two years, supporting the qRT-PCR results. This study provides useful information on flooding tolerance in soybeans.

Phytophthora root rot attributable to infection by the soil-borne oomycete Phytophthora sojae causes serious damage to susceptible soybeans grown in poorly drained soil. Management of this disease depends primarily on Rps (resistance to P. sojae) resistance genes. The
objective
of this study was to map resistance to two P. sojae isolates (40412 and 2457) in a Daepung×Socheong2 recombinant inbred line population. Of these two varieties, Socheong2 is resistant to the two isolates, whereas Daepung is susceptible. Single-marker analysis of variance and linkage analyses using a high-density genetic map identified different resistance loci for each isolate. A genomic region of 36.2~37.4 Mbp on chromosome 3 was identified as being associated with resistance to isolate 40412, explaining 18% of the phenotypic variance (PV), whereas, a 2.1~2.6-Mbp region on chromosome 18 was significantly associated with resistance to isolate 2457, accounting for approximately 26% of the PV. An additional region of 53.1~53.3 Mbp on chromosome 18 was also significantly associated with resistance to isolate 2457. All three loci coincide with genomic regions where an Rps gene or partial resistance have been mapped in previous studies. The respective locus showed significance for only one or the other of the isolates, indicating an isolate-specific interaction. From this finding, it can be inferred that isolates 40412 and 2457 are characterized by different avirulence genes, and that Socheong2 has at least two Rps genes that interact with each isolate. The finding of multiple Rps loci specific to an isolate within a single soybean genotype is a unique discovery. Socheong2 will accordingly be a useful genetic source for breeding resistance to multiple P. sojae isolates.

An allo-octoploid strawberry (Fragaria × ananassa Duch.) is one of the most important vegetable crops in Korea. However, there were few genomic researches of strawberry due to polyploidy and complexity of its genome. In this study, we aimed to construct a genetic linkage map of strawberry using single nucleotide polymorphism (SNP) markers that were developed through a next-generation sequencing (NGS) analysis. Two strawberry varieties, ‘Sulhyang’ and ‘Senga-sengana’, were used as a maternal and a paternal parent, respectively, and their F1 generation consisting of 94 individuals was used for construction of a genetic linkage map. A total of 19.0 Gbp (‘Sulhyang’) and 21.8 Gbp (‘Senga-sengana’) of genomic sequences were obtained through NGS analysis. Subsequently, approximately 87,000 SNPs were identified and 1,154 primer sets for high-resolution melting (HRM) analysis were designed through bioinformatic analysis. In result, a total of 224 polymorphic HRM markers were developed and 205 markers were mapped on the genetic linkage map of strawberry, which total length was 800.8 cM and the number of linkage groups were 30. This SNP-based genetic linkage map and the 224 SNP markers will be very helpful for the genomic and genetic researches of allo-octoploid strawberry.

The rice recombinant inbred lines derived from Milyang23 and Gihobyeo cross were used in genetic mapping and QTL analysis studies. In this study, we developed a new 101 CAPS markers based on the SNPs in the whole genome region between these varieties. As a result, the total genetic distance and average distances were 1,696.97 cM and 3.64 cM, respectively. In comparison to the distance of the previous genetic map constructed based on 365 DNA markers, the new genetic map was found to have a decreased distance. The map was applied for the detection of QTLs on all seven traits relevant to diameter of stem internode, length of culms, length of panicles and the number of panicles including the correlation analysis between each trait. The QTLs results were similar to the report in previous studies, whereas the distance between the markers was narrowed and accuracy increased with the addition of 101 CAPS markers. A total of 9 new QTLs were detected for stem internode traits. Among them, qI1D-6 had higher LOD of 5.1 and phenotype variation of 50.92%. In this experiment, a molecular map was constructed with CAPS markers using next generation sequencing showing high accuracy for markers and QTLs. In the future, developing more accurate QTL information on stem internode diameters with various agriculturally important traits will be possible for further rice breeding.

The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vast sequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage of the Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred population derived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported 219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internode diameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stem diameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), and fourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score and explained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much more markers can be developed by using SNP information acquired in this study, which will enable construction of high-density genetic map and more accurate QTL analysis of important agronomical traits with MGRIL population.