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 Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

2021 ◽  
Author(s):  
Dong Cao ◽  
Dongxia Wang ◽  
Shiming Li ◽  
Yun Li ◽  
Ming Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Energy Crop ◽  
Hexaploid Triticale ◽  
Genome Wide ◽  
Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

scholarly journals Is useful research data usually shared? An investigation of genome-wide association study summary statistics

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0229578 ◽  
Author(s):  
Mike Thelwall ◽  
Marcus Munafò ◽  
Amalia Mas-Bleda ◽  
Emma Stuart ◽  
Meiko Makita ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Research Data ◽  
Genome Wide Association ◽  
Summary Statistics ◽  
Genome Wide

scholarly journals Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽  
2020 ◽  
Author(s):  
Yanhua Zhang ◽  
Yuzhe Wang ◽  
Yiyi Li ◽  
Junfeng Wu ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Carcass Traits ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

scholarly journals 0004 GENOME-WIDE ASSOCIATION STUDY FOR SNORING IDENTIFIES NOVEL GENETIC FACTORS AND BIOLOGICAL LINKS TO SLEEP APNEA AND OBESITY

SLEEP ◽  
2017 ◽  
Vol 40 (suppl_1) ◽  
pp. A2-A2 ◽  
Author(s):  
JM Lane ◽  
I Vlasac ◽  
S Redline ◽  
D Ray ◽  
M Rutter ◽  
...  
Keyword(s):  
Sleep Apnea ◽  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide
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