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期刊论文 7

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N-糖基化 1

全基因组关联研究 1

基因组学 1

糖组学 1

聚糖 1

遗传学 1

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A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 321-330 doi: 10.15302/J-FASE-2014037

摘要： Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population. Of these, 38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition. By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis, 26 genes were found to contain or be near to such SNPs. Among them, the gene is merely 87 bp away from the significant SNP, Hapmap30383-BTC-005848. Hence, we report herein genotype-phenotype associations to further validate the genetic effects of the gene. By pooled DNA sequencing of 14 unrelated Holstein sires, a total of 18 with seven novel SNPs were identified. Among them, nine SNPs were in the 5′ regulatory region, one in exon 6 and the other in the 3′ UTR and 3′ regulatory region. A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population. The results showed that these SNPs were statistically significant for more than two traits [ <(0.0001-0.0267)]. In addition, mRNA expression analyses revealed that was ubiquitous in eight different tissues, with a relatively higher expression level in the mammary gland than in other tissues. These findings, therefore, provide strong evidence for association of variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

关键词： GWAS     functional annotation     Chinese Holstein     milk production traits     C14H8orf33 gene     single nucleotide polymorphisms     association study    

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Genome-wide association studies: inherent limitations and future challenges

null

《医学前沿（英文）》 2012年 第6卷 第4期   页码 444-450 doi: 10.1007/s11684-012-0225-3

摘要：

Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.

关键词： genome-wide association studies (GWAS)     genetic variant     cancer     limitation     challenge    

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A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

《农业科学与工程前沿（英文）》 2014年 第1卷 第2期   页码 137-143 doi: 10.15302/J-FASE-2014014

摘要： Meat quality is an important trait in the pig industry. To identify genomic regions and haplotype blocks responsible for meat quality traits in pigs, a genome-wide association study was conducted for five traits including intramuscular fat content, pH at 45 min and 24 h, drip loss within 24 h and water-holding capacity in 231 Yorkshire barrows using illumina porcine 60k SNP chips. The results showed that a total of 344 single nucleotide polymorphisms (SNP) were significantly associated with five meat quality traits ( <1×10 ). Moreover, 323 SNPs were within the reported QTL regions, of which 21 were novel. Also, 158 SNPs fell into the proximal region of meat quality related genes. In addition, 25 haplotype blocks based on 116 SNPs were revealed with SNP combination patterns for five traits. Our study added new SNP information for identification of meat quality traits in pigs and will help elucidate the mechanisms of meat quality in pigs.

关键词： Pig     GWAS     meat quality trait     SNP    

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Spectral reflectance indices as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait associations

Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 296-308 doi: 10.15302/J-FASE-2019269

摘要：

The application of spectral reflectance indices (SRIs) as proxies to screen for yield potential (YP) and heat stress (HS) is emerging in crop breeding programs. Thus, a comparison of SRIs and their associations with grain yield (GY) under YP and HS conditions is important. In this study, we assessed the usefulness of 27 SRIs for indirect selection for agronomic traits by evaluating an elite spring wheat association mapping initiative (WAMI) population comprising 287 elite lines under YP and HS conditions. Genetic and phenotypic analysis identified 11 and 9 SRIs in different developmental stages as efficient indirect selection indices for yield in YP and HS conditions, respectively. We identified enhanced vegetation index (EVI) as the common SRI associated with GY under YP at booting, heading and late heading stages, whereas photochemical reflectance index (PRI) and normalized difference vegetation index (NDVI) were the common SRIs under booting and heading stages in HS. Genome-wide association study (GWAS) using 18704 single nucleotide polymorphisms (SNPs) from Illumina iSelect 90K identified 280 and 43 marker-trait associations for efficient SRIs at different developmental stages under YP and HS, respectively. Common genomic regions for multiple SRIs were identified in 14 regions in 9 chromosomes: 1B (60–62 cM), 3A (15, 85–90, 101–105 cM), 3B (132–134 cM), 4A (47–51 cM), 4B (71–75 cM), 5A (43–49, 56–60, 89–93 cM), 5B (124–125 cM), 6A (80–85 cM), and 6B (57–59, 71 cM). Among them, SNPs in chromosome 5A (89–93 cM) and 6A (80–85 cM) were co-located for yield and yield related traits. Overall, this study highlights the utility of SRIs as proxies for GY under YP and HS. High heritability estimates and identification of marker-trait associations indicate that SRIs are useful tools for understanding the genetic basis of agronomic and physiological traits.

关键词： genome-wide association study (GWAS)     heat tolerance     spectral reflectance     spring wheat    

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近十二年人类蛋白质N-糖基化的全基因组关联研究综述 Review

Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko

《工程（英文）》 2023年 第26卷 第7期   页码 17-31 doi: 10.1016/j.eng.2023.03.013

摘要： 接下来，在第3节中，总结、分类并归纳了当前N-糖基化全基因组关联研究（GWAS）的结果，这些研究提供了有关糖基化群体变异遗传调控的新知识。

关键词： 糖组学     聚糖     N-糖基化     基因组学     遗传学     全基因组关联研究    

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Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness

Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun

《工程管理前沿（英文）》 2016年 第3卷 第1期   页码 30-38 doi: 10.15302/J-FEM-2016008

摘要： Frequent traffic accidents constitute a major danger to human beings. The accident-prone driver who has the stable physiological, psychological, and behavioral characteristics is one of the most prominent causes of traffic accidents. The internal link between the individual characteristics and the accident proneness has been a difficult point in the accident prevention research. The authors selected accident-prone drivers as cases and safe drivers as controls (case-control group) from 18,360 drivers who were enrolled from three public transportation incorporations of China using area stratified sampling method. The case-control groups were 1:1 matched. The authors performed genome-wide association study (GWAS) by 179 cases and 179 controls using the U.S. Affymetrix Genome-Wide Human Mapping SNP 6.0 Array. The authors observed that the gene frequencies of 34 single-nucleotide polymorphisms (SNPs) in three regions of cases were higher than those in the control ( <10 ). The authors then tested two independent replication sets for strong association 6 SNPs in 349 pairs of case-control drivers using the U.S. ABI 3730 sequencing method. The results indicated that SNP rs6069499 within linked CBLN4 gene are strongly associated with accident proneness ( =6.37×10 ). According to CBLN4 gene mainly involved in adrenal development and the regulation of secretion, the authors performed 12 biochemical parameters of the blood using radioimmunoassay. The levels of dopamine (DA) and adrenocorticotropic (ACTH) hormone showed significant differences between accident-prone drivers and safe drivers ( =0.03, =0.01). It is suggested that the accident-prone drivers may have the idiosyncrasy of susceptibility.

关键词： accident proneness     genome-wide association study (GWAS)     dopamine (DA)     ACTH     susceptibility gene     traffic accident epidemiology     accident prevention     traffic safety     three-dimensional model    

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Development of Machine Learning Methods for Accurate Prediction of Plant Disease Resistance

Qi Liu,Shi-min Zuo,Shasha Peng,Hao Zhang,Ye Peng,Wei Li,Yehui Xiong,Runmao Lin,Zhiming Feng,Huihui Li,Jun Yang,Guo-Liang Wang,Houxiang Kang,

《工程（英文）》 doi: 10.1016/j.eng.2024.03.014

摘要： The traditional method of screening plants for disease resistance phenotype is both time-consuming and costly. Genomic selection offers a potential solution to improve efficiency, but accurately predicting plant disease resistance remains a challenge. In this study, we evaluated eight different machine learning (ML) methods, including random forest classification (RFC), support vector classifier (SVC), light gradient boosting machine (lightGBM), random forest classification plus kinship (RFC_K), support vector classification plus kinship (SVC_K), light gradient boosting machine plus kinship (lightGBM_K), deep neural network genomic prediction (DNNGP) and densely connected convolutional networks (DenseNet), for predicting plant disease resistance. Our results demonstrate that the three plus kinship (K) methods developed in this study achieved high prediction accuracy. Specifically, these methods achieved accuracies of up to 95% for rice blast (RB), 85% for rice black-streaked dwarf virus (RBSDV), and 85% for rice sheath blight (RSB) when trained and applied to the rice diversity panel I (RDPI). Furthermore, the plus K models performed well in predicting wheat blast (WB) and wheat stripe rust (WSR) diseases, with mean accuracies of up to 90% and 93%, respectively. To assess the generalizability of our models, we applied the trained plus K methods to predict RB disease resistance in an independent population, rice diversity panel II (RDPII). Concurrently, we evaluated the RB resistance of RDPII cultivars using spray inoculation. Comparing the predictions with the spray inoculation results, we found that the accuracy of the plus K methods reached 91%. These findings highlight the effectiveness of the plus K methods (random forest classification plus kinship (RFC_K), support vector classification plus kinship (SVC_K), and light gradient boosting machine plus kinship (lightGBM_K)) in accurately predicting plant disease resistance for RB, RBSDV, RSB, WB, and WSR. The methods developed in this study not only provide valuable strategies for predicting disease resistance but also pave the way for using machine learning to streamline genome-based crop breeding.

关键词： Predicting plant disease resistance (PPDR)     Genomic selection (GS)     Machine learning (ML)     Genome-wide association study (GWAS)    

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标题 作者 时间 类型 操作

A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

期刊论文

Genome-wide association studies: inherent limitations and future challenges

null

期刊论文

A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

期刊论文

Spectral reflectance indices as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait associations

Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS

期刊论文

近十二年人类蛋白质N-糖基化的全基因组关联研究综述

Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko

期刊论文

Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness

Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun

期刊论文

Development of Machine Learning Methods for Accurate Prediction of Plant Disease Resistance

Qi Liu,Shi-min Zuo,Shasha Peng,Hao Zhang,Ye Peng,Wei Li,Yehui Xiong,Runmao Lin,Zhiming Feng,Huihui Li,Jun Yang,Guo-Liang Wang,Houxiang Kang,

期刊论文