인디카 벼는 일조시간이 짧은 열대지역에서 주로 재배하며, 자포니카 벼는 일조시간이 긴 한국, 일본, 및 중국(동북부 지역)을 포함하는 온대지역에서 재배한다. 최근 동남아 열대지역에서 자포니카 쌀에 대한 수요가 증가함에 따라 농촌진흥청은 필리핀 국제미작연구소(IRRI)와 공동으로 열대지역에 적응하는 다수성 온대 자포니카 벼 품종을 개발하고 있다. 일반적으로 자포니카 벼를 단일조건인 열대지역에 재배하면 이앙 후 바로 개화가 촉진되어 극조기 출수가 유도된다. 따라서 열대지역에 적응하는 자포니카 벼를 개발하기 위해서는 단일조건에서도 충분히 생장한 후 출수를 하는 특성이 우선적으로 필요하다. 본 연구는 국내 자포니카형 벼 품종인 ‘일품’과 미국에서 육성한 인디카형 벼인 ‘Zenith’를 교배한 F9 RIL 180 계통을 이용하여 필리핀의 단일조건하에서 재배하면서 출수기에 관련한 양적형질유전자좌(QTL) 분석을 수행한 바, 그 결과는 다음 과 같다. 1. 단일조건하에서 출수일수(파종~출수)에 관여하는 2종의 QTL(qHD6-SD와 qHD6-LD)을 탐색하였다. 2. 정밀지도제작 결과 qHD6-SD와 qHD6-LD은 모두 6번 염색체 Hd1 유전자를 포함하는 98 kb 영역에 존재하는 동일한 QTL인 것으로 나타났다 3. 시험계통을 필리핀 단일 조건에서 재배하였을 때 qHD6- SD 또는 qHD6-LD에서 Zenith allele형을 보유한 계통들은 일 품 allele형을 가진 계통들 보다 출수일수가 평균 8일 정도 길었다. 3. 시험계통을 한국의 장일 조건에서 재배하였을 때 qHD6- SD 또는 qHD6-LD에서 Zenith allele형을 보유한 계통들은 일품 allele형을 가진 계통들보다 출수일수가 평균 8일 정도 짧 았다. 4. 이러한 특성은 기존에 보고된 Hd1 유전자의 특성과 유사하여 qHD6-SD 및 qHD6-LD 은 Hd1 유전자일 가능성이 높은 것으로 나타났으며, 본 시험에서 사용한 Zenith는 nonfunctional Hd1 allele을 보유하는 것으로 추정되었다. 5. 이러한 결과를 통해 열대지역에 적응하는 자포니카 벼 육종연구에서 극조기 출수를 방지하고 충분한 출수일수를 확보하여 수량을 높이기 위해서는 인디카 벼가 주로 보유하고 있는 non-functional Hd1 allele을 반드시 도입해야 함을 재확인 하였다.

Pleurotus eryngii, an edible white-rot fungus, is cultivated widespread in Eurasia, northern Africa and China. It occupies the second position in the world mushroom market. Despites the importance, the small numbers of studies have been done. To promote the availability of P. eryngii, it is important to know the genome and organization of the fungus. In this study, the whole genome sequence of P5 monokaryon from P. eryngii KNR2312 strain was sequenced using Next Generation Sequencing (NGS) strategy. Identified 222 SSR markers based on newly known genome information and various type of markers used to construct the map consisted of 12 linkage groups (LGs) spanning 1047.8 cM. Using composite interval mapping, 71 quantitative trait loci (QTL)s were identified on 12 linkage groups (LG) for nine traits such as yield, quality, cap color and earliness in four different populations. Clusters of more than five QTLs for various traits were identified on three genomic regions on LG 1, 7, and 9. The largest cluster was identified on LG 1 in the range from 65.4 to 110.4 cM. We performed the genes prediction analysis responsible for yield in the LG1 genomic region with highest logarithm of the odd (LOD) scores The identified genes were involved in biomass degradation and synthesis and signal transduction. However, the region was wide to identifie the genes crucial role in important trait, we need to narrow down. To improve the resolution of QTL mapping, we enlarge the populations crossing with additional 205 monokaryons. Find mapping of QTLs will increases the accuracy and efficiency of interpret the genomic region and enhance the usefulness of genomic information. [Supported by a grant from the IPET (213007-05-1-SBI30), MIFAFF, Republic of Korea.]

고추의 적색소는 고추의 상품성을 가늠하는 중요한 척도이면서 식재료 뿐 아니라 상업적으로도 다양하게 활용되고 있다. 본 연구는 적색소 성분의 함량과 관계하는 QTL 마커를 개발하기 위하여 적색소 성분 분석을 위한 mapping 집단을 육성하였고, 적색소 성분에 대한 QTL mapping을 수행하였다. 적색소 분석을 위한 mapping 집단인 ‘만다린’과 ‘블랙클러스터’를 양친으로 하는 F7 RIL 집단에서의 색도(ASTA value) 분포는 1.64에서 117.26의 범주에 있으며 그 분포 양상은 정규분포를 보여 QTL분석에 적합한 것으로 확인되었다.Mapping 집단의 양친들에 대해서 454 GS-FLX pyrosequencing을 이용한 NGS를 수행하였고, 그 결과 ‘만다린’과 ‘블랙클러스터’각각 120.44Mb와 142.54Mb의 염기서열 데이터를 확보할 수 있었으며, ‘만다린’에서 1,025개, ‘블랙클러스터’에서 1,059개의 SNP들을 확보하게 되었다. 이 SNP들을 HRM 분석에 용이하도록 프라이머를 제작하여 유전자 지도 작성을 수행한 결과 총 246개의 SNP 마커를 이용하여 약 512cM을 설명할 수 있는 21개 연관군의 유전자 지도가 작성되었다. 분석 집단 93계통들에서 측정된 ASTA 값을 이용하여 수행한 QTL 분석 결과 총 6개의 QTL 을 확인하였다. 이들 QTL과 근접한 마커들은 향후 고추의 적색소 함량 연구에 매우 유용한 정보로 활용될 것이며, 아직까지 개발된 바 없는 적색소 함량 연관 마커 개발에 가능성을 열어줄 것으로 기대한다.

In here, we screened drought tolerant varieties with modified leaf water loss rate assay and visual drought tolerant phenotype in the greenhouse conditions with more than 800 varieties. Among these varieties, Samgang, Gumei4 and Apo showed the lowest of leaf water loss rate and strong drought tolerant phenotype. To identify drought QTLs with Samgang variety, we developed the doubled-haploid (DH) population consist of 101 lines derived from a cross the drought tolerant cultivar Samgang and the drought sensitive cultivar Nagdong. To score the drought phenotype degrees of this population, we withheld water for 6 weeks and treated the watering for 7 days. After watering, visual phenotype was observed 1 to 9 degree according to the standard evaluation system for rice, IRRI. Drought sensitive parent Nagdong was almost died and was scored as 9 degree, while tolerant parent Samgang showed slightly leaf tip drying phenotype and was scored as 3 degree in our experimental conditions. Three main QTLs were detected on chromosome 2, 6, and 11 with this visual phenotype. We also measured relative water contend of these population under drought stress conditions, and got one main QTL on chromosome 11. The QTL loci on chromosome 11 with flanking markers RM26755-RM287 has a function for visual phenotype and relative water content under drought conditions.

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.

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.

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.

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

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

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.

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.

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.

Grain size is a major determinant of grain yield in rice. In a previous study, a QTL for grain width(GW), qgw1 was detected on chromosome 1 using 96 BC3F8 lines derived from a cross between ‘Hwaseongbyeo’ as a recurrent parent and ‘O. rufipogon’ as a donor parent. At this locus, the O. rufipogon allele increased GW. Among the 96 introgression lines, three ILs with the O. rufipogon qgw1 locus showed significantly increase in grain width compare to the recurrent parent. One of the three lines, CR572 was selected and crossed to ‘Hwaseongbyeo’. A total of 494 F2:3 were evaluated for grain width and agronomic traits in the field. QTL analysis in 494 F2:3 lines indicated that QTL for grain width was located in the interval RM495–RM5443. To narrow down the position of qgw1, substitution mapping using F4 lines with different cross-over breakpoints in the region is underway. The result will be discussed.

In this study, we were conducted the construction of the framework map using SSR markers in the F2 population derived from a cross between waxy corn inbred line (02S6140) and sweet corn inbred line (KSS22), and also identifying of QTLs associated with eating quality traits by employing genetic linkage map of F2:3 population. The linkage map was constructed using 295 SSR markers on the 158 F2 individuals derived from a cross of 02S6140 and KSS22. The map comprised a total genomic length of 2,626.5cM in ten linkage groups and an average distance between markers of 8.9cM. Chi-square test revealed that 254 markers (86.1%) associating with all ten chromosomes exhibited a segregation of 1:2:1 Mendelian ratio. A total of 10 QTLs each for pericarp thickness (PER), amylose content (AMY), dextrose content (DEX), and sucrose content (SUC) were detected in the 158 F2 families. The number of QTL per each trait was ranged from 2 to 4, and also phenotypic variance was ranged from 4.26 to 30.71%. For PER, 4 QTLs were found to be controlled by four genomic regions at locations chromosomes 4, 5, 8, and 9 contributing 10.43, 6.71, 6.74, and 7.79% of phenotypic variance, respectively. While 2 QTLs for AMY, DEX, SUC traits, were found to be controlled by two genomic regions at locations chromosomes 4, 6, 8, and 9 contributing between 4.26 and 30.71% of phenotypic variance, respectively. Among them, 4 QTLs, such as qAMY4 (10.43%), qAMY9 (19.33%), qDEX4 (21.31%), and qSUC4 (30.71%), may be considered as a major QTLs, while the remaining six QTLs might be regarded as minor QTLs. In our study, qAMY9 for amylase content was detected on chromosome 9 in marker intervals phi027-umc1634, which was the same locus as encoding wx1 gene. Thus qAMY9 may be thought very useful molecular marker for selecting amylase content trait. The other QTLs may be thought very useful molecular marker for eating quality traits. The resulting genetic map will be useful in dissection of quantitative traits and the identification of superior QTLs from the waxy hybrid corn, and also this study may provide valuable information for the further identification and characterization of genes responsible for eating quality-related traits in waxy corn and sweet corn.

In order to clarify the chromosomal location of quantitative trait loci (QTL) associated with the yield and agronomic traits in waxy corn and sweet corn (Zea maysL.), we were conducted identifying of QTLs associated with yield and agronomic traits by employing genetic linkage map of F2:3 population. A total of 14 QTLs each for days to silking (DTS), plant height (PH), ear height (EH), ear height ratio (ER), ear length (L-Ear) and kernel setting length (L-Sear) were detected in the 158 F2 families. The number of QTL per each trait was ranged from 1 to 6, and also phenotypic variance was ranged from 3.55 to 16.86%. For DTS, one QTLs was found to be controlled by genomic regions at locations chromosomes 1 contributing 9.21% of phenotypic variance. While three QTLs for PH, were found to be controlled by 3 genomic regions at locations chromosomes 1 and 2 contributing 6.68, 6.85 and 8.17% of phenotypic variance, respectively. For EH, six QTLs were found to be controlled by 6 genomic regions at locations chromosomes 1, 7, 8 and 10 range from 3.55 to 11.44% of phenotypic variance. The one QTLs for ER was found at locations chromosomes 1 contributing 7.25% of phenotypic variance. For L-Ear, two QTLs were found to be controlled by 2 genomic regions at location chromosome 7 and 10 contributing 7.40 and 11.63% of phenotypic variance, respetively. The one QTLs for L-Sear was found at locations chromosomes 3 contributing 16.86% of phenotypic variance. Among them, three QTLs, such as qEH8 (11.44%), qLEar10 (11.63%), and qLSear3 (16.86%) may be considered as a major QTLs, while the remaining 11 QTLs might be regarded as minor QTLs. This study may provide valuable information for the further identification and characterization of genes responsible for agronomic traits in waxy corn and sweet corn.

1. 선행 연구에서 염색체 3번의 RM60~RM231 부근에서 종자중, 수당립수에 관여하는 QTL이 탐지되었고, 이를 확인하기 위하여 이 지역에 크기와 위치가 다른 O. glaberrima 단편이 이입된 5 계통을 선발하여 표현형을 조사하였다. 실험 결과 계통별로 출수기, 임실률, 수당립수, 종자중을 제외한 형태적 특성들이 밀양23호와 비슷한 양상을 보였다. 이는 대부분의 염색체 지역이 밀양23호로 회복되었기 때문이라고 보여진다. 2. 유전자의 위치를