scholarly journals An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade inACEand putative multilocus association betweenACE,A2M, andLRRTM3

2009 ◽  
Vol 150B (5) ◽  
pp. 721-735 ◽  
Author(s):  
Todd L. Edwards ◽  
Margaret Pericak-Vance ◽  
Johnny R. Gilbert ◽  
Jonathan L. Haines ◽  
Eden R. Martin ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Candidate Genes ◽  
Association Analysis ◽  
Risk Haplotype

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

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.

scholarly journals Prevalence, Patterns, and Genetic Association Analysis of Modic Vertebral Endplate Changes

2017 ◽  
Vol 11 (4) ◽  
pp. 594-600 ◽  
Author(s):  
Rishi Mugesh Kanna ◽  
Rajasekaran Shanmuganathan ◽  
Veera Ranjani Rajagopalan ◽  
Senthil Natesan ◽  
Raveendran Muthuraja ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Association ◽  
Association Analysis ◽  
Disc Degeneration ◽  
Lumbar Disc ◽  
Nucleotide Polymorphisms ◽  
Lumbar Disc Degeneration ◽  
Vertebral Endplate ◽  
Genetic Association Analysis ◽  
Study Population

<sec><title>Study Design</title><p>A prospective genetic association study.</p></sec><sec><title>Purpose</title><p>The etiology of Modic changes (MCs) is unclear. Recently, the role of genetic factors in the etiology of MCs has been evaluated. However, studies with a larger patient subset are lacking, and candidate genes involved in other disc degeneration phenotypes have not been evaluated. We studied the prevalence of MCs and genetic association of 41 candidate genes in a large Indian cohort.</p></sec><sec><title>Overview of Literature</title><p>MCs are vertebral endplate signal changes predominantly observed in the lumbar spine. A significant association between MCs and lumbar disc degeneration and nonspecific low back pain has been described, with the etiopathogenesis implicating various mechanical, infective, and biochemical factors.</p></sec><sec><title>Methods</title><p>We studied 809 patients using 1.5-T magnetic resonance imaging to determine the prevalence, patterns, distribution, and type of lumbar MCs. Genetic association analysis of 71 single nucleotide polymorphisms (SNPs) of 41 candidate genes was performed based on the presence or absence of MCs. SNPs were genotyped using the Sequenome platform, and an association test was performed using PLINK software.</p></sec><sec><title>Results</title><p>The mean age of the study population (n=809) was 36.7±10.8 years. Based on the presence of MCs, the cohort was divided into 702 controls and 107 cases (prevalence, 13%). MCs were more commonly present in the lower (149/251, 59.4%) than in the upper (102/251, 40.6%) endplates. L4–5 endplates were the most commonly affected levels (30.7%). Type 2 MCs were the most commonly observed pattern (n=206, 82%). The rs2228570 SNP of VDR (<italic>p</italic>=0.02) and rs17099008 SNP of MMP20 (<italic>p</italic>=0.03) were significantly associated with MCs.</p></sec><sec><title>Conclusions</title><p>Genetic polymorphisms of SNPs of VDR and MMP20 were significantly associated with MCs. Understanding the etiopathogenetic mechanisms of MCs is important for planning preventive and therapeutic strategies.</p></sec>

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

2022 ◽  
Author(s):  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Yibin Qiu ◽  
Donglin Ruan ◽  
Jie Wu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Large Scale ◽  
Major Gene ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Backfat Thickness ◽  
Lean Meat ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks

2005 ◽  
Vol 110 (7) ◽  
pp. 1324-1333 ◽  
Author(s):  
S. J. Szalma ◽  
E. S. Buckler ◽  
M. E. Snook ◽  
M. D. McMullen
Keyword(s):  
Chlorogenic Acid ◽  
Candidate Genes ◽  
Association Analysis ◽  
Acid Accumulation ◽  
Maize Silks

Parsing the genetic heterogeneity of chromosome 12q susceptibility genes for Alzheimer disease by family-based association analysis

Neurogenetics ◽  
2006 ◽  
Vol 7 (3) ◽  
pp. 157-165 ◽  
Author(s):  
Ping-I Lin ◽  
Eden R. Martin ◽  
Carrie A. Browning-Large ◽  
Donald E. Schmechel ◽  
Kathleen A. Welsh-Bohmer ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Association Analysis ◽  
Genetic Heterogeneity ◽  
Susceptibility Genes ◽  
Family Based
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