The next-generation sequencing (NGS) technology is being used for more effective genetic mapping and genome analysis. In this study, we performed whole-genome sequencing on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new cleaved amplified polymorphic sequence (CAPS) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. Approximately, sequences of 60x coverage of the Nipponbare reference genome on average were obtained following Illumina sequencing. Totally, 1,726,798 SNPs between Milyang23 and Gihobyeo were detected. Among them, 149 SNP were selected for CAPS markers and located on genetic map with 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. Newly 6 QTLs were detected for culm length (CL) and stem diameter (ID) traits including the first internode diameter (I1D), third internode diameter (I3D), and fourth internode diameter (I4D). Among those QTLs, qI1D5 and qCL5 had relatively higher LOD score and explained 8.99% and 4.24% of total variation. This study showed that the NGS allowed the rapid discovery of a large number of SNPs for CAPS marker. Only very small portion of SNPs through re-sequencing were used in this study. Furthermore, the results of QTL analysis described above shows relevance of molecular markers in mapping genes for useful traits.

Rice cultivation by direct seeding allows reduced labour and production costs in addition to other benefits. However the success of this rice production method can be limited by uneven fields with poor drainage or heavy rainfall at sowing leading to early flooding conditions slowing germination and hindering crop establishment. Hence, the need to improve tolerance to anaerobic conditions in both rainfed and irrigated rice ecosystem after direct seeding. In this study QTL analysis was performed to identify QTLs associated with tolerance derived from Vietnamese variety Tai Nguyen (TN) under anaerobic conditions during germination. The population derived from a cross between TN (tolerance indica lines) and Anda (susceptible japonica), was used for collection of phenotypic data based on the survival rates of the seedlings at 21 days after sowing under 10cm of water. A total of 286 F2:3 families of the population were used for QTL mapping and the genotyping was carried out with the infinium 6K SNP-chip based on the illumina infinium platform. Two significant QTLs associated with the AG trait were detected on chromosomes 1 and 11, respectively. In Particular, the QTL on chromsome 1 had an LOD score of 7.45 and R2 of 14.21%. We plan to confirm the identified QTLs in further studies and develop varieties with improved anaerobic germination ability using advanced backcross lines.

The seed shattering played a key role in the crucial step of rice domestication. Because it has been important to increase the yield human had to select the rice varieties and species with low shattering degree. The shattering habit of rice is considered to be under the relatively simple genetic control compared with other characteristics related to domestication. Several recessive genes associated with the formation of an abscission layer, sh2, sh4 and sh-h on chromosomes 1, 3 and 7, have been reported. In addition, the grain shattering of rice is considered to be caused by seed abscission. The morphology of the abscission layer can differ in many different rice varieties that show varying degrees of shattering. Accordingly, it is important to elucidate the molecular mechanism to determine why some varieties do not have abscission layers and have an easy-shattering trait. In this study, analysis of QTL for grain shattering was performed to determine the location of QTLs on the whole chromosomes of rice. Also, we tried to construct a physical map for qPs6

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.

In this study, 80 F7:8 recombinant inbred lines (RIL), derived from a cross between dent corn and waxy corn, were evaluated for 10 grain yield and eating-related traits over a two-year period. A total of 39 quantitative trait loci (QTLs) and 74 epistatic interactions were confirmed in 2011 and 2012. All QTLs detected in 2011 and 2012, qAC9 (amylose content), qEH4 (ear height), qSEL6 (setted ear length), and q100KW10 (fresh 100 kernel weight) had higher phenotypic variance and were observed in both years; therefore, they may be considered major QTLs. We reported that the QE interaction affects (QTLs and environmental changes) for qEH4, qSEL6, and q100KW10 in discussion. Some new QTLs identified in this study were located on different loci compared with other studies. The genetic region (bin 4.08) strongly controls plant height and ear height, and results from pleiotropy and/or tight linkage. qST3 (including stem thickness) and qEH3 were co-located within two common adjacent simple sequence repeat (SSR) markers (umc2275 and umc1273), whereas qEL6 (ear length) and qSEL6 were co-located within two common adjacent SSR markers (umc2309 and bnlg238). Thus, these SSR markers are a useful selection tool for screening grain yield and yield component traits.

본 연구는 강원도 농업기술원 옥수수연구소에서 튀김옥 수수 품종개발을 위하여 육성한 79개의 자식계통들에 대하 여 대표적인 분자마커인 SSR마커를 이용하여 집단구조 및 association mapping 분석을 실시하였다. 집단구조에 대한 분 석 결과에서 79개의 튀김옥수수 자식계통들은 groups I, II, III, IV, admixed group으로 구분되었다. 4개의 옥수수 자식 계통은 group I에 포함되었고, Group II는 총 17개의 자식계 통들이 포함되었다. 그리고 6개의 자식계통들은 Group III에 포함되었으며, 22개의 자식계통들은 Group IV에 포함되었 다. 그리고 admixed group에는 30개 옥수수 자식계통들이 포함되었다. 튀김옥수수 자식계통들에 대하여 50개 SSR 마 커와 10개의 양적 형질 사이에서 association mapping 분석 을 하였다. Q GLM 분석에서는 0.01의 유의수준에서 92개의 marker-trait association을 확인하였으며, 반면에 Q+K MLM 분석에서는 0.01의 유의수준에서 6개의 marker-trait association 을 확인되었다. 본 연구에서 79개의 튀김옥수수 자식계통들 에 대한 집단구조 및 association mapping 분석의 결과는 앞 으로 강원도농업기술원 옥수수연구소에서 튀김옥수수 품종개 발을 위한 계통 육성 및 교배조합 구성 등에 유용한 정보를 제공할 것으로 기대한다.

Reckless development policy, which has continued during the past several decades, caused landscape damage. In order to solve this problem, it is very urgent to conserve the habitat and to establish systematic database. Recently, various researches related to landscape damage have been conducted actively and the necessity of landscape ecological planning based on the biotop mapping has been issued as one of the solutions. Therefore, the purpose of this study is to select the study area, which is located in Guji-meon, Dalseong-gun, Daegu and will be formed into Daegu Science Park, and then to develop and apply the landscape ecological planning model based on biotop mapping in district unit. The results are as follows. Fist of all, according to the results of biotop classification with field survey and literature review, total 13 biotop and total 63 biotop types were classified. According to the first evaluation with B-VAT, total 19 biotop types were classified I grade including natural river with abundant plants(BA) and so on. While V grade, which has lowest value, was classified 16 biotop types including vegetable garden adjacent to river(BC). Also the second evaluation, we analyzed total 30 areas such as 1a, 1b grades, which had special meaning for the conservation of species and biotop. Next, 2a, 2b, 2c grades were analyzed total 82 areas. Secondly, in the compliance with Ecological landscape planning, we divided landscape planning model into two parts such as setting of improvement goal and detailed implement plan. For instance, setting of improvement goal, we classified 9 parts such as conservation region and parts of detailed implement plan, we classified total 28 planning indicators with 4 view such as the region which should be special protected from nature and landscape. Lastly, with the developed landscape model we applied to research areas, made maps, and differentiate proposals in each region. Specially, the final master plan was made to help understand the contents of detailed landscape planning. This study will be a useful data, which can solve the landscape damage problem systematically and control it landscape-friendly with biotop classification, evaluation, landscape ecological planning model, and application method which we developed.

A long-term wind resource map was made to provide the key design data for the 2.5 GW Korean West-South Offshore Wind Project, and its reliability was validated. A one-way dynamic downscaling of the MERRA reanalysis meteorological data of the Yeongwang-Gochang offshore was carried out using WindSim, a Computational Fluid Dynamics based wind resource mapping software, to establish a 33-year time series wind resource map of 100 m x 100 m spatial resolution and 1-hour interval temporal resolution from 1979 to 2012. The simulated wind resource map was validated by comparison with wind measurement data from the HeMOSU offshore meteorological tower, the Wangdeungdo Island meteorological tower, and the Gochang transmission tower on the nearby coastline, and the uncertainty due to long-term variability was analyzed. The long-term variability of the wind power was investigated in inter-annual, monthly, and daily units while the short-term variability was examined as the pattern of the coefficient of variation in hourly units. The results showed that the inter-annual variability had a maximum wind index variance of 22.3% while the short-term variability, i.e., the annual standard deviation of the hourly average wind power, was 0.041±0.001, indicating steady variability.

The objective of this study was to make a map of farmland vulnerability to flood inundation based on morphologic characteristics from the flood-damaged areas. Vulnerability mapping based on the records of flood damages has been conducted in four successive steps; data preparation and preprocessing, identification of morphologic criteria, calculation of inundation vulnerability index using a fuzzy membership function, and evaluation of inundation vulnerability. At the first step, three primary digital data at 30-m resolution were produced as follows: digital elevation model, hill slopes map, and distance from water body map. Secondly zonal statistics were conducted from such three raster data to identify geomorphic features in common. Thirdly inundation vulnerability index was defined as the value of 0 to 1 by applying a fuzzy linear membership function to the accumulation of raster data reclassified as 1 for cells satisfying each geomorphic condition. Lastly inundation vulnerability was suggested to be divided into five stages by 0.25 interval i.e. extremely vulnerable, highly vulnerable, normally vulnerable, less vulnerable, and resilient. For a case study of the Jinju, farmlands of 138.6km2, about 18% of the whole area of Jinju, were classified as vulnerable to inundation, and about 6.6km2 of farmlands with elevation of below 19 m at sea water level, slope of below 3.5 degrees, and within 115 m distance from water body were exposed to extremely vulnerable to inundation. Comparatively Geumsan-myeon and Sabong-myeon were revealed as the most vulnerable to farmland inundation in the Jinju.

분위사상법(QM, Quantile Mapping)은 GCM(Global Climate Model) 자료의 계통적 오차를 보정하여 보다 신뢰성 높은 자료로 재생성하기 위해 활용되고 있다. 이 기법은 사상(mapping)시키려는 대상(object) 자료의 통계분포모수가 정상적(stationarity)이라는 가정 하에 대상 자료의 누적확률분포(CDF, Cumulative Distribution Function)를 목표(target) CDF에 통계적으로 투영시키는 것이 일반적이다. 따라서 GCM에서 제공되는 미래 기후시나리오의 강우시계열과 같이 비정상성(non-stationarity)을 갖는 장기 시계열자료에 대한 적용에는 문제점을 보이고 있다. 본 연구에서는 비정상성을 갖는 장기시계열자료의 오차보정을 위해 통계분포모수에 경향성을 부여하는 비정상성 분위사상법(NSQM, Nonstationary Quantile Mapping)을 적용하였다. NSQM 적용을 위한 확률분포로 수문분야에서 광범위하게 쓰이고 있는 Gamma 분포를 선정하였으며, 대상 시나리오는 CCCma(Canadian Centre for Climate modeling and analysis)에서 제공하고 있는 CGCM3.1/T63모형의 20C3M(reference scenario)과 SRES A2 시나리오(projection scenario)를 활용하였다. 한강유역 내 관측기간이 충분한 10개의 지상관측소로부터 강우량을 수집하였다. 또한 6월과 10월 사이에 연강수량의 65% 이상이 집중되는 한반도의 계절성을 반영하기 위해 홍수기(6∼10월)와 비홍수기(11∼5월)를 구분하였고, 기준기간(Baseline)은 1973∼2000년, 전망기간(Projection)은 2011∼2100년으로 구분하였다. 다양한 목표분포의 설정을 통하여 NSQM의 적용성을 평가하고자 하였으며, 전망기간은 FF시나리오(Foreseeable Future Scenario, 2011∼2040년), MF시나리오(Mid-term Future Scenario, 2041∼2070년), LF시나리오(Long-term Future Scenario, 2071∼2100년)의 3개의 구간으로 설정하여 기준기간과 전망기간의 연평균강우량에 대한 경향성분석을 실시하였다. 그 결과 NSQM이 FF시나리오에서 330.1mm(25.2%), MF시나리오에서 564.5mm(43.1%), LF시나리오에서 634.3mm(48.5%)로 증가하는 전망결과를 나타내고 있었다. 정상성기법을 적용한 결과, 전망기간 중 전체적으로는 동일한 평균값을 갖는 목표통계모수를 사용한다고 하여도, 전망전반부에서 과다하고, 후반부에서 오히려 과소한 전망을 보여주고 있었다. 이러한 결과는 비정상성기법을 사용함으로써 상당부분 개선될 수 있음을 확인하였다.

eLoran 시스템의 구축을 위해서는 기존 LORAN-C 설비의 보완과 데이터채널, dLoran 기준국, ASF 데이터베이스 등의 추가가 필요하다. 특히 항만접근 시 eLoran을 이용한 정밀 위치측정을 위해서는 항만 해역에 대한 ASF 맵이 반드시 이용자에게 제공되어야 한다. 본 연구에서는 eLoran 시스템의 주요 오차 요인인 항만에서의 ASF를 효율적으로 생성 및 보완하기 위하여, ASF 예측모델과 실측치를 이용한 ASF 맵 생성기법에 대해 연구하였다. 포항 LORAN-C 주국(9930M)에서 송신신호와 LORAN-C 수신기의 수신신호를 각각 세슘원자시계를 기준으로 측정하는 전파지연 측정법을 적용하여 ASF 실측치를 얻었고, ASF 예측맵은 불규칙한 지형을 적용한 몬테스 모델로 구현하였다. 본 논문에서는 영일만 해상 12 개 측정점에서의 ASF 실측값과 ASF 모델링을 통해 획득한 예측값의 옵셋을 보정하여 영일만의 ASF 맵을 생성하였다.

Excessive water stress can cause severe damage to sorghum and results in significant yield reduction. The aim of this study is to identify quantitative trait loci (QTL) for excessive water stress in sorghum. As a first step, two out of 21 bmr mutants were selected for their superior agronomic performance and Chlorophyll a fluorescence OJIP transient, and were crossed with an elite Korean cultivar, Hwangkeumchal, to construct mapping populations. One hundred ten out of 236 SSR primers showed polymorphism between two parens, which cover ten chromosomes of sorghum from different published SSR linkage maps of sorghum. Development of recombinant inbred lines from the crosses ‘25M2-0698 x Hwangkeumchal’ and ‘25M2-0404 x Hwangkeumchal’ are in progress using the single seed descendent method for generation acceleration.

Rice hulls remain closed throughout the ripening period to maintain internal humidity of the grains. An Open-hull sterile mutant was induced by N-methyl-N-nitrosourea(MNU) treatment on Sinsunchalbyeo rice, a japonica type. This mutant showed open hulls even in the ripening stages and fully mature grains. In addition, several altered characteristics were observed, including of narrowed palea, decreased grain size, partial pollen sterility and erect panicle. Microscopic analysis showed that the palea was positioned slightly inside the lemma, and the size of palea decreased in the mutant. Genetic analysis of F2 and F3 segregation populations derived from the cross between the Open-hull sterile mutant (Oryza sativa ssp. japonica) and Milyang23 (O. sativa ssp. indica) indicated that the Open-hull trait was controlled by a single recessive allele. The fine-mapping with STS (sequence tagged site) markers revealed that the mutant gene was located on the short arm of chromosome 3. We were able to narrow it down until 30.6Kb where three candidate genes were found.

Our study is performed to confirm the level of genetic diversity and population structure with 80 maize inbred lines (40 waxy inbred lines and 40 flint inbred lines) and to explain the genetic basis of agronomic traits using an association mapping. The 200 SSR loci are confirmed a total of 1,610 alleles in total 80 maize inbred lines. The average number of alleles per locus was 8.05. The average GD was 0.72. The average PIC value was 0.68. The average MAF was 0.40. Population structure was revealed for K=2. Total 80 maize inbred lines were divided by groups I, II and admixed group. The 14 waxy inbred lines were assigned to group I. The 45 inbred lines include 5 waxy inbred lines and 40 flint inbred lines were contained to group II. The 21 waxy inbred lines were contained in the admixed group with lower than membership threshold 0.8. Association mapping between 200 SSR markers and 10 phenotypic traits of waxy/flint maize inbred lines were performed by Q GLM and Q+K MLM. In significant level at 0.01, 72 SSR markers were associated with 10 phenotypic traits using Q GLM. The 4 marker-trait association were detected in Q+K MLM. The results derived from this study will be used for designing efficient new maize breeding programs.

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.

NGS costs are decreasing rapidly, and beneficial application of the technology to plant genomics seems inevitable. Trying to interpret the agriculturally important traits like yield is actively in progress all across the globe. However, the current stage of bio-informatic technology as applied to the interpretation of agricultural trait appears not yet at a level of maturity to justify widespread plant genome sequencing for user-friendly molecular breeding. It is necessary to construct dense mutation block (DMB) based molecular breeding system for selecting plants with optimal agricultural performance; as well as for identifying useful quantitative trait loci (QTLs). Firstly, we screened and selected DMBs-specific INDEL markers obtained from SNV density profiles using 42 genome sequences of Korean cultivar and public sequences of 24 japonica rice cultivars. Secondly, we analyzed the genetic similarity between 288 Korean cultivars using 113 DMB-specific INDEL markers, which could differentiate on agarose gel by PCR. And we are going to integrate 360 INDEL markers up to 30 per each chromosome. Finally, we selected 40 founder lines considering the importance of the breeding, the purpose of use, and plant ecotype. To construct rice nested association mapping population we crossed each founder lines with the pollen of Hwayoungbyeo which was most commonly used in korean rice breeding program. F2 seed multiplication and generation iteration are ongoing.

The early senescence mutant was isolated from the japonica rice Koshihikari through Ethyl-methane-sulfonate (EMS) mutagenesis. The early senescence phenotype was controlled by a single recessive gene, tentatively symbolized as es-k. Using an F2 population derived from a cross between the mutant and Milyang23 and molecular markers, we mapped the es-k locus to the long arm of chromosome 7 between STS markers 147-1 and 147-2 with a physical distance of 66-kb. The symptom of early senescence appeared even before heading, while appeared during ripening in wild-type. Physiological characteristics of the es-k mutant before initiation of senescence was similar to the wild-type. However, after heading, es-k mutants started to exhibit a significant decrease in chlorophyll and soluble protein content compared to the wild-type. The wild-type leaf color appeared normal irrespective of temperature treatment, while the leaf of es-k mutant appeared pale-green at the low temperature and dark-green at the high temperature. During dark-induced senescence, mutant did not show significant differences compared to normal type. The results show that es-k is sensitive to temperature but not to light.

고추 탄저병은 국내에서 아주 피해가 심한 병 중의 하나로 본 연구팀은 십수 년 동안 탄저병 저항성에 대해 유전분석을 수행하는 동시에 저항성 품종 육성에 노력을 기울여 왔다. 이전에 사용하였던 탄저병 저항성 소재는 Capsicum baccatum 종의 PBC81 accession이었는데, 이와 가장 교잡화합성이 높았던 C. annuum 종의 SP21 계통을 모친으로 사용하여 종간 교잡을 수행하였고, 이에 대한 BC1F1과 BC1F2 분리집단에서 QTL mapping을 수행하여 두 가지의 탄저병(Colletotrichum acutatum과 C. capsici)에 대한 각각의 저항성 주동 QTL을 탐색함과 동시에 연관된 분자표지를 개발하였다. 본 연구에서는 탄저병 저항성 소재로 PBC81이 아닌 PI594137과 AR을 사용하여 NGS re-sequencing을 수행한 후 대량의 SNP를 탐색하고자 하였다. PI594137은 C. baccatum 종에 속하며, PBC81보다 좀 더 broad spectrum resistance를 보인다. AR은 AVRDC에서 분양 받은 재료인데, C. chinense Jacq. PBC932의 열성 저항성을 C. annuum에 도입한 계통이다. 탄저병 저항성 QTL mapping은 Golden aji(C. baccatum, 탄저병 이병성)와 PI594137의 F2 분리집단과 SP211(C. annuum, 탄저병 이병성)과 AR의 F2 분리집단에서 수행할 계획이어서 각각의 양친 사이(Golden aji vs. PI594137과 SP211 vs. AR)에서 SNP를 탐색하였다. NGS re-sequencing을 통해 읽혀진 염기서열 총 길이는 PI594137이 40.5Gbp, Golden aji가 12.1Gbp, AR이 12.8Gbp, SP211이 11.5Gbp였다. 이 염기서열을 사용하여 생물정보학적 분석((주)씨더스에 의뢰)을 수행하였는데, PI594137과 Golden aji 사이에서 333,816개, AR과 SP211 사이에서 1,218,595개의 SNP를 최종적으로 탐색할 수 있었다. 탐색된 SNP는 탄저병 저항성 QTL mapping 분석에 유용하게 사용될 수 있을 것이다.