De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data

Jo, Yeonhwa,Choi, Hoseong,Bae, Miah,Kim, Sang-Min,Kim, Sun-Lim,Lee, Bong Choon,Cho, Won Kyong,Kim, Kook-Hyung The Korean Society of Plant Pathology 2017 Plant Pathology Journal Vol.33 No.5

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

중국과 브라질의 대두 무역 동향 분석과 예측

장수환,전주람,장유운 한국 포르투갈-브라질 학회 2018 포르투갈-브라질 연구 Vol.15 No.1

China is a major importer of soybean taking about 60% of world soybean trade. China's soybean import growth has continued steadily over more the 20 years. This is due to the decrease in the rural population, changes in the livestock industry policy, and changes in dietary caused by urbanization and income increase. Brazil is the main exporter of soybean to China. The amount of soybean imported from Brazil has been increasing significantly in last decade. The production costs per soybean unit in Brazil are relatively inexpensive and the Brazilian soybean has higher protein content than American soybean. These are the main reasons of the increasing Brazilian soybean exports to China. However, it is predicted that China's soybean demand growth rate will decrease because of the decrease in the population growth rate and the increase in vegetarian diet. And in Brazil, even though the area harvested has been expanding and pesticide usage has been increasing, that agricultural productivity has not reached that level. In this paper, we consider various variables surrounding soybean trade between China and Brazil. Especially, the future changes in China’s soybean demand are forecasted by using STELLA model applying the relationship between the meat consumption and the increase in soybean demand using.

Effects of Heat Treatment on Soybeans With and Without the Gene Expression for the Kunitz Trypsin Inhibitor: Chick Growth Assays

Burnham, L.L.,Kim, I.H.,Hancock, J.D.,Lewis, A.J. Asian Australasian Association of Animal Productio 2000 Animal Bioscience Vol.13 No.12

A total of 864 broiler chicks were used at Kansas State University and the University of Nebraska to determine the effects of heat treatment of two soybean genotypes on the growth performance. The soybeans were Williams 82 variety with (+K) and without (-K) gene expression for the Kunitz trypsin inhibitor. Heat treatment (autoclaving at $121^{\circ}C$ and $1.1kg/cm^2$) was applied for 0, 3, 6, 12, 18, and 24 min, resulting in a $2{\times}6$ factorial arrangement of treatments. Station and station treatment effects occurred, indicating that response in nutritional value of the soybean genotypes to heat treatment varied from year to year and location to location. However, the interactions were in magnitude of response rather than direction of response, with greater reductions in trypsin inhibitor concentrations for the soybeans heat processed at the Nebraska location. Pooled data indicated that -K supported greater (p<0.001) ADG, ADFI and gain/feed than the +K genotype. As the length of heat treatment increased, the ADG, ADFI, and the gain/feed ratio increased for chicks fed both soybean genotypes (p<0.0001). However, heating the -K soybeans resulted in a greater response in ADG, ADFI, and gain/feed than heating the +K soybeans (genotype heat treatment interaction, p<0.001). Pancreatic weights (mg pancreas/g of BW) of chicks fed -K soybeans were reduced compared to those from chicks fed +K (p<0.001). Increasing heat treatment decreased pancreas weights in chicks fed both soybean genotypes (p<0.001). Chicks fed heated soybeans in the Nebraska experiment had lower pancreatic weights than chicks fed heated soybeans in the Kansas experiment (station heat treatment interaction, p<0.0001). Chick growth performance was improved and pancreatic weights decreased by feeding raw -K soybeans versus raw +K soybeans, and by increasing heat treatment of both soybean genotypes. However, the response to heat treatment was not independent of genotype. Both +K and -K soybeans heated for 24 min supported similar ADG, ADFI, gain/feed, and pancreas weights, although chicks fed raw +K soybeans had lower growth performance than chicks fed -K soybeans. In conclusion, raw -K soybeans supported greater growth performance in broiler chicks than raw +K soybeans, although this advantage was lost when both soybean genotypes were heated for 24 min. Heat treatment of +K soybeans supported similar growth performance to heated -K soybeans, even though +K soybeans supported lower rates and efficiencies of gain than -K soybeans when fed raw.

Analysis of Isoflavone, Phenolic, Soyasapogenol, and Tocopherol Compounds in Soybean [Glycine max (L.) Merrill] Germplasms of Different Seed Weights and Origins

Kim, Eun-Hye,Ro, Hee-Myong,Kim, Sun-Lim,Kim, Hong-Sig,Chung, Ill-Min American Chemical Society 2012 Journal of agricultural and food chemistry Vol.60 No.23

<P>This study investigated the functional compounds, including isoflavones, phenolics, soyasapogenols, and tocopherols, that were detected in 204 soybean [Glycine max (L.) Merrill] germplasms. The soybean samples were divided into three groups according to origin: America, China, and Korea. The soybean samples were also classified into three groups on the basis of 100-seed weight: small (<13 g), medium (13–24 g), and large (>24 g). Among the soybean germplasms, CSRV121 (Bosukkong) had the highest level of isoflavone content (4778.1 μg g<SUP>–1</SUP>), whereas CS01316 had the lowest isoflavone content (682.4 μg g<SUP>–1</SUP>). Of the soybeans from the three different countries of origin, those from Korea showed the highest average concentration of total isoflavones (2252.6 μg g<SUP>–1</SUP>). The small seeds had the highest average total isoflavone concentration (2520.0 μg g<SUP>–1</SUP>) of the three different seed sizes. Among the 204 soybean germplasms, CS01405 had the highest content of total phenolics (5219.6 μg g<SUP>–1</SUP>), and CSRV017 (Hwangkeumkong) had the lowest phenolic content (654.6 μg g<SUP>–1</SUP>). The mean concentrations of total phenolic compounds were 2729.1 μg g<SUP>–1</SUP> in American soybean seeds, 1680.4 μg g<SUP>–1</SUP> in Chinese soybean seeds, and 1977.6 μg g<SUP>–1</SUP> in Korean soybean seeds. Of the soybean seeds from the three different countries of origin, American soybean seeds had the highest average concentration of total phenolic compounds, and Korean varieties showed the second highest value. Small soybean seeds had the highest average content of total phenolic compounds (2241.7 μg g<SUP>–1</SUP>), whereas medium-sized (1926.8 μg g<SUP>–1</SUP>) and large (1949.9 μg g<SUP>–1</SUP>) soybeans had lower concentrations of phenolic compounds. In whole soybean germplasms, the level of total soyasapogenols was higher in CS01173 (1802.3 μg g<SUP>–1</SUP>) and CS01346 (1736.8 μg g<SUP>–1</SUP>) than in the other types of soybeans. The mean concentrations of total soyasapogenol were 1234.0 μg g<SUP>–1</SUP> in American, 1294.5 μg g<SUP>–1</SUP> in Chinese, and 1241.5 μg g<SUP>–1</SUP> in Korean soybean varieties. Chinese soybean varieties showed the highest mean concentration of total soyasapogenol, and Korean soybean seeds showed the second highest level. The medium-seed group had the highest soyasapogenol content (1269.3 μg g<SUP>–1</SUP>) of the seeds that were grouped by size. A larger amount of soyasapogenol B than soyasapogenol A was detected. In whole soybeans, CS01202 showed the highest level of total tocopherols (330.5 μg g<SUP>–1</SUP>), whereas CSRV056 (Pungsannamulkong) had the lowest content (153.3 μg g<SUP>–1</SUP>). Chinese soybeans had the highest average concentration of total tocopherols (255.1 μg g<SUP>–1</SUP>). By comparison, the medium-sized Chinese soybean group had the highest (256.1 μg g<SUP>–1</SUP>) average total tocopherol content.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jafcau/2012/jafcau.2012.60.issue-23/jf300463f/production/images/medium/jf-2012-00463f_0007.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jf300463f'>ACS Electronic Supporting Info</A></P>

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data

조연화,최호성,Miah Bae,김상민,김선림,이봉춘,조원경,김국형 한국식물병리학회 2017 Plant Pathology Journal Vol.33 No.5

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

조선시대의 대,소두와 그 가공식품

최덕경 ( Choe Deog Gyeong ) 대구사학회 2003 대구사학 Vol.72 No.-

Beans have been in the spotlight for a long time as important crops as one part of the five grains- rice, millet, barley, foxtail millet and beans. In fact, the book of Qiminyaoshu(齊民要術) mainly refers to various uses of soybeans(大豆) and red beans(小豆). First of all, they basically were much the same as other crops which had functions of fundamental foods, but their leaves and processed stuffs came to be also used very importantly and diversly at every home at all seasons. These facts meaned that soybeans and red beans were so available that demands for them increased rapidly day by day in those days. In this script, it will be defined how to change trends of processed soybeans of which the place of origin is the Korean Peninsula. As everyday knows, these days, processed soybeans are so various and popular fascinating the citizens. This suggests that many parts of this country have been suited for dynamic soybean culture. If the soil of Korean Peninsula has been so suitable for growing soybeans after the primitive age, it is necessary to find out how soybeans have been processed and used up to this day. There are some evidences to prove that Korean Peninsula is the home of soybeans. For example, our ancestors have made soybeans malts and soy sauces from soybeans, according to the historical informations of Chinese. In addition, in the days of Koryo, bean sprouts and bean curds are used regularly as similarly as processed soybeans of the present day. Actually, most kinds of processed soybeans in these modem days were already in existence at that time. Especialy, referring to many kinds of farming books(農書), farmer diaries(日記) and Yigui(儀軌), processed soybeans were widely used from the Royal Court even to the general public in early days of the Choson era. These facts do not only emphasize the importance of soybeans and red beans, but also make it possible to guess the abundant amount of consumption of soybeans and red beans in previous days to the Choson era. In the fore part, I pointed out that soybeans and red beans played roles of locomotive to the rapid progress of the Korean agricultural economy. Besides, for reference of this script, soybeans and red beans were favorite sorts of health foods rather than simple foods. Furthermore, they have come to be used as wage of the government official(祿俸), article essential to a marriage(婚需品), prize for remarkable result(賞品), and military supply(軍糧). They have been even processed to side dishes(副食), vegetables(菜蔬) and household medicines(常備藥). Like these, soybeans and red beans have been taken regularly because they have been much more useful than any other crops. Owing to these various merits of soybeans and red beans, they have been necessities of general public lives as hardy wild crops capable of being used in a famine as well as basic farm products to support his and her families. Their fundamental economic roles might be regarded as trivial things to some degree, like the tip of an iceberg, compared with other various additional roles. Judging from these facts, we can see tha soybeans and red beans have performed various important functions at that time. For these reasons, so many farmers have grown soybeans and red beans from early days in the Choson ers. As result, the abundant supply of those versatile crops could have maintained elasticity subsisting farming communities upon scanty bean foods under the calamity of war. There are several reasons that soybeans and red beans could have been excellent foods in a famine. At first, they have had various effective values. Second, as producing power of other similar staple grains increase rapidly, roles of soybeans and red beans have changed from chief articles of foods to condiments, fermented soybeans, health foods and vegetable dishes so on. In short, they have come to get special tastes. These days, Korea is very famous for processed soybeans because the soil of Korean Peninsula has been suitab

우리나라 콩 논재배 기술과 기술과 정책

이영호,한상수 한국콩연구회 2002 韓國콩硏究會誌 Vol.19 No.2

In 2000, the production amount of soybean in Korea was 118 thousand tons and the demand of soybean for food and processing was 412 thousand tons, and the self supply rate of soybean for food and processing was 28.2%. The Korean government set a goal to increase the self supply rate for fooe and processing to 50% by 2004. However, the soybean production was decreased continuously every year, because of lower income than other summer crops and lower price comparability comparing with imported soybeans. The major problem of soybean production is small farming size of 9.6a per farm household and 0nly 43% of farm households cultivated soybean for selling in 2000. A total of 3,852 farm households in Korea and 1,724 farm households in Jeju Province cultivated over one hectare. The average farming size of soybean in Jeju Province was 86.6 are. The labor productivity of soybean in 2000 was 8,300 won per hour and it was similar with those of cash crops and less than those of rice and malting barley. Therefore, more efforts are needed to decrease labor input comparing with rice and malt barley. The rice stock is increasing continuously because the rice consumption per capita has been decreased 3 to 4 kg per year recently. The rice consumption per capita was 88.9 kg in 2000. The cultivation of soybean and forage crops in paddy field was recommended from 2002 to decrease rice production. The Korean government increased doubly purchasing price of soybean produced in paddy fields to compensate the income gap between soybean and rice using forward-pricing system. The rate of suitable land among paddy fields for soybean cultivation is 30.8% and the southwestern regions has more suitable lands than the other regions. The paddy upland cycling cropping for soybean is two years maximum, because of lower yield, more weed emergence, and decreasing of organic matters in soil. The selection of tolerant varieties to excessive soil water, improvement of water drainage, and cautious application of herbicides are advised the soybean cultivation in paddy fields. The cultivated area of soybean production in paddy fields is 2,110 ha in this year and the average yield is estimated 1.88 ton per hectare.

Evaluation of Forage Yield and Quality in Wild Soybeans (Glycine soja Sieb. and Zucc.)

( Eun Ja Lee ),( Hong Jib Choi ),( Dong Hyun Shin ),( Chan Ho Kwon ),( J Grover Shannon ),( Jeong Dong Lee ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.1

Wild soybeans (Glycine soja Sieb. & Zucc.) are generally higher in protein and lower in oil with potential advantages as forage than cultivated soybeans. This study was conducted to evaluate forage yield and quality of wild soybeans. Three wild soybeans were compared to three cultivated soybeans for forage yield and quality at the full bloom stage, full pod stage, and full seed stage (R6) of development. The wild soybeans had significantly lower forage yield than cultivated soybeans at R6 which was determined to be the best stage to harvest based on forage quantity and quality. Wild soybean also had lower crude fat (2.0%) and crude protein (17.7%) concentration than cultivated soybean (5.7 and 21.3%, respectively) at the R6 stage. There were no significant differences for neutral detergent fiber, acid detergent fiber and relative feed value among growth stages between cultivated and wild soybean. The neutral detergent fiber was 40.2 and 40.4%, acid detergent fiber was 26.1% and 27.5%, and relative feed value was 161 and 158 at R6 stage for cultivated and wild soybean, respectively. Wild soybean had less forage yield at harvest time but had similar forage quality comparable to cultivated soybean. However, wild soybeans have smaller and softer stems for potentially improved palatability and feed intake than cultivated soybeans. Therefore, it will be a good genetic source to improve forage characteristics of soybean.

Isoflavone Content and its Relationship with Other Seed Quality Traits of Soybean Cultivars Collected in South Korea

Sun-Lim Kim,Hee-Youn Chi,Jung-Tae Kim,Yeong-Ho Lee,Nam-Kyu Park,Jong-Rok Son,Si-Ju Kim 韓國作物學會 2006 Korean journal of crop science Vol.51 No.1

The 117 soybean cultivars were collected from nine provinces in Korea, and various seed quality traits along with isoflavone contents were evaluated to elucidate their relationship. The 100-seed weight of the black soybean (31.2 g) was significantly higher (p<0.05) than yellow soybeans (28.6 g). The composition of genistein, daidzein, and glycitein accounted for 75.8, 22.8, and 1.4 % of total isoflavone in yellow soybean cultivars, while their compositions in black soybeans were 58.5, 39.7, and 1.8%, respectively. The mean contents of total isoflavone in yellow and black soybean were l,561.6~mug~;g-1~;and~;l,018.3~mug~;g-1 . The isofalvone content showed significant variation among cultivars when classified by the seed size. In the yellow soybeans, total isoflavone content was higher in small size soybean cultivars (1,776.0~mug~;g-1) and medium size soybean cultivars (1,714.3~mug~;g-1) compared to large size ones (1,518.5~mug~;g-1) . Genistein content was proved as the major factor determining the relationship between isoflavone content and 100-seed weights (r =-0.206*). Daidzein and glycitein, however, showed no significant relationship with the 100-seed weights. Isoflavone content was not significantly correlated with color parameters L (lightness) and a (redness) values, but color parameter b (yellowness) was positively correlated with glycitein (r=0.264*) in the yellow soybeans, while its negative correlation between daidzein (r=-0.245*) and total isoflavone (r=-0.256*) were observed in black soybeans. However, these findings suggested that the seed color value may not serve as an effective parameter for estimating the isoflavone intensity of the soybeans. Variation of protein and lipid contents between yellow soybeans (n=58) and black soybeans (n=59) was relatively stable, however, protein and lipid contents have no significant relationship with isoflavone content.

선녹콩 개체간 및 개체내 단백질 함량 변이

임무혁,정명근 한국작물학회 2008 Korean journal of crop science Vol.53 No.-

Soybean [Glycine max (L.)] is a major source of protein for human and animal feed. Inter- and intragenotype variation of soybean protein has been investigated by soybean researchers. However, limited sample amount of soybean single seed there is no report that investigated intra-plant variation of soybean protein within soybean plant. Recently a non-destructive NIR (near-infrared reflectance) spectroscopy using single seed grain to analyze seed protein was developed. The objectives of this study were to understand variation of seed protein content within plant and to determine the amount of minimum sample size which can represent protein content for a soybean plant. Frequency distribution of protein content within plant showed normal distribution. There was an intra-cultivar variation for protein content in soybean cultivar Seonnogkong. Difference of protein content among single plants of Seonnokong was recognized at 5% level. Seeds in lower position on plant stem tended to accumulate more protein than in higher position. There was significant difference for protein content between sample size 5 seeds and sample size of more than 5 seeds (10, 20, 30, 40, and 50 seeds) at a soybean plant with 57 seeds however no difference was recognized among sample size (5, 10, 20, and 30 seeds) at a soybean plant with 33 seeds. Around 20% seeds of soybean from single plant needed to determine the protein content to represent protein content of single soybean plant. This study is the first one to report evidence of intra-plant variation for protein content which detected by non-destructive NIR spectroscopy using single seed grain in soybean. Soybean [Glycine max (L.)] is a major source of protein for human and animal feed. Inter- and intragenotype variation of soybean protein has been investigated by soybean researchers. However, limited sample amount of soybean single seed there is no report that investigated intra-plant variation of soybean protein within soybean plant. Recently a non-destructive NIR (near-infrared reflectance) spectroscopy using single seed grain to analyze seed protein was developed. The objectives of this study were to understand variation of seed protein content within plant and to determine the amount of minimum sample size which can represent protein content for a soybean plant. Frequency distribution of protein content within plant showed normal distribution. There was an intra-cultivar variation for protein content in soybean cultivar Seonnogkong. Difference of protein content among single plants of Seonnokong was recognized at 5% level. Seeds in lower position on plant stem tended to accumulate more protein than in higher position. There was significant difference for protein content between sample size 5 seeds and sample size of more than 5 seeds (10, 20, 30, 40, and 50 seeds) at a soybean plant with 57 seeds however no difference was recognized among sample size (5, 10, 20, and 30 seeds) at a soybean plant with 33 seeds. Around 20% seeds of soybean from single plant needed to determine the protein content to represent protein content of single soybean plant. This study is the first one to report evidence of intra-plant variation for protein content which detected by non-destructive NIR spectroscopy using single seed grain in soybean.