Genome-wide association studies approach and post-GWAS study in rice

Gang Li,Min-Young Yoon,Won-Hee Ra,Jae-Wan Park,Qiang He,Aye Aye Khaing,Xiao-Qiang Wang,Win Htet Oo,Feng-Peng Li,Byoung Kook Yun,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.

Genetic Diversity Analysis of Mungbean Accessions from East and Central Asia Using SSR Markers

Gang Li,Soon-Wook Kwon,Yu Mi Choi,Yong-Jin Park 한국국제농업개발학회 2011 韓國國際農業開發學會誌 Vol.23 No.2

Transcriptome profiling of Shindongjin and Sugary mutant at grain-filling stages using RNA-Seq

Feng-Peng Li,Min-Young Yoon,Gang Li,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying developmental seeds. In the study, the seeds of 10th day after flowering (DAF) were conducted RNA-Seq of the variety Shindongjin and Sugary mutant using RNA-seq technique. Approximately 202 and 214 million high-quality paired-end reads (101-bp in size) were generated in Shindongjin and Sugary mutant, respectively. Comprehensive analysis on the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism of starch biosynthesis in seeds. Quantitative real-time PCR was also used to validate the expression profiles of 28 rice genes encoding six classes of enzymes, viz., ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme at different developmental grain- filling stages (DAF 1-14) between Shindongjin and Sugary mutant. The results showed that the expression of most of starch synthesis genes were up-regulated except the cytosolic AGPase small subunit2b (AGPS2b), which sharply decreased at grain-filling stages in Sugary mutant. These results will expand our understanding of the complex molecular and cellular events in rice grain-filling stages and provide a fundamental understanding of future studies on developmental endosperm in rice and other cereal crops.

Haplotype analysis of major blast resistance (R) genes in rice; Pi9, Pia, and Pib

Won-Hee Ra,Gang Li,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Rice blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive rice diseases worldwide. Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several genes. A total of 13 major blast resistance (R) genes were reported in a number of Korean rice varieties using molecular markers. The Pi-ta gene, which locates near to the centromere of chromosome 12, was haplotyping using 1790 accessions including cultivated and wild varieties in previous research. However, the genetic variations of other R genes in rice still not clear. Three R genes, Pi9, Pia, and Pib on chromosome 6, 11 and 2 respectively, were resequenced among 84 accessions of rice core set. Different types of halotype among the 84 accessions were detected. Some new SNPs and InDels found in exon part of R genes were expected to result into amino acid changes following analysis of the genetic code variations, and the germplam in this rice core set which are resistance to blast were explored. We are expecting to develop the new functional markers and incorporate of resistance genes into existing rice cultivars and finally these apply outcomes in breeding rice resistance to blast diseases.

A comparative study of three collocation point methods for odd order stochastic response surface method

Li, Dian-Qing,Jiang, Shui-Hua,Cheng, Yong-Gang,Zhou, Chuang-Bing Techno-Press 2013 Structural Engineering and Mechanics, An Int'l Jou Vol.45 No.5

This paper aims to compare three collocation point methods associated with the odd order stochastic response surface method (SRSM) in a systematical and quantitative way. The SRSM with the Hermite polynomial chaos is briefly introduced first. Then, three collocation point methods, namely the point method, the root method and the without origin method underlying the odd order SRSMs are highlighted. Three examples are presented to demonstrate the accuracy and efficiency of the three methods. The results indicate that the condition that the Hermite polynomial information matrix evaluated at the collocation points has a full rank should be satisfied to yield reliability results with a sufficient accuracy. The point method and the without origin method are much more efficient than the root method, especially for the reliability problems involving a large number of random variables or requiring complex finite element analysis. The without origin method can also produce sufficiently accurate reliability results in comparison with the point and root methods. Therefore, the origin often used as a collocation point is not absolutely necessary. The odd order SRSMs with the point method and the without origin method are recommended for the reliability analysis due to their computational accuracy and efficiency. The order of SRSM has a significant influence on the results associated with the three collocation point methods. For normal random variables, the SRSM with an order equaling or exceeding the order of a performance function can produce reliability results with a sufficient accuracy. The order of SRSM should significantly exceed the order of the performance function involving strongly non-normal random variables.

Minimum life-cycle cost design of ice-resistant offshore platforms

Li, Gang,Zhang, Da-Yong,Yue, Qian-Jin Techno-Press 2009 Structural Engineering and Mechanics, An Int'l Jou Vol.31 No.1

In China, the oil and natural gas resources of Bohai Bay are mainly marginal oil fields. It is necessary to build both ice-resistant and economical offshore platforms. However, risk is involved in the design, construction, utilization, maintenance of offshore platforms as uncertain events may occur within the life-cycle of a platform under the extreme ice load. In this study, the optimum design model of the expected life-cycle cost for ice-resistant platforms based on cost-effectiveness criterion is proposed. Multiple performance demands of the structure, facilities and crew members, associated with the failure assessment criteria and evaluation functions of costs of construction, consequences of structural failure modes including damage, revenue loss, death and injury as well as discounting cost over time are considered. An efficient approximate method of the global reliability analysis for the offshore platforms is provided, which converts the implicit nonlinear performance function in the conventional reliability analysis to linear explicit one. The proposed life-cycle optimum design formula are applied to a typical ice-resistant platform in Bohai Bay, and the results demonstrate that the life-cycle cost-effective optimum design model is more rational compared to the conventional design.

Nonlinear free vibration of heated corrugated annular plates with a centric rigid mass

Yong-Gang Wang,Dan Li,Ze-Jun Feng 국제구조공학회 2010 Structural Engineering and Mechanics, An Int'l Jou Vol.34 No.4

A computational analysis of the nonlinear free vibration of corrugated annular plates with shallow sinusoidal corrugations under uniformly static ambient temperature is examined. The governing equations based on Hamilton’s principle and nonlinear bending theory of thin shallow shell are established for a corrugated plate with a concentric rigid mass at the center and rotational springs at the outer edges. A simple harmonic function in time is assumed and the time variable is eliminated from partial differential governing equations using the Kantorovich averaging procedure. The resulting ordinary equations, which form a nonlinear two-point boundary value problem in spatial variable, are then solved numerically by shooting method, and the temperature-dependent characteristic relations of frequency vs. amplitude for nonlinear vibration of heated corrugated annular plates are obtained. Several numerical results are presented in both tabular and graphical forms, which demonstrate the accuracy of present method and illustrate the amplitude frequency dependence for the plate under such parameters as ambient temperature, plate geometry, rigid mass and elastic constrain.

Preventive Effects of Aspirin on Cardiovascular Complications in Prostate Cancer Cases after Endocrinotherapy

Li, Xiao-Xia,Zhang, Yong-Gang,Wang, Dong,Chen, Yun-Fang,Shan, Yan-Hua Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.12

Objective: To explore the preventive effect of aspirin on the cardiovascular complications in prostate cancer after endocrinotherapy. Materials and Methods: A total of 92 patients with prostate cancer were divided into observation group (n=44) and control group (n=48). The control group was treated with medical castration plus anti-androgenic drugs. Based on the above treatment, the observation group was added aspirin. The follow-up duration was 2 years. The changes of partial prothrombin time (PT), activated partial thromboplastin time (APTT), platelet aggregation rate (PAG), prostate-specific antigen (PSA) and serum testosterone (T) before and after treatment as well as incidence of cardiovascular disease were observed. Results: The 2-year survival rates of patients without cardiovascular disease in observation group and control group were 95.45% (42/44) and 72.92% (35/48), respectively, and significant difference was presented between two groups by comparison to the survival rates ($x^2=8.5453$, p=0.0035). There was no statistical significance between two groups as well as before and after treatment regarding PT (p>0.05). After treatment, APTT went down and PAG was gradually on the rise in control group, while PAG down and APTT on the rise increasingly in observation group. Significant differences were presented between two groups as well as before and after treatment (p<0.01). Both PSA and T levels were decreased significantly in two groups after treatment (p<0.01), but there was no statistical significant between two groups (p>0.05). Conclusions: Application of endocrinotherapy in prostate cancer can easily lead to occurrence of cardiovascular disease, but cardiovascular complications can be prevented by aspirin, without affecting the effect of endocrinotherapy.

Stanniocalcin-1 protects bovine intestinal epithelial cells from oxidative stress-induced damage

Li-ming Wu,Rui Guo,Lin Hui,Yong-gang Ye,Jing-mei Xiang,Chun-yun Wan,Miao Zou,Rui Ma,Xiao-zhuan Sun,Shi-jin Yang,Ding-zong Guo 대한수의학회 2014 Journal of Veterinary Science Vol.15 No.4

Chronic enteritis can produce an excess of reactive oxygenspecies resulting in cellular damage. Stanniocalcin-1(STC-1)reportedly possesses anti-oxidative activity, the aim of thisstudy was to define more clearly the direct contribution ofSTC-1 to anti-oxidative stress in cattle. In this study, primaryintestinal epithelial cells (IECs) were exposed to hydrogenperoxide (H2O2) for different time intervals to mimic chronicenteritis-induced cellular damage. Prior to treatment with 200μM H2O2, the cells were transfected with a recombinantplasmid for 48 h to over-express STC-1. Acridine orange/ethidium bromide (AO/EB) double staining and trypan blueexclusion assays were then performed to measure cell viabilityand apoptosis of the cells, respectively. The expression of STC-1and apoptosis-related proteins in the cells was monitored byreal-time PCR and Western blotting. The results indicated thatboth STC-1 mRNA and protein expression levels positivelycorrelated with the duration of H2O2 treatment. H2O2 damagedthe bovine IECs in a time-dependent manner, and this effectwas attenuated by STC-1 over-expression. Furthermore, overexpressionof STC-1 up-regulated Bcl-2 protein expression andslightly down-regulated caspase-3 production in the damagedcells. Findings from this study suggested that STC-1 plays aprotective role in intestinal cells through an antioxidant mechanism.

High-throughput pyrosequencing of complete chloroplast genome of Chrysanthemum boreale M.

Gang Li(리강),Cheol Soon Park(박철순),Kyeong Ho Yeon(연경호),Yong-Jin Park(박용진) 한국약용작물학회 2012 한국약용작물학회 학술대회논문집 Vol.2012 No.1