Powdery mildew disease caused by Leveillula taurica is a serious fungal threat to greenhouse pepper production. In contrast to most epiphytic powdery mildew species, L. taurica is an endophytic fungus which colonizes in the mesophyll tissues of the leaf. In the genus Capsicum, several studies have been conducted to identify resistance sources to L. taurica. In previous studies, five quantitative trait loci (QTLs) for powdery mildew resistance have been identified. An F2 population derived from self-pollination of the commercial cultivar Capsicum annuum ‘PM Singang’ was used for genetic analysis of powdery mildew resistance. Resistance of the F2 plants was tested under the natural environmental conditions. Sporulation intensity on infected leaves was used as a disease scale to assign resistance levels to plants, where 0-5% is Resistant, 6-15% Moderate resistant and 16-100% Susceptible. A total of 83 F2 plants were evaluated for resistance. The results showed that 59 plants were resistant, 10 susceptible and 14 moderately resistant. If we consider MR as S, segregation ratio fitted to a single dominant resistance gene model. In the future study, closely linked molecular marker will be developed and tested to locate this gene. The developed marker will be used to identify the powdery mildew resistance gene.

Root-knot nematode, Meloidogyne incognita is a virulent pest of solanaceaous crops worldwide. The M. incognita resistance gene Me7 derived from Capsicum annuum CM334, is located on chromosome 9. In the present study, an F2 population derived from a cross between ECW03R and CM334 was used to locate the Me7 gene. An F2 population was inoculated using approximately 1,000 second-stage juveniles per individual plant. Phenotype screening was done 45 days after inoculation by using gall index system. The phenotype study of 503 F2 individual showed 391 resistant and 112 susceptible plants. The 3:1 phenotypic ratio confirmed that resistance phenotype is controlled by a single dominant gene. Previously reported two markers were tested to reveal the linkage of markers to phenotype. Two markers, CAPS_F4R4 and SCAR_PM6a were located at 4.3 and 2.7 cM from the resistance gene, respectively. Additional SNP markers were developed using CM334 reference genome information to narrow down the position of the gene, but no closer markers could be developed due to errors of DNA sequence assembly. The closest marker was positioned on telomere of the chromosome 9 long arm, where tens of other NB-LRR genes are clustered. NB-LRR genes are being used as candidates to identify the Me7 gene.

In the rice inflorescence development, timing of inflorescent meristem abortion, conversion of the rachis branch meristem to the terminal spikelet meristem and shift to lateral meristem identity determine the overall architecture of the rice panicle (keda-Kawakatsu et al. 2009). Cheng et al. (2011) reported that quantitative trait loci (QTLs) have major effects on panicle apical abortion in rice. However, there have been very few reports about panicle tip mutants. Therefore, this research is conducted to fine map mutant gene and perform functional analysis of mutant gen. Hwacheongbyeo (japonica rice) seed was treated with ethyl methane sulfonate (EMS) for inducing mutation. Two F2 population (Japanica mutant crossed with wild type and Japanica mutant crossed with Milyang 23, Indica type) were established for Phenotyping and genomic analysis. STS markers in crop molecular Breeding laboratory. Additional STS markers for fine mapping were developed based on the Nipponbare genome sequence (http://rgp.dna.affrc.go.jp/blast/runblast.html). All F2 generations showed the segregation of normal plants and mutant following a ratio of 3:1 suggesting the mutant phenotype is caused by a single recessive gene. Initial BSA test made using STS markers confirmed the mutant gene is found in the long arm of chromosome 8. Panicle tip mutant gene, pnt has pleotropic effect which has been manifested in significant reduction of tiller development starting from late stage of vegetative growth and pronounced effect on possession of stay green nature of the rice during the vegetative stage of development. The only significant difference observed within panicle traits is the number of spikelet on primary branch and spikelet fertility. The first primary branch which contain aborted spikelet and elongated distance between spikelet is the most affected structure in the panicle.

Foxglove aphid, Aulacorthum solani (Kaltenbach), is a Hemipteran insect that infected a wide variety of plants worldwide and caused serious yield losses in crops. The foxglove aphid resistance gene, Raso2 was previously mapped from PI 366121 (Glycine soja Sieb. and Zucc.) to a 26cM marker interval on soybean chromosome 7. The development of additional genetic markers, which are mapped closer to Raso2 were required to accurately position the gene to improve the effectiveness of marker assisted selection. The objective of this study was to narrow down the putative QTL region, which is responsible to foxglove aphid resistance in PI366121 using recently developed high-density 180K Axiom SoyaSNP genotyping array. One hundred and forty one F8-derived F12 recombinant inbred lines developed from a cross of susceptible Williams 82 and resistant PI 366121, were used to generate a fine map of Raso2 interval. The phenotyping of antibiosis and antixenosis was done through choice and no-choice assays with total plant damage (TPD) and primary infestation leaf damage (PLD). The composite interval mapping analysis showed that the physical interval between two flanking makers, which was corresponding to Raso2, was narrowed down to 500kb on the Williams 82 genome assembly (Glyma2.0), instead of 4Mb in the previous report using Goldengate assay. In the Raso2 interval, there are about 60 candidate genes, including 4 of NBS-containing putative R genes. This result could be useful in breeding for new foxglove aphid resistant soybean cultivars.

The depletion of stratospheric ozone has resulted in increased amount of ultraviolet-B radiation (UV-B: 280-320 nm) reaching the Earth’s surface and could cause significant biological effect in plants. In this study, putative quantitative trait loci (QTL), which is responsible to UV-B resistance in soybean, was identified using recently developed high-density 180K Axiom SoyaSNP genotyping array. A population of 115 recombinant inbred lines (RILs) derived from a cross between susceptible Keunolkong and resistant Iksan 10 was analyzed. A total 8,970 polymorphic SNP markers were used to construct linkage map. The both parents and RILs were grown with supplemental UV-B radiation in a greenhouse condition. Three categories of UV-B induced morphological damage, degree of leaf chlorosis, leaf shape change, and total plant damage were evaluated. Using composite interval mapping analysis, one major QTL associated with all of the phenotypic traits was detected on 7.7cM of soybean chromosome 7 with 22 of LOD score accounting for about 60% of phenotypic variance. Also, the allele from Iksan 10 were responsible for the UV-B resistance. Thus, the UV-B resistance QTL on chromosome 7 from Iksan 10 was designated to qUVBR1, corresponding to 30kb on the Williams 82 genome assembly (Glyma2.0) including 7 candidate genes. This result could be useful in breeding for new foxglove aphid resistant soybean cultivars. In addition, these results provided useful information not only for marker-assisted selection for UV-B resistance soybean, but also for the future identification of putative candidate genes, responsible for UV-B resistance in soybean.

The fruit shape is an important character in tomato. OVATE is one of genes controlling fruit elongation in tomato. Two loci suppress the ovate mutation, sov1 and sov2, on chromosome 10 and chromosome 11 respectively. sov1 appears to control neck constriction in the fruits (Rodriguez et al, 2013). We sequenced the genomes of Gold Ball Livingston and Yellow Pear using the Illumina Hiseq 2000 generating 101 PE reads and developed molecular markers tightly linked to sov1. The locus was confirmed by fruit shape index analysis, marker genotyping and progeny testing of recombinants. We find mapped sov1 to a 145 kb interval corresponding to a region comprising two candidate genes. One of the candidate genes for sov1 is SlOFP20 another member of the Ovate Family Protein class. Although there is no difference expression of SlOFP20 in the parents at anthesis, when the gene is expressed very high, the mutation appears to be a 34 kb promoter deletion of SlOFP20 in Yellow Pear, conferring a pear shaped and neck-constricted fruit.

Rice embryo contains valuable materials which are related to human health and industrial material, thus controlling embryo size is more and more important in the field of rice breeding. Especially, main health-aid components such as γ -aminobutyric acid (GABA), tocopherol and vitamins showed positive-correlation with embryo size. We obtained three enlarged embryo character mutants derived from Hwacheongbyeo (Korean japonica cultivar) by treatment of chemical mutagen, N-methyl-N-nitrosourea(MNU). These three mutants were named according to their embryo size as ge-m, ge, ge-s. The result of allelism test between Hwacheongbyeo, ge-m, ge and ge-s represented that the embryo size of ge and ge-s was controlled by the same gene(Giant embryo, GE). Through GE locus sequencing of three mutants, we found that each of ge and ge-s mutant has a point mutation, causing non synonymous amino acid substitution. On the other hand, ge-m mutant, the embryo of which featured intermediate size in between those of Hwacheongbyeo and ge, turned out to be non-allelic to the GE locus, suggesting it is likely a novel gene, which influences rice embryo development through a different mechanism than GE gene. Fine mapping of ge-m is currently in progress. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

Pepper mottle virus (PepMoV) is frequently occurring virus in pepper field. PepMoV infected plants show symptoms including mosaic leaf, distortion of foliage and fruit deformation. The dominant gene Pvr7 from Capsicum annuum ‘9093’ confers resistance to PepMoV. Previous research reveals that Pvr7 is located in 10 chromosome and linked to the dominant potyvirus resistance gene Pvr4 and Tomato spotted wilt virus (TSWV) resistance gene Tsw. To identify the Pvr7 gene, we constructed an intraspecific F2 mapping population from a cross between C. annuum ‘9093’ (PepMov resistant) and C. annuum ‘Jejujaerae’ (PepMoV susceptible). Resistance of F2 plants were screened with green flouorescent protein (GFP) tagged PepMoV. Genomic DNA was extracted from F2 individuals and markers were developed using C.annuum ‘CM334’ whole genome sequence (WGS). Several single nucleotide polymorphism (SNP) markers that were co-segregated with Pvr7 were developed. We are expecting that this Pvr7 SNP marker can be used to breeding PepMoV resistant cultivars and fine mapping of Pvr7.

Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a significant disease in most rice cultivation areas. The present study was performed to identify new BB R-gene conferring resistance to Korea Xoo isolates, derived from IR65482-7-216-1-2 and to construct a physical map of the candidate gene. An F2 population derived from a cross between 11325 and Anda was used to determine the exact position of the nearest recombination event to the target region. The position of the R-gene was delimited by flanking markers, RM1233 and RM5766, on chromosome 11. Of the 56 markers designed in the flanking region, 20 were selected as anchor markers and the R-gene was mapped to a 295kb region on chromosome 11. To narrow down the interval spanning the R-gene, an additionally SSR marker, 20 STS markers, and CAPS marker between RM27320 and ID55.05-79 were developed using rice reference genome information. From the result the gene was defined by RM27320 and ID55.WA18-5 located in the BAC clone OSJNBa0036K13. The physical distance between these two markers is approximately 80kb. In a further study, gene expression analysis against listed candidate genes was investigated using semi-quantitative transcription PCR. These results will useful for future disease breeding as well as gene function studies regarding resistance genes.

Tsw, a single dominant resistant gene against Tomato spotted wilt virus (TSWV), has been mapped on chromosome 10 in Capsicum chinense species. Previously reported molecular markers linked to the Tsw gene are not transferable for all pepper breeding materials. To develop additional markers and do genome-based fine mapping of the Tsw gene, approaches of mapping comparison, pooled transcriptome analysis, and genome walking were applied. Eleven additional SNP molecular markers tightly linked to the Tsw gene were developed using tomato and pepper whole genome sequencing databases. Among them, four SNP markers, SNP7715-1, SNP68-1, SNP17918-1, and SNP1072-1, showed no recombination in two segregating populations of F2 ‘Telmo’ (210 individuals) and ‘SP’ (843 individuals). Three scaffold sequences from the C. annuum BAC database and two BAC clones from the BAC library of C. annuum ‘CM334’ covering the Tsw gene were identified by transcriptome analysis and genome walking. A pepper scaffold sequence covering three pepper scaffold sequences was identified from a final version of the C. annuum BAC database. The Tsw gene was delimited within 149 kb by alignment analysis of two BAC clone sequences and the pepper scaffold sequence. A total of 22 predicted genes were resided in the target region between SNP7715-1 and SNP1072-1 co-segregating markers. Among them, five predicted genes showing annotations of CC/TIR-NBS-LRR resistance proteins, mRNA-6, mRNA-7, mRNA-11, mRNA-12, and mRNA-13, were identified. The transcriptome analysis and gene expression study showed that the mRNA-13 was expressed in ‘PI152225’ but was absent in ‘Special’, demonstrating the mRNA-13 could be a strong candidate gene for the Tsw gene. This result will be favorable for cloning the Tsw gene and developing cultivars which carry the TSWV-resistance gene.

The architecture of rice panicle is primarily determined by the arrangement of branches and spikelets, and it directly affects grain yield. We identified a mutant for panicle apical abortion from a japonica cultivar Hwacheongbyeo treated with N-methyl-N-nitrosourea. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as a slight reduction in plant height, narrow and dark green leaf blades, and small erect panicles with clear panicle apical abortion compared to the wild-type plants. Genetic analysis revealed that the panicle apical abortion was controlled by a single recessive gene, which is tentatively designated as paa. The paa gene was fine mapped at an interval of 71 kb flanked by STS markers aptn3 and S6685-1 at the long arm of chromosome 4. Sequence analysis of the candidate genes within the delimited region showed a single base-pair change corresponding to an amino acid substitution from glycine to glutamic acid. We expect that the paa gene will be a clue to uncover the molecular mechanism of panicle apical abortion and to maintain the panicle identity for grain yield in rice breeding programs.

Spikelets per panicle (SPP) is one of the most important traits associated with rice yield. In this study, IL28, a near isogenic line (NIL) developed by introgressing chromosomal segments from ‘Moroberekan’ into ‘Ilpumbyeo’ showed significantly higher number of spikelets per panicle than the recurrent parent, ‘Ilpumbyeo’. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that a QTL for spikelets per panicle, qSPP6 was located in the interval RM3430 - RM20580. The Moroberekan allele increased SPP. The fact that QTLs for panicle length and the number of secondary branches were mapped in the same interval as qSPP6 appears to indicate that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qSPP6 using F3 lines was conducted. Substitution mapping with 41 F3 lines further narrowed the interval containing not only qSPP6 for spikelets per panicle but also qNDW6 for node width to about 680-kb between markers RM20521 and RM20572 based on Nipponbare genome sequence. The locus, qSPP6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qSPP6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in the breeding program.

The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is one of the most serious insect pests affecting cultivated rice (Oryza sativa L.) in temperate regions of East Asia. To understand the genetic basis of the GRH resistance, a F2 population derived from across between a highly resistant variety,Cheongnam and a susceptible variety, Junambyeo was analyzed by genetic analysis and association mapping. GRH resistance was evaluated using the F2 populations. The results showed that a single dominant gene in Cheongnam. DNA from 22 F2 individuals being either resistant or susceptible were pooled to produce bulk resistant and bulk susceptible DNA samples. Parents and bulks were screened with 192 SSR markers and twolinked SSRmarker, RM6082 and RM20145 were identified.Subsequent mapping in the original mapping population showed that thelocusis flanked by the SSR markers, RM20130 and RM20152 on chromosome 6. To physically map this locus, the-linked markers were landed on the artificial chromosome clones of the reference cv., Nipponbare, released by the International Rice Genome Sequencing Project. The DNA markers found to be closely linked to Grh3 would be useful for marker-assisted selection for the improvement of resistance to GRH in rice.

Grain size is one of the most important trait determining yield in cereal crops, apart from number of grains per panicle, number of panicles per plant and 1000 seed weight. Other than grain characteristics, plant architecture is another very important factor influencing yield by affecting the amount plant surface area directly exposed to the sun light. Erect panicle is important morphological characteristic which helps in enhancing the yield by allowing sun light to fall directly on leaves unlike curved panicle which blocks sunlight and consequently reduce photosynthesis. A small round grain and erect panicle mutant was obtained by treating Hwacheong rice (japonica) with MNU (N-methyl-N-nitrosourea) chemical mutagen. Through bulked segregant analysis (BSA) using STS (Sequence-Tagged Sites) and SS-STS (Sub-species Specific Sequence-Tagged Site) markers we located the mutated gene on the long arm of chromosome 7 and narrowed down candidate region to 168.75kbp through fine mapping. Mutant manifested characteristics like reduced grain size and plant height, dense and erect panicle and relatively erect plant compared to the wild type. When we crossed the mutant with its parent (Hwacheong), F1 panicle and grain characteristics showed intermediate phenotype, therefore, we concluded that wild type allele of this gene shows incomplete dominance. Scanning electron microscopy(SEM) result shows that increase in width of mutant grain, which changes its shape, is due to increase in width of glume cells. Phenotypic examination shows that dense and erect panicle phenotype is result of reduction in length of rachis, primary and secondary branch.

Spikelets per panicle is one of the most important trait associated with rice yield component. In this study, IL28, near isogenic line (NIL) developed by introgressing chromosomal segments from Moroberekan into Ilpumbyeo, showed significantly higher number of spikelets per panicle than the recurrent parent Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo, indicated that a QTL for spikelets per panicle, qspp6, located in the interval RM3430 – RM20580. The fact that QTLs for panicle length and secondary branch number were mapped in the same interval as that for qspp6 indicated that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qspp6 using F4 lines was conducted. As a result, substitution mapping with ten F4 lines further narrowed the interval containing qspp6 to about 429kb between marker RM20521 and RM20562 based on the japonica genome sequence. The locus, qspp6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qspp6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in an applied breeding program.