Shoot-fresh-weight (SFW) is one of the parameters, used to estimate the total plant biomass yield in soybean. Understanding the genetic and molecular basis of SFW could help increase the total biomass production. In this particular study, we identified QTLs associated with SFW in a Recombinant Inbred Line (RIL) population derived from interspecific cross of PI483463 and Hutcheson. A total of 551 (535 SNP and 16 SSR) markers, were found to be polymorphic between the parental lines and were used to screen the RILs to develop the genetic map. Linkage analysis and QTL mapping were performed using with the software QTL IciMapping version 4.0, with the minimum LOD score of 3.0 and estimating the likelihood of a QTL and its corresponding effects at every 1cM. QTLs with LOD value > threshold LOD, as determined by 1000 permutation tests at p > 0.05 were considered as significant QTLs. The analysis identified a total of 5 QTLs associated with shoot fresh weight over two environments, with the phenotypic variation (PV) ranging from 6.34 to 21.32%, and the additive effect from -0.54 to 0.33. Among these QTLs, qFW1314_19_1 had the largest LOD scores, with PV of 21.32%. Interestingly, three QTLs, qFW2013_19_1, qFW2014_19_1, and qFW1314_19_1 identified on chromosome 19(L), showed negative additive effects, indicating the contribution from the wild parent PI483463. The QTLs identified in this study can be the targets to identify the candidate genes for the SFW and can help in developing cultivars with increased biomass potential.

Leaves are the organ for photosynthesis, respiration and transpiration, and have a major effect on crop yield. Therefore, leaf shape and structure are important agronomic traits in breeding for ideal type plant. We obtained a new abaxially rolled leaf mutant from Ilpum(Oryza sativa ssp. japonica) by the treatment of ethyl methane sulfonate(EMS). The abaxially rolled leaf mutant showed reduced plant height and panicle length, increased tiller number and panicle number than Ilpum. LRI(Leaf rolling index) analysis showed that the mutant have high value compared to the wild-type. In cross section analysis, the mutant was observed to have increased of bulliform cell number and size, and led to the outcurved leaf rolling. The phenotypes of the F1 plants derived from the cross between the mutant and Ilpum were normal. In F2 population, segregation ratio between the wild type and the mutant was 3:1. This genetic analysis indicated that leaf rolling is controlled by single recessive gene. Bulked segregant analysis(BSA) and genetic mapping were conducted using F2 population derived from the cross between mutant and Milyang23(Oryza sativa ssp. indica). According to the results, the gene was located on the long arm of chromosome2. Fine mapping is in progress.

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.

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops including Brassica oleracea. Therefore, it is important to identify resistance gene for CR disease and apply it to breeding of Brassica crops. In this study, we applied genotyping-by-sequencing (GBS) technique to construct high resolution genetic map and mapping of clubroot resistance (CR) genes. A total of 18,187 GBS markers were identified between two parent lines resistant and susceptible to the disease, of which 4,103 markers were genotyped in all 78 F2 plants generated from crossing of both parent lines. The markers were clustered into nine linkage groups spanning 879.9 cM, generating high resolution genetic map enough to refine reported reference genome of cabbage. In addition, through QTL analysis using 78 F2:3 progenies and mapping based on the genetic map, two and single major QTLs were identified for resistance of race 2 and race 9 of P. brassicae, respectively. These QTLs did not show collinearity with CR loci found in Chinese cabbage (Brassica rapa) but roughly overlapped with CR loci identified in cabbage for resistance to race 4. Taken together, genetic map and QTLs obtained in this study will provide valuable information to improve reference genome and clubroot resistance in cabbage.

Seed weight (SW), often expressed as 100-seed weight (HSW), is an important yield component in soybean and has been found to show positive correlation with seed yield. It is shown to behave as a quantitative trait controlled by many loci that are largely unclear. In this study, we represent the identification of chromosomal regions controlling the seed weight in soybean. We used a Recombinant Inbred Line (RIL) population, consisting of 188 lines derived from a cross of a wild soybean PI483463 (HSW: 0.85g) and a cultivated soybean cultivar Hutcheson (HSW: 14.05g) to identify the chromosomal regions controlling the SW trait. The population, along with parental samples and check, William82 (HSW: 21.2g) was grown for four years and phenotype data was recorded postharvest. A total of 535 SNP and 16 SSR markers, polymorphic between the parents were employed to genotype the RILs using Golden gate assay to develop the linkage map. Whole genome QTL scanning identified a total of 17 QTLs, spanning 10 chromosomes for the 100-seed weight. All these QTLs explained phenotypic variation (PV) in the range of 3.77 to 12.33%. Of the 17 QTLs, 2 QTLs qSWA1-1 and qSWD2-1, found to be the consistent QTLs, expressing in all the four environments. The QTL qSWD2-1 explained highest contribution to the total PV with 10.04 -12.23 %. The remaining 15 QTLs were identified in at least one environment with PV ranging up to 10.39%. The findings from this study will provide useful information to understand the genetic and molecular basis of SW and facilitate further genomic research leading to the yield improvements in soybean.

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.

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbred lines ‘835’ (susceptible) and ‘B2’ (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-years experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.

This paper evaluates the applicability of a simple kriging with local means(SKLM) for highresolution spatial mapping of monthly mean temperature and rainfall in South Korea by using AWS observations in 2013 and elevation data. For an evaluation purpose, an inverse distance weighting(IDW) which has been widely applied in GIS and cokriging are also applied. From explanatory data analysis prior to spatial interpolation, negative correlations between elevation and temperature and positive correlation between elevation and rainfall were observed. Bias and root mean square errors are computed to compare prediction performance quantitatively. From the quantitative evaluation, SKLM showed the best prediction performance in all months. IDW generated abrupt changes in spatial patterns, whereas cokriging and SKLM ref lected not only the topographic effects but also the smoothing effects. In particular, local characteristics were better mapped by SKLM than by cokriging. Despite the potential of SKLM, more extensive comparative studies for data sets observed during the much longer time-period are required, since annual, seasonal, and local variations of temperature and rainfall are very severe in South Korea.

In recent years, meteorological disasters have frequently occurred in rural areas. As a result, there have been growing concerns over the protective measures needed. In order to avoid natural risks and damage, and to strengthen countermeasure to meteorological disasters, local governments needs to be prepared. Therefore, this paper seeks to prevent meteorological disasters through mapping of inundation vulnerability in agricultural land, Chungcheongnam-do. In doing so, this study were considered 5 variables (i.e. precipitation, region of altitude below 50m, region of slope gradient is below 10 degree, distance from river within less 50m) for creating vulnerability map. The precipitation was excluded in five variables. Since, the precipitation which include Daily maximum precipitation, 2-Daily maximum precipitation, summer precipitation was not any correlation among them. The results of analysing four variables, exclusive of precipitation, were showed that the agricultural lands where located in Dangjin, Buyeo, Hongseong and Asan were low correlation of inundation vulnerability by overlapping analysis. Moreover, The correlation analysis was showed low correlation between each factors and the annual average area of agricultural lands’ inundation, whereas, the correlation analysis which was overlapping each factor showed high correlation. In conclusion, in order to create reliable vulnerability map in agricultural lands, Chungcheongnam-do, it must be considered to overlap analysis of the four main factors such region of altitude below 50m, region of slope gradient is below 10 degree, distance from river within less 50m. We suppose that this study’s analysis can help to set the preparedness site of agricultural lands inundation.

본 연구에서는 홍수위험도 작성을 위한 낙동강 유역에서의 도달시간을 산정하였다. 현재 국내에서 제작되고 있는 홍수위험지도는 홍수범람범위 및 홍수심을 표출하는 것을 목적으로 하는 Flood Hazard Map이다. 최근 발생하고 있는 홍수피해는 태풍이나 국지성 호우에 의한 피해가 대부분으로 이를 대비하기 위해서는 실시간 홍수예보가 중요하며, 나아가서는 실시간 홍수위험도 예측이 필요한 실정이다. 특히 실시간 홍수예경보가 이루어지고 있는 대하천의 경우 4대강 살리기 사업으로 인해 보 설치 및 하천 준설 등으로 인해 하천환경이 변화되어 하천의 흐름특성이 변화되었다. 따라서 변화된 하천 단면의 적용 및 보 등의 내부구조물을 고려한 수리학적 분석을 통한 실시간 홍수예경보 및 홍수위험도 작성이 필요하다. 본 연구에서는 현재 제작되고 있는 Flood Hazard Map들이 홍수범람범위와 침수심의 제한된 정보만을 포함하고 있는 한계를 벗어나 다양한 범람 시나리오에 대한 불확실성을 고려한 홍수위험도를 작성하기 위한 요소 중 홍수파 도달시간을 산정하였다. 도달시간 산정을 위해 본 연구에서는 FLDWAV 모형을 사용하였으며 태풍 산바 사상을 통한 검증 후 가상 홍수 시나리오에 대한 낙동강 유역에서의 도달시간을 산정하였다. 또한, 4대강 살리기 사업으로 설치된 보의 영향을 분석하기 위해 보 설치 전·후를 비교하였다. 홍수에 대한 여러 가지 불확실성이 있겠지만 홍수 발생시 중요하게 고려되는 홍수심, 유속 등을 추가로 고려하여 이를 바탕으로 나아가 불확실성을 고려한 홍수위험도를 작성하고자 한다.

사회기반시설의 방재 및 안전성 평가에 있어 지중 침투수의 흐름 또는 누수경로의 발달은 매우 중대한 현안이다. 따라서 지하에 선택적으로 집중된 유로의 3차원적 경로 파악 기술은 특별히 노후 댐 및 제방에서의 내적 침식과 터널 및 하천 등에서의 지하수 유출 문제와 관련하여 핵심적인 사안이라 할 수 있다. 현재 국내에서는 이러한 지중 누수 취약대 파악을 위해 전기비저항 탐사를 필두로 다양한 탐사기법들이 시행되고 있으나, 보다 구체적인 집중된 경로를 매핑하는 것은 어려움이 있는 실정이다. 본 연구에서는 국제대댐회(ICOLD)에서 소개된 전자기장 탐사의 일종인 Willowstick 탐사를 국내에 최초로 적용하고, 기술의 타당성을 비교 분석하였다. Willowstick 탐사는 누수경로가 발달한 것으로 추정되는 부지에서 상부와 하부의 저수지 또는 침출수(또는 지하수, 하천수 등)에 전극봉을 설치하고 AC회로를 구성하여 전류를 흘려보낸 후, 지표면에서 측정 그리드를 구성하여 유도된 자기장을 GPS기반의 위치 정보와 함께 측정하는 방법을 사용한다. 측정된 자기장의 등고선도는 선택적 유로가 없을 경우 수치해석적으로 예측된 자기장 등고선도와 비교함으로서 비(ratio)를 구하고 다양한 전기적 왜곡요소들에 대한 필터링을 거쳐 집중되고 있는 유로를 역산해석을 통해 3차원적으로 찾는 기법이다. 연구 대상 부지는 높이 70m의 콘크리트 표면차수벽형 석괴댐인 Y댐 하류 배면부로 설정하였다. 본 현장은 건설 당시 침투수량 계측을 목적으로 집수옹벽과 침투수량 측정실을 시공하였으나 집수옹벽 내 지중 수위가 침투수량 계측 가능 높이에 도달하지 않아 지중의 선택적 누수 경로를 따라 하류 하천으로 일정량의 침투수가 소산되고 있는 것으로 추정되었다. 집수옹벽과 침투수량 측정실을 중심으로 댐 하류부에 대한 Willowstick 전자기장 탐사와 고 정밀도 3차원 전기비저항 탐사, 그리고 댐 배면부에 설치된 지하수위공 3개소에서의 계측 경시변화 분석을 수행하였다. 현장적용 연구의 예비분석 결과, Willowstick 탐사를 통해 댐 배면부에서 지배적인 유로의 3차원적 경로를 매핑하였으며, 집수옹벽의 기초 하단을 통해 침투수가 소산되고 있는 것으로 파악되었다. Willowstick 탐사는 지중 지하수로 포화된 수면을 찾기보다는 선택적으로 집중되어 흐르는 누수경로의 3차원적 파악이 우수한 것으로 판단된다. 이에 반해 3차원 전기비저항 탐사는 지중 포화대 존재 시 포화영역의 거시적인 파악과 지하수면의 파악이 우수한 것으로 판단되나, 3차원적인 집중적 유로 파악은 쉽지 않은 것으로 검토되었다. 향후 고가의 보강비용 수반이 예상되는 곳의 지중 누수경로 매핑을 위해서는 비교적 장비와 절차가 간편한 Willowstick 탐사는 적용성이 양호할 것으로 판단된다. 추후 검증을 위해 대상 지반에 대한 시추 지반조사 및 시험을 수행할 예정이며, 연구대상 부지를 확장하여 복합적 적용성을 검토할 예정이다.

본 연구의 목적은 범죄적으로 취약한 지역을 대상으로 지역주민들이 범죄에 대하여 느끼는 불안(걱정)과 두려움, 공포심에 대한 노출 및 잠재적 고충지점(터치포인트)의 도출과 이를 기반으로 한 퍼소나와 범죄두려움지도를 개발하고, 궁극적으로는 범죄예방을 위한 개선사업에 반영하기 위함이다. 연구의 대상지역은 서울시 금천구 가산동 및 독산동 일대이며, 이 지역은 용도지역 상 주거지역과 준공업지역(소공장 밀집지역)이 혼재되고 외국인 근로자들이 다수 거주하고 있는 특성을 지닌다. 터치포인트와 퍼소나는 기본적으로 모두 대상지역의 이해관계자의견조사와 관찰조사를 기반으로 작성하였다. 범죄두려움지도 역시 이해관계자의견조사와 관찰조사를 통한 범죄취약성 요인을 기반으로 하였지만 지역주민의 의견강도와 직간접적 관련성 등도 세분화하여 반영하였고 대상지역의 물리적 여건 및 현황분석과 경찰청 Hot Spot 등의 자료를 함께 고려하여 범죄두려움지수로 계량화하였다. 그리고 이를 대상지역의 공간(지점 및 가로)에 배분하여 범죄두려움지도를 제작하였다. 본 연구를 통하여 개발한 범죄취약지역 터치포인트와 퍼소나, 범죄두려움지도는 향후 안전도시와 관련된 계획수립과 범죄예방디자인사업 등을 수행 시 매우 유용할 것으로 보이며, 특히 범죄두려움지도는 현재 경찰청 Hot Spot 지도가 가지는 제약과 한계점을 보완할 수 있을 것으로 사료된다.

최근 기상이변에 의한 자연재해의 발생빈도가 증가하고 있으며 피해규모 또한 대형화·광역화되고 있다. 최근 10년간 자연재해 원인별 피해규모는 태풍(57.1%), 호우(31.3%), 대설(11.5%)이 차지하고 있어 이에 대한 대책이 시급하다. 우리나라는 자연재해에 의한 피해에 대응하기 위해 풍수해보험을 시행하고 있다. 풍수해보험은 소방방재청이 주관하며 민간보험사가 운영하는 정책보험으로 보험계약자가 부담해야 하는 보험료의 일부를 국가 및 지방자치단체에서 보조함으로써 국민이 저렴한 보험료로 예기치 못한 풍수해에 대해 능동적으로 대처할 수 있도록 하는 선진국형 재난관리제도이다. 풍수해보험의 대상 재해는 자연재해대책법 제2조 제3항에서 정의한 태풍, 홍수, 호우, 강풍, 풍랑, 해일, 대설이며, 크게 홍수, 강풍, 대설로 분류할 수 있다. 홍수에는 태풍, 호우, 홍수, 해일이 포함되고, 강풍에는 태풍, 강풍, 풍랑이 포함되며, 이렇게 분류된 홍수, 강풍, 대설은 각각 위험도분석을 통해 풍수해보험관리지도에 반영된다. 본 연구에서는 이러한 풍수해보험관리지도의 보험요율 산정시 필요한 목적물별 피해율을 어떻게 분석하고, 이를 위한 보험목적물 DB 구축과 GIS 분석하는 방법에 대하여 연구하였다. 본 연구에서 구축한 풍수해 보험의 보험목적물은 단독주택, 공동주택, 온실을 대상으로 하였으며 우리나라 전역의 광범위한 데이터를 어떻게 구축하고, 이 데이터를 실제 시스템으로 어떻게 운영할 것인지에 대하여 제시하였다.

Chrysanthemums (Asteraceae) are important ornamental crops in worldwide that are well known as commercial valuable cultivars for cut flowers, potted plants, and garden flowering plants. Genus chrysanthemum consisted of 41 species that are mostly distributed in East Asia. Chrysanthemum has diverse ploidy levels with the basic chromosome number of x=9 from 2n=2x=18 (diploid) to 2n=10x=90 (decaploid). Fluorescence in situ hybridization (FISH) is a useful tool for studying the distribution of ribosomal DNAs. In this study, we have confirmed ploidy level by chromosome counting method. The somatic metaphase chromosome numbers were observed 2n=2x=18 in Chrysanthemum boreale, and 2n=6x=54 in C. indicum and C. zawadskii. More detailed Karyotype was constructed based on FISH method using 5S and 45S rDNA probes. Two (2) loci of 5S rDNA signals were detected in interstitial region of long arm chromosome in C. boreale and six (6) loci were in C. indicum and C. zawadskii. All of 45S rDNAs were located in terminal region of short arm chromosome which were visualize in six (6) loci in C. boreale and C. indicum and twelve(12) loci in C. zawadskii. In this study, it was the main topic to perform physical mapping of the location of 5S and 45S rDNA. Three of wild chrysanthemum showed variations in number of ribosomal DNAs. In the present investigation will help to further study of genome sequencing project in chrysanthemum.

An important worldwide plant source of dietary protein and oil, modern breeding and improvement of soybean is suffered from a narrow cultivated germplasm relative to other crop species likely because of underuse of wild soybeans as breeding resources. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important adaptive genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soybean SNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the AxiomÒ SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161markers were of good quality for genotyping. Of the converted SNPs, 82.6% 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb with the 297 inter-SNP spacings of >100 kb and with 812 kb of the largest spacing, thereby suggesting that our array is likely suitable for GWAS of soybean germplasm. This array is being used to construct high-density genetic map in populations generated from intermatings of two cultivated and two wild soybeans, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps

Rice mesocotyl is the region between the coleoptile node and point of union of the culm with the root. The mesocotyl is one of the important factor contributing to rice seedling emergence from soil in direct seedling. Several quantitative trait loci (QTLs) for mesocotyl elongation of rice had been reported in few studies. However, association mapping of mesocotyl elongation QTL was not conducted. For that reason, we detected QTLs for mesocotyl elongation in agar and soil conditions and confirmed the potentials of QTLs using chromosome substitution lines (CSSLs). Backcross inbred line (BILs) and chromosome segment substitution lines (CSSLs) derived from a cross between Kasalath and Nipponbare were employed to detect QTLs for mesocotyl elongation in rice. A total of 12 QTLs for mesocotyl elongation were detected on chromosome 1, 3, 6, 7, 9 and 12 using 98 BILs in agar and soil conditions. Two QTLs, qMel-1 and qMel-3 were consistently detected in both conditions. For substitution mapping of qMel-1 and qMel-3, across was made between 2 CSSLs, CSSL-6 and CSSL-15. Our results showed that the qMel-1 was located between two markers RM5448 and RM5310 on chromosome1 and the qMel-3 was located between RM15859-RM15974 on chromosome3. To understand factors controlling mesocotyl elongation, cell expansion and division of rice mesocotyl were investigated. Moreover, microarray analysis was conducted to select candidate genes using near-isogenic lines for two QTLs. 194 genes were up- and down regulated in rice mesocotyl.

Downy mildew, caused by P. cubensis, is one of the most devastating diseases in cucumber (Cucumis sativus) worldwide. Due to the variation and mutation of the races of P. cubensis, host resistance in cucumber has been lost in recent years, so the identification of new sources of resistance is one of the most important targets in cucumber breeding programs. Moderate levels of resistance against downy mildew has been identified in different cucumber varieties. In this study, we identified new downy 2mildew resistance QTLs in cucumber using F2 mapping populations originated from the hybridization between breeding lines of cucumber. We used both classical QTL mapping based on SSR markers and GBS (gentyping based sequencing) based QTL mapping. In this presentation, detailed information about downy mildew resistance related QTL will be presented

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.

There is a growing number of plant genomes that are being sequenced, but most of these available assemblies do not cover the entire genome mainly due to the highly repetitive sequences found in most plant genomes. Nevertheless, these repeats, although a challenge in assembly algorithms, provide relevant information about a genome’s history that could help explain its structure and complexity. Here, we cytogenetically mapped previously and presently characterized major repeats of Panax ginseng genome, including several LTR retrotransposons (PgDel2, PgDel3, PgTat1, PgTat2, PgTork) and one tandem repeat, PgTR Fluorescence in situ hybridization (FISH) results showed differential accumulation of Ty3/gypsy LTR retrotransposons into different chromosomal regions or subgenomes, suggesting a non-random preferential amplification of retrotransposons in these regions and an allopolyploid origin of P. ginseng. In silico analysis based on 1x whole genome sequence reads suggests that PgTR is the most abundant tandem repeat in ginseng, which was further corroborated by FISH analysis. More importantly, its unique distribution pattern among the 24 ginseng chromosomes, coupled with the non-random distribution of LTR retrotransposons and rDNA arrays, allowed us to discriminate and characterize each individual ginseng chromosome. These different newly characterized cytogenetic markers allowed reorganization of previously reported ginseng karyotype with better resolution, demonstrating the irutility in ginseng chromosome identification. These information give us insight about the genomic structure of P. ginseng, and should be useful for future comparative cytogenetics studies among closely related species to unravel its genomic history. This work was supported by the Next-Generation BioGreen21 Program (No. PJ008202), Rural Development Administration, Republic of Korea.

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.