As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.

This study is to raise the utilization of genetic resource of wheat (Triticum aestivum) landrace by evaluating genetic variation related to end use quality of the Far East. Allelic composition of HMW-glutenin subunits encoded by genes of Glu-1 loci associated with bread baking quality was investigated in 324 wheat landrace genetic resources originated from Korea, China, and Japan. The most frequent combination of HMW-glutenin subunits were Glu-A1c, Glu-B1b in Korean and Japanese resources, but Glu-A1a and Glu-B1c were the most in Chinese resources. By using the Glu-1 score system, 24 accessions were evaluated as 10 out of 10. As for genetic diversity, represented by polymorphic information content(PIC) index, the level of variation of Korean landrace(0.245) was lower than that in China(0.569) and Japan(0.294). When it comes to unique composition, Glu-B1f(13+16) and Glu-D1f(2+10) subunits are only in Chinese resources. Glu-B1d(6+8), Glu-B1e(20), Glu-D1b(7+8), and Glu-D1c (7+9) subunits are only in Korean resources. Consequently, this study showed that Chinese landrace collection was the most highly diverse and had distinctive characteristics compared to Korean and Japanese one. Especially, some resources having preferable genetic stock or high Glu-1 score can be valuable for wheat breeding program.

Stem rust of wheat caused by Puccinia graminis f. sp. Tritici is historically one of the most important diseases of crops worldwide. The objective of this study was to screen the growth habits and yield of wheat accessions in Korea winter condition. We collected ninety stem rust resistant germplasms from USDA-Grain and planted for the characteristics of growth and yield in 2013. We measured the growth characteristics such as the plant type, leaf color, heading date, stem length, spike length, awn length, number of spikelet, number of tiller, and 1,000 kernel weight (g). Early maturity is most important wheat breeding target in double cropping system such as Korea. Heading dates of ninety cultivars ranged from May 17 to June 7. The Keumkang control cultivar headed on May 23. Heading dates of seventeen accessions had as early as Keumkang control (May 23). The numbers of semi-erect and intermediate type for growth habit were 45 and 33 respectively. The 1000 kernel weights were also measured. Mean 1000 kernel weights ranged from 16.7g (Webster) to 41.8g (123 A1C2). The average of stem length was 100.2cm and Keumkang was 58.4cm. These results showed that A4849-60P-7P-1P (Chile), MG 31492 (Ethiopia), 1338.F.6.C.3.B (Kenya), 1203 A1C2 (Kenya), and II-90-20/3-1R-1M- 3R (Mexico) were best lines for agronomic characteristic such as early heading date and grain yield

본 연구는 야생콩과 재배콩의 교잡 후대 집단에서 25계통을 선발하여 사료 수량 및 품질을 평가하여 사료용 콩 품종육성 가능성을 검토하였으며, 그 결과를 요약하면 다음과 같다. 먼저, 야생콩과 재배콩 교잡종의 조사료 수확시기별 수량 및 품질 검정에서 교잡종을 대조품종인 재배콩과 비교하여 보았을 때 사료의 수량이나 품질을 고려하면 협비대기인 R6에 가장 우수한 것으로 평가가 되었다.야생콩과 재배콩의 교잡후대 계통에 대한 사료 수량 및 품질평가에서 대조품종과 비슷하거나 유의적인 차이가 없는 수량이 높은 계통을 선발할 수 있었으며, 가식부위 생체중은 대조품종인 재배콩 보다 교잡종이 상대적으로 높은 것으로 평가가 되었다. 교잡종에 대한 사료품질을 평가한 결과 AFGC의 두과 건초 품질 등급기준에 따라 나누었을 때, 특등급의 조건인 조단백질 함량 19% 이상, NDF 함량 40% 미만, ADF 함량 31% 미만, DDM 65% 이상, DMI 3.0% 이상, RFV 151 이상을 모두 충족시키는 계통을 선발할 수 있었고, 이들중 몇몇 계통은 수량도 우수한 것으로 평가가 되었다. 따라서, 재배콩과 야생콩의 교잡을 통해 사료 수량 및 품질이 우수한 사료용 콩을 개발할 수 있을 것으로 판단된다.

Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.

딸기 유전자원 중 원예적 특성이 우수하여 육종 소재로 활 용 가능성이 높은 19품종을 대상으로 완숙된 과실을 부위별 (과피 및 과실 전체)로 안토시아닌 함량을 분석하고 색차계를 이용하여 비파괴적인 방법으로 안토시아닌 고함유 계통을 선 발할 수 있는지에 대하여 검토하였다. 그 결과 딸기의 과피는 22.04～87.16 mg · 100 g -1 FW, 과실 전체는 1.98～30.16 mg · 100 g -1 FW의 범위에 분포하여 측정 부위와 유전자원에 따라 안토시아닌 함량의 변이가 큼을 알 수 있었다. 과실 전 체를 기준으로 하였을 때, 조사된 유전자원 중 ‘Sachinoka’, ‘Tamar’, ‘Amaou’, ‘Summerberry’ 순으로 안토시아닌 함량 이 높게 나타났다. 과피와 과실 전체 부위의 안토시아닌 함량 간의 상관계수가 0.867로 높아 과피를 기준으로 하여 과실 전 체의 안토시아닌 함량을 추정할 수 있을 것으로 생각된다. 또 한 과실 전체의 안토시아닌 함량과 측정된 색차계의 L*값 (-0.791) 및 b*값(-0.772)에서 높은 역의 상관관계를 보였다. 따라서 향후 딸기 육종 프로그램에서 안토시아닌 고함유 계 통을 신속하게 선발할 때, 색차계를 보조적인 방법으로 활용 할 수 있을 것으로 판단된다.

With the rapid development of sequencing technologies, next-generation sequencing is widely utilized for molecular breeding in several crops including rice. We performed whole genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. In total, 2,448 million raw reads were generated with over 58x coverage of Nipponbare genome. We mapped the reads from each of the ten accessions onto genomic sequence of japonica rice cultivar, Nipponbare. We detected 3,144,016 SNPs, which estimated to be one per 2.2kb on average. We found SNPs in genes that have been reported to be involved in rice flowering time regulation and bacterial blight resistance among ten rice accessions. Unmapped region against Nipponbare genome occupied about 1 ~ 2% in each accession. Over 50% of the unmapped region were found in the repeat region. The minimum length of gap in all accessions were 1bp and the maximum length of gap was 45,967bp in Ilpum. We also identified 3,497 possible gene loss events within these unmapped regions. The frequency of gene loss in each chromosome ranged from 33 on chromosome 5 to 913 on chromosome 11. The genetic variations we detected among ten rice accessions will provide invaluable resources for identification of genes associated with diverse traits of agronomical importance for molecular breeding.

This study was conducted to assess the genetic diversity and population structure of 70 amaranth accessions collected from South and Southeast Asia using 14 simple sequence repeat (SSR) markers. In total, 67 alleles were detected, with an average of 4.79 per locus. Rare alleles comprised a large portion (46.3%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. The mean major allele frequency (MAF), genetic diversity (GD) and polymorphic information content (PIC) of the 14 SSR loci were 0.77, 0.36, and 0.34, respectively. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbor-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. All 70 accessions showed a clear relationship to each cluster without any admixtures. We observed a relatively low extent of genetic exchange within or among amaranth species from South and Southeast Asia. The genetic diversity results could be used to identify amaranth germplasms and so facilitate their use for crop improvement.

본 연구는 우리나라에서 보존하고 있는 구기자(Lycium chinesis Miller) 유전자원 131점의 잎과 줄기를 에탄올로 추출한 후 페놀화합물의 함량을 측정하여 비교 분석하기 위하여 수행되었다. 구기자 잎의 페놀 함량은 8.8~14.9mgg1을 보였으며 11.6~13.5mgg1 사이에는 약 60%의 유전자원이 분포되어 있었다. CB03286-89 유전자원은 총 페놀함량이 14.9±0.3mgg1으로 가장 높은 반면 CBP03310-250은 8.8±0.2mgg1으로 가장 낮은 함량을 보였다. 줄기에 대한 총 페놀함량은 6.8~12.4mgg1의 함량 범위를 보이고 있으며 잎보다는 상대적으로 다소 낮은 것으로 나타났다. 구기자 잎의 페놀화합물 중 33가지 물질을 정량 분석한 결과 China collection No.1에서 가장 높게 나타났으며 99797 수집종에서 가장 낮게 나타났다. (+)catechin 함량은 CB03286-89에서 가장 많았다. Myricetin은 Geumsan jaerae, Japan No.1, China collection No.1, CL32-13, CB04329-13, China collection No.12 그리고 CB03286-89 등에서 분석되었지만 나머지 구기자 유전자원의 잎에서는 검출되지 않았다. 줄기에 대한 페놀화합물은 잎에 비하여 상대적으로 함량이 적었으며 99797 수집종이 가장 많은 함량을 보였으나 CB04329-13에서는 가장 적은 함량을 보였다. (+)catechin 함량은 Japan No.1이 231.0±0.5ugg1으로 가장 높았으며, myricetin은 Japan No.1, China collection No.1, China collection No.12, CB03286-89 및 99797에서 분석되었지만 나머지 구기자 유전자원의 줄기에서는 검출되지 않았다.

Advances in genome sequencing technologies have aided discovery of millions of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDels), which are an invaluable resource to analyze genetic diversity in a population. We performed whole-genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. A total of 2,447 million raw reads were generated with over 58x coverage and detected 3,240,025 DNA polymorphisms between the Korean rice accessions and Nipponbare as reference genome. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). Potential SNPs were classified into two types, homozygous SNP and heterozygous SNP, which approximately 87% of the total was homozygous SNPs from ten accessions and heterozygous SNPs accounted for 13%. According to annotation of DNA polymorphisms, 634,620 SNPs were found in gene region, and only 169,738 SNPs were occurred in coding region. Altogether, 86,251 non-synonymous SNPs were located on 76,891 genes. We also examined genes which had at least one SNP in all ten accessions. It was estimated that the total of 290 genes had one or more non-synonymous SNPs and 25 genes had only synonymous SNPs. These genes were functionally classified based on gene ontology (GO). These DNA polymorphisms obtained from our result will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.

Soybean is desirable as a forage crop because of it has high protein and oil concentration. Wild soybean, a progenitor of cultivated soybean, has a softer stem and higher protein content in seed than cultivated soybean. There is little information on yield and forage quality for wild soybean and its derivatives. The objective of this study was to determine the forage yield and quality of wild soybeans and selected soybeans derived from a cross G. max ×G. soja. Forage yield and quality were assessed for three grain soybean cultivars, three wild soybeans and three selected lines from G. max×G. soja. Forage quality attributes such as crude protein (CP), crude fat (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF), digestible dry matter (DDM), dry matter intake (DMI) and relative feed value (RFV) were determined at the R2, R4 and R6 developmental stages. Forage yield and CF were highest at stage R6 in G. max, G. soja and selected G. max×G. soja lines. CP content was similar between R2 and R4 but increased sharply after R4 and peaked at R6 in G. max and selected lines from G. soja×G. max. On the other hand, CP content was similar between R4 and R6 stage in wild soybeans. Generally, NDF and ADF were highest at stage R4 but decreased at stage R6. DDM, DMI, and RFV increased between R4 and R6. These results suggest that R6 was the optimal harvest stage to provide forage of highest quality and yield. A study was conducted in 2011 to evaluate forage yield and quality at stage R6 in 25 lines from PI483463 (G. soja)×Hutcheson (G. max) and four cultivated grain soybeans. Hutcheson had the highest forage yield with 24.7t/ha infresh weight (FW) among grain soybeans. Line W11 had the highest forage yield(25.7t/ha,FW) among G. soja×G. max selections and four other lines had similar forage yield compared to Hutcheson. Generally the 25 lines from this G. max×G. soja cross had thinner main stems and branches than cultivated soybeans. When the 25 lines were evaluated for their feed quality as per forage grade by AFGC, nine lines rated prime grade and all 25 lines were classified as forage Grade 1. Results of this study indicate crosses between wild and cultivated soybean show promise for improving soybean as a forage crop.

Genus Taraxacum has been widely used as a folkloric medicine for treatment of diverse diseases. The genetic diversity and relationship among 32 accessions belonging to five Taraxacum species (T. mongolicum T. coreanum, T. coreanum var. flavescens, T. officinale and T. laevigatum) which collected from field, mountain, island and seaside of Korea were evaluated using ISSR markers. A total of 142 ISSR loci detected in the overall species were all polymorphic loci (100%) and interspecies polymorphisms obtained from Korean native and naturalized species were 98.2% and 94.5%, respectively. The genetic similarity matrix (GSM) among 32 accessions ranged from 0.025 to 0.860 with an average of 0.303. According to the clustering analysis, the Korean native species and naturalized species were divided two major clusters. In addition, the different species were divided into independent groups except for the T. coreanum and T. coreanum var. flavescens, and all the 32 accessions could be classified into 7 categories. The study findings indicate that Taraxacum accessions have a high genetic diversity and the dandelion accessions as breeding materials can be effectively utilized for the improvement of Taraxacum breeding.

우리나라에서 수집한 재래종 조 26계통들에 대하여 9개의 AFLP primer조합을 사용하여 유전적 다양성 및 계통유연관계를 분석한 결과는 다음과 같다. 1. 분석에 이용한 9개의 AFLP primer조합들은 국내에서 수집한 조 26계통들에서 총 170개의 DNA단편을 나타내었고, 이중에서 145개의 단편(85.3%)들은 다형성을 나타내었다. 9개의 AFLP primer조합들에서 측정된 유전적 다양성 값(Hs)은 1.84에서 6.80의 범위로 나타나, 평균 3.85값을 나타내었다. 강원지역에서 수집한 조 계통(Group 1)들은 평균 3.39의 유전적 다양성 값을 나타내었고, 경기도 등 타 지역에서 수집한 조 계통들(Group 2)은 평균 2.99의 유전적 다양성 값을 나타내었다. 2. 국내에서 수집된 재래종 조 26계통들은 유전적 유사성 73% 수준에서 크게 두 개의 그룹으로 구분되었다. Group I은 유전적 유사성 76.8% 수준에서 강원도에서 수집한 13계통들과 경기도에서 수집한 1계통을 포함하고 있었으며, Group II는 유전적 유사성 78.9% 수준에서 강원도에서 수집한 2계통들과 타 지역에서 수집한 10계통들을 포함하고 있었다. 본 연구결과는 우리나라에서 수집한 재래종 조 계통들에 대한 유전적 다양성 및 계통유연관계 이해 그리고 이들 자원의 수집 및 보존 등에 유용한 정보를 제공할 것으로 기대된다.

In this study, simple sequence repeat (SSR) analyses were utilized for evaluation of genetic diversity and discrimination of 17 accessions. Five cultivars, which were developed from Korea, and 12 foreign accessions, which were collected from China, Japan, Russia and USA, were evaluated by nine markers out of 22 SSR markers. A total of 39 alleles were detected, ranging from 2 to 8, with an average of 4.3 alleles per locus. The expected heterozygosity and PIC values were 0.627 and 0.553, with a range from 0.21 (GB-PG-078) to 0.76 (GB-PG-142) and from 0.19 (GB-PG-078) to 0.70 (GB-PG-142), respectively. Four makers out of nine SSR markers, GB-PG-026, GB-PG-043, GB-PG-142 and GB-PG-177, were selected as key factors for discrimination of Korean ginseng cultivars and foreign accessions. All of Korean ginseng cultivars and foreign accessions were individually by the combination of four SSR markers. Consequently, the SSR markers developed in this study may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and foreign accessions.

본 연구는 우리나라에서 자생 및 재배되고 있는 들깨와 차조기의 재배형 및 잡초형 계통들에 대하여 종자발아에 대한 변이 양상을 구명하기 위해 재배형 들깨 102계통, 잡초형 들깨 41계통 그리고 잡초형 차조기 19계통들에서 측정된 종자발아율 및 발아세는 다음과 같다. 1. 재배형 들깨는 저온처리 조건에서 1%에서 99%의 발아율을 나타내어 평균 73%±24를 나타내었으나, 비저온처리조건에서는 0%에서 98%의 발아율을 나타내어 평균 45%±26를 나타내었

The genetic diversity and the genetic relationship among 30 genetic resources of T. officinale and T. coreanum collected from 20 regions in Korea were evaluated by using ISSR markers. Out of 127 loci detected overall, 122 were identified to be polymorphic with a rate of 96.0% at the 30 individuals. The intraspecific polymorphism between T. officinale and T. coreanum was 92.6% and 88.2%, respectively. The genetic similarity matrix (GSM) revealed a wide range of variablility among the 30 accessions, spanning from 0.179 to 922. According to the clustering analysis, different species T. officinale and T. coreanum, were divided into independent groups and all of the accessions could be classified into 7 categories. Especially, all of the mountain collected accessions belonged to independent groups. The study findings indicate that T. officinale and T. coreanum accessions have a high genetic diversity and accordingly carry a germ-plasm qualifying as good genetic resources for breeding.

In this study, 15 simple sequence repeat (SSR) markers were used to analyze the population structure of 55 mungbean accessions (34 from South Asia, 20 from West Asia, 1 sample from East Asia). A total of 56 alleles were detected, with an average of 3.73 per locus. The mean of major allele frequency, expected heterozygosity and polymorphic information content for 15 SSR loci were 0.72, 0.07 and 0.33 respectively. The mean of major allele frequency was 0.79 for South Asia, and 0.74 for West Asia. The mean of genetic diversity and polymorphic information content were almost similar for South Asian and West Asian accessions (genetic diversity 0.35 and polymorphic information content 0.29). Model-based structure analysis revealed the presence of three clusters based on genetic distance. Accessions were clearly assigned to a single cluster in which >70% of their inferred ancestry was derived from one of the model-based populations. 47 accessions (85.56%) showed membership with the clusters and 8 accessions (14.54%) were categorized as admixture. The results could be used to understanding the genetic structure of mungbean cultivars from these regions and to support effective breeding programs to broaden the genetic basis of mungbean varieties.

The polymorphism and the genetic relationships among 32 genetic resources of genus Nelumbo from Korea, Japan, China, USA, India, Thailand and Gabong were thoroughly investigated and extensively examined using ISSR markers. Out of 103 loci detected overall, 94 were identified to be polymorphic with a rate of 91.2%. The genetic similarity matrix revealed a wide range of variability among the 32 accessions, spanning from 0.227 to 0.833. The study findings indicate that the Nelumbo accessions have a high genetic diversity, and accordingly carry a germplasm qualifying as good genetic resources for cross breeding. According to the clustering analysis, different subspecies, N. nucifera and N. lutea, were divided into independent groups and all of the N. nucifera accessions could be classified into five categories. Compared to RAPD analysis, ISSR method showed a clearer picture of polymorphism among the accessions and exhibited a definite distinction even among the subspecies. In this respect, ISSR analysis is considered to be more effective in differentiating the accessions and subspecies of the genus Nelumbo than RAPD test.