Comparison and Analysis of Main Effects, Epistatic Effects,and QT x Environment Interactions of QTLs for Agronomic Traits Using DH and RILs Populations in Rice

Xinhua Zhao,Yang Qin,Baoyan Jiav,Suk-Man Kim,Hyun-Suk Lee,Moo-Young Eun,김경민,손재근 한국작물학회 2010 Journal of crop science and biotechnology Vol.13 No.4

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross ‘Samgang x Nagdong’, were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population,respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).

Lack of Association Between the Matrix Metalloproteinase-2 -1306C>T Polymorphism and Breast Cancer Susceptibility: a Meta-analysis

Yang, Lu,Li, Ning,Wang, Siyu,Kong, Yanan,Tang, Hailin,Xie, Xinhua,Xie, Xiaoming Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.12

Background: Since inconsistent results have been reported regarding the relation between the matrix metalloproteinase-2 (MMP-2) -1306C>T polymorphism and susceptibility for breast cancer, we performed a meta-analysis to investigate the issue. Materials and Methods: An internet search of PubMed and EMBASE was performed to identify eligible studies. Pooled odds ratios (ORs) with their corresponding confidence intervals (CIs) were calculated to evaluate any association between MMP-2 -1306C>T polymorphism and breast cancer susceptibility. Results: Nine case-control studies were included in the meta-analysis, involving 9,858 cases and 10,871 controls. Overall, there was no evidence of any association between the MMP-2 -1306C>T polymorphism and breast cancer susceptibility in different genetic models (T-allele vs C-allele: OR=0.95, 95%CI, 0.82-1.10, p=0.49; TT vs CC: OR=1.03, 95%CI, 0.90-1.19, p=0.66; TT+TC vs CC: OR=0.93, 95%CI, 0.78-1.10, p=0.38; TT vs TC+CC: OR=1.02, 95%CI, 0.89-1.17, p=0.77). In the subgroup analysis by ethnicity, CC was associated with a significant increase in breast susceptibility among Latin-Americans in the dominant model (OR=0.61, 95%CI, 0.40-0.93, p=0.02), but the association disappeared in other models. No significant association was observed among Europeans, East Asians and others in different genetic models. In the subgroup analysis by their source of controls, no significant association between MMP-2 -1306C>T polymorphism and breast cancer susceptibility was noted among population-based studies and hospital-based studies in different genetic models. Conclusions: The results of this meta-analysis suggest that MMP-2 -1306C>T polymorphism is not associated with breast cancer susceptibility, although the association among Latin-Americans in the dominant model was significant.

Damage analysis of arch dam under blast loading

Xinhua Xue,Xingguo Yang,Wohua Zhang 사단법인 한국계산역학회 2013 Computers and Concrete, An International Journal Vol.12 No.1

This paper examines the dynamic response of an arch dam subjected to blast loading. A damage model is developed for three dimensional analysis of arch dams. The modified Drucker-Prager criterion is adopted as the failure criteria of the damage evolution in concrete. Then, Xiluodu arch dam serves as an example to simulate the failure behaviors of structures with the proposed model. The results obtained using the proposed model can reveal the reliability degree of the safe operation level of the high arch dam system as well as the degree of potential failure, providing a reliable basis for risk assessment and risk control

QTL detection and MAS selection efficiency for lipid content in brown rice (Oryza sativa L.)

Yang Qin,김석만,Xinhua Zhao,이현석,Baoyan Jia,김경민,은무영,손재근 한국유전학회 2010 Genes & Genomics Vol.32 No.6

Rice lipid content as one of important ingredients of functional food and industrial products has become an entirely new target in the rice breeding programs worldwide. A genetic linkage map spanning 12 rice chromosomes with an average interval of 10.51 cM between markers was created using 172 DNA markers, which intended to elucidate genetic basis of lipid content in brown rice by QTL detection. Eight QTLs related to lipid content with LOD from 2.52 to 7.86 were mapped on chromosome1, 2, 3, 5, 6, 7 and 9 using a doubled haploid (DH) population from a cross of ‘Samgang/Nagdong’ with field experiments for five years. Two QTLs of qLC5.1 and qLC6.1in the intervals 5014‐5024 and 6011‐RM19696 were repeatedly detected over four years at average LOD scores of 4.85 and 4.21, respectively. Five of eight QTLs tend to increase the lipid content from ‘Samgang’ alleles. Epistatic and environmental effects played important roles and explained 42.20% of phenotype variations. Three QTLs of qLC6.1, qLC7.1 and qLC9.1collectively explained much than 27% of phenotype variations and increased 0.25% of lipid content and, showed much than 85% of selection efficiency for the lines with high lipid contents in the F7 population from a cross of ‘Samgang/Nagdong’. Thus it provides the sufficient possibility to realize QTLs pyramiding and to promote process of rice breeding.

Earthquake safety assessment of an arch dam using an anisotropic damage model for mass concrete

Xinhua Xue,Xingguo Yang 사단법인 한국계산역학회 2014 Computers and Concrete, An International Journal Vol.13 No.5

The seismic safety of concrete dams is one of the important problems in the engineering due to the vast socio-economic disasters which may be caused by collapse of these infrastructures. The accuracy of the risk evaluation associated with these existing dams as well as the efficient design of future dams is highly dependent on a proper understanding of their behaviour due to earthquakes. This paper develops an anisotropic damage model for arch dam under strong earthquakes. The modified Drucker-Prager criterion is adopted as the failure criteria of the dynamic damage evolution of concrete. Some process fields and other necessary information for the safety evaluation are obtained. The numerical results show that the seismic behaviour of concrete dams can be satisfactorily predicted.

QTL mapping for developmental behavior at different stages in rice

Xinhua Zhao,Yang Qin,Hyun-Suk Lee,Young-Hie Park,Yu-Jin Ji,Tae-Heun Kim,Hee-Yeon Park,Jae-Keun Sohn 한국작물학회 2008 한국작물학회 학술발표대회 논문집 Vol.2008 No.10

A population of 120 double-haploid lines derived from Samgang/Nagdong was used for analyzing the developmental behaviors of plant height and tiller number by conditional mapping via composite interval approaches at five growth stages of rice. The traits were normally distributed with transgressive segregations in both directions. A total of 4 QTLs associated with plant height were identified in 40th/initial, 50th/40th and 60th/50th periods, respectively. The qph7.1 was observed in 50th/40th and 60th/50th periods, with increasing effects from Samgang and Nagdong alleles, respectively. This indicated that an individual gene or genes at the same genomic region might have opposite genetic effects at various growth stages. Five QTLs associated with tiller number were identified in four stages except 60th/50th stage. Four of five increasing effects of QTLs were from Nagdong alleles. Six of nine QTLs for two traits were detected before 60 days. It was evident that the expression of QTLs for plant height and tiller number was more active at early stages than at maturity stage. Furthermore, QTLs identified at early stages showed opposite additive effects on plant height and tiller number. These results provided a possible genetic explanation for the negative correlation between two traits.

Identification for quantitative trait loci controlling grain shattering in rice

Yang Qin,김석만,Xinhua Zhao,Baoyan Jia,이현석,김경민,은무영,진일두,손재근 한국유전학회 2010 Genes & Genomics Vol.32 No.2

Seed shattering is an important factor causing loss of grain yield before and during rice harvest. In the present study, the quantitative trait loci regarding shattering scale, breaking tensile strength (BTS) and abscission layer (AL), the parameters evaluating seed shattering habit by hand gripping, a digital force gauge and observation on AL, respectively, were identified by using an doubled haploid line (DHL) population from a cross between a loose-shattering type Tongil variety,‘Samgang’, and a moderately difficult shattering japonica variety,‘Nagdong’. Eight QTLs consisted in four QTLs for shattering scale, two QTLs for AL, each one QTL for pulling and bending strength were detected on six chromosomes,respectively. Among them, Qss1 with flanking markers RM6696 and RM476 explained 31% of phenotype variation in shattering scale. Furthermore, two new QTLs controlling shattering habit, Qss5-2 and Qal5-1, were located on chromosome 5 at the interval 5028−5037 and 5021-RM289. They explained 10% and 12% of phenotype variations, respectively. A total of eleven digenic epistatic loci were identified for four parameters. The identification of QTLs affecting seed shatter-ing habits is favorable to thoroughly dissect the genetic mechanism of the shattering habit and to apply for marker-assisted selection in rice breeding system of specific regions.

Memantine Improves Cognitive Function and Alters Hippocampal and Cortical Proteome in Triple Transgenic Mouse Model of Alzheimer’s Disease

Xinhua Zhou,Liang Wang,Wei Xiao,Zhiyang Su,Chengyou Zheng,Zaijun Zhang,Yu Qiang Wang,Benhong Xu,Xifei Yang,Maggie Pui Man Hoi 한국뇌신경과학회 2019 Experimental Neurobiology Vol.28 No.3

Memantine is a non-competitive N-methyl-D-aspartate receptor (NMDAR) antagonist clinically approved for moderate-to-severe Alzheimer’s disease (AD) to improve cognitive functions. There is no report about the proteomic alterations induced by memantine in AD mouse model yet. In this study, we investigated the protein profiles in the hippocampus and the cerebral cortex of AD-related transgenic mouse model (3×Tg-AD) treated with memantine. Mice (8-month) were treated with memantine (5 mg/kg/bid) for 4 months followed by behavioral and molecular evaluation. Using step-down passive avoidance (SDA) test, novel object recognition (NOR) test and Morris water maze (MWM) test, it was observed that memantine significantly improved learning and memory retention in 3xTg-AD mice. By using quantitative proteomic analysis, 3301 and 3140 proteins in the hippocampus and the cerebral cortex respectively were identified to be associated with AD abnormalities. In the hippocampus, memantine significantly altered the expression levels of 233 proteins, among which PCNT, ATAXIN2, TNIK, and NOL3 were up-regulated, and FLNA, MARK 2 and BRAF were down-regulated. In the cerebral cortex, memantine significantly altered the expression levels of 342 proteins, among which PCNT, PMPCB, CRK, and MBP were up-regulated, and DNM2, BRAF, TAGLN 2 and FRY1 were down-regulated. Further analysis with bioinformatics showed that memantine modulated biological pathways associated with cytoskeleton and ErbB signaling in the hippocampus, and modulated biological pathways associated with axon guidance, ribosome, cytoskeleton, calcium and MAPK signaling in the cerebral cortex. Our data indicate that memantine induces higher levels of proteomic alterations in the cerebral cortex than in the hippocampus, suggesting memantine affects various brain regions in different manners. Our study provides a novel view on the complexity of protein responses induced by memantine in the brain of AD.

Comparison and Analysis of Main Effects, Epistatic Effects, and QTL ${\times}$ Environment Interactions of QTLs for Agronomic Traits Using DH and RILs Populations in Rice

Zhao, Xinhua,Qin, Yang,Jia, Baoyan,Kim, Suk-Man,Lee, Hyun-Suk,Eun, Moo-Young,Kim, Kyung-Min,Sohn, Jae-Keun 한국작물학회 2010 Journal of crop science and biotechnology Vol.13 No.4

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross 'Samgang x Nagdong', were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population, respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).

Carbonation Model and Prediction of Polyvinyl Alcohol Fiber Concrete with Fiber Length and Content Effects

Zuyun Luo,Xinhua Yang,Heli Ji,Chuanchuan Zhang 한국콘크리트학회 2022 International Journal of Concrete Structures and M Vol.16 No.2

Durability is an important aspect of reliability of concrete structures. In order to establish the carbonation model of polyvinyl alcohol (PVA) fiber concrete including the influences of PVA fiber length and volume content, a series of accelerated carbonation experiments were carried out on the normal concrete specimens and PVA fiber concrete specimens with fiber lengths of 3 mm, 6 mm, 12 mm and 18 mm and fiber volume contents of 0.1%, 0.3%, 0.5%, 0.75%, 1.0% and 1.5%, respectively. The experimental conditions remained at temperature of 20 ℃, humidity of 70%, and carbon dioxide concentration of 20%. It was found that the addition of PVA fibers could improve the carbonation resistance of concrete considerably. Within the investigated range of fiber length and content, the carbonation resistance of concrete is first strengthened and then weakened with increasing PVA fiber length or content. The quadratic carbonation depth prediction model could characterize the influences of PVA fiber length and content better than the linear model. The carbon dioxide diffusion equation was established by introducing a PVA fiber influence factor and its parameters were determined from the carbonation depth prediction model. The carbonation process of PVA fiber concrete under the accelerated carbonation experiment condition was simulated. Both the model and the numerical method were validated by comparison between the experimental and numerical results. Finally, the influences of added PVA fibers on the carbonation life and durability of reinforced concrete components were further studied numerically. The results showed that compared with the normal concrete component, the durability of PVA fiber concrete components is significantly improved.