scholarly journals An Association Study of 22 Candidate Genes in Psoriasis Families Reveals Shared Genetic Factors with Other Autoimmune and Skin Disorders

2009 ◽  
Vol 129 (11) ◽  
pp. 2637-2645 ◽  
Author(s):  
Tiphaine Oudot ◽  
Fabienne Lesueur ◽  
Mickaël Guedj ◽  
Rafael de Cid ◽  
Steven McGinn ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Factors ◽  
Skin Disorders ◽  
Shared Genetic

Identification of Potential Pleiotropic Genes for Immune and Skeletal Diseases Using Multivariate MetaCCA Analysis

2021 ◽  
Vol 23 ◽  
Author(s):  
Pei He ◽  
Rong- Rong Cao ◽  
Fei- Yan Deng ◽  
Shu- Feng Lei
Keyword(s):  
Association Study ◽  
Canonical Correlation ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Summary Statistics ◽  
Immune Disease ◽  
Histocompatibility Complex ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Shared Genetic

Background: Immune and skeletal systems physiologically and pathologically interact with each other. The immune and skeletal diseases may share potential pleiotropic genetics factors, but the shared specific genes are largely unknown Objective: This study aimed to investigate the overlapping genetic factors between multiple diseases (including rheumatoid arthritis (RA), psoriasis, osteoporosis, osteoarthritis, sarcopenia and fracture) Methods: The canonical correlation analysis (metaCCA) approach was used to identify the shared genes for six diseases by integrating genome-wide association study (GWAS)-derived summary statistics. Versatile Gene-based Association Study (VEGAS2) method was further applied to refine and validate the putative pleiotropic genes identified by metaCCA. Results: About 157 (p<8.19E-6), 319 (p<3.90E-6) and 77 (p<9.72E-6) potential pleiotropic genes were identified shared by two immune disease, four skeletal diseases, and all of the six diseases, respectively. The top three significant putative pleiotropic genes shared by both immune and skeletal diseases, including HLA-B, TSBP1 and TSBP1-AS1 (p<E-300) were located in the major histocompatibility complex (MHC) region. Nineteen of 77 putative pleiotropic genes identified by metaCCA analysis were associated with at least one disease in the VEGAS2 analysis. Specifically, majority (18) of these 19 putative validated pleiotropic genes were associated with RA. Conclusion: The metaCCA method identified some pleiotropic genes shared by the immune and skeletal diseases. These findings help to improve our understanding of the shared genetic mechanisms and signaling pathways underlying immune and skeletal diseases.

scholarly journals Identification of genetic factors controlling phosphorus utilization efficiency in wheat by genome-wide association study with principal component analysis

2020 ◽  
Author(s):  
Luqman Bin Safdar ◽  
Muhammad Jawad Umer ◽  
Fakhrah Almas ◽  
Siraj Uddin ◽  
Qurra-tul-Ain Safdar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Principal Component ◽  
Utilization Efficiency ◽  
Genome Wide Association ◽  
Genome Wide ◽  
P Utilization ◽  
P Utilization Efficiency

ABSTRACTDespite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.KEY MESSAGEWe report two new loci for P utilization efficiency on chromosomes 3A and 4A of wheat. The prioritized candidate genes at these loci can be investigated by molecular biology techniques to improve P efficiency in wheat and grass relatives.

scholarly journals Association Study of Puberty-Related Candidate Genes in Chinese Female Population

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Gideon Omariba ◽  
Junhua Xiao
Keyword(s):  
Next Generation Sequencing ◽  
Association Study ◽  
Candidate Genes ◽  
Genetic Factors ◽  
Transition Period ◽  
Female Population ◽  
Number Of Genes ◽  
Puberty Onset ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Puberty is a transition period where a child transforms to an adult. Puberty can be affected by various genetic factors and environmental influences. In mammals, the regulation of puberty is enhanced by the hypothalamic-pituitary-gonadal axis (HPG axis). A number of genes such as GnRH, Kiss1, and GPR54 have been reported as key regulators of puberty onset. In this study, we have conducted an association study of puberty-related candidate genes in Chinese female population. Gene variations reported to be related with some traits in a population may not exist in others due to different genetic and ethnic backgrounds, hence the need for this kind of study. The genotyping of SNPs was based on multiplex PCR and the next-generation sequencing (NGS) platform of Illumina. We finally performed association study using PLINK software. Our results confirmed that SNPs rs34787247 in LIN28, rs74795793 and rs9347389 in OCT-1, and rs379202 and rs10491080 in ZEB1 genes showed a significant association with puberty. With the result, it is reasonable to conclude that these genes affect the process of puberty in Shanghai Chinese female population, yet the mechanism remains to be investigated by further study.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

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