scholarly journals Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley

2020 ◽  
Author(s):  
Hao Luo ◽  
Camilla Beate Hill ◽  
Gaofeng Zhou ◽  
Xiao-Qi Zhang ◽  
Chengdao Li
Keyword(s):  
Association Studies ◽  
Missense Variant ◽  
Binding Activity ◽  
Genome Wide Association ◽  
Yield Potential ◽  
Genome Wide Association Studies ◽  
Hordeum Vulgare L ◽  
Coleoptile Length ◽  
Dna Binding Activity ◽  
Genome Wide

Abstract BackgroundDrought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions. ResultsIn this study, we detected large genetic variation in a panel of 328 diverse barley (Hordeum vulgare L.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were geminated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. The Squamosa promoter-binding-like protein 3 gene (SPL3) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity. ConclusionThis study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.

Abstract P112: Genes in Genome-wide Association Study-identified Loci and Risk of Atherosclerosis in Adolescents and Young Adults

Circulation ◽  
2017 ◽  
Vol 135 (suppl_1) ◽  
Author(s):  
Changwei Li ◽  
Shengxu Li ◽  
James E Hixon
Keyword(s):  
Genome Wide Association Study ◽  
Sequence Data ◽  
Association Studies ◽  
Statistical Significance ◽  
Missense Variant ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Common Snps ◽  
Single Marker Analysis ◽  
Genome Wide

Background: Genome-wide association studies (GWASs) have identified multiple genomic loci associated with atherosclerotic diseases. However, specific genes underlying the observed associations are largely unknown. Objectives: We aimed to examine the associations between genes that harbor variants in high LD with index variants in GWAS-identified loci and pathologically determined atherosclerosis in major arteries from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study. Methods and Results: Data for 1,938 single nucleotide polymorphisms (SNPs) from 28 genes were retrieved from whole exome sequence data. Atherosclerosis was confirmed by postmortem examination of major arteries from 1,005 young persons (aged 15-34 years) who died from non-cardiovascular causes. Logistic regression was used to evaluate associations between common SNPs and atherosclerosis controlling for age and sex. Gene-based analysis was conducted using Sequence Kernel Association Test (SKAT) method to test the combined effect of rare and common variants on atherosclerosis controlling for age and gender. All analyses were performed separately in blacks and whites. Statistical significance was determined by false positive discovery rate (FDR) method. In gene-based analyses, BUD13 ( P =1.11х10 -2 ) and COL4A1 ( P =3.58х10 -2 ) were associated with atherosclerosis among young blacks; none of the 28 genes was associated with atherosclerosis in whites. In single marker analysis of common SNPs, LRP1 missense variant rs7397167 ( P =8.50х10 -3 ), COL4A1 variant rs16975492 ( P =4.60х10 -3 ), STK32B variant rs168985 ( P =4.00х10 -3 ), and SMARCA4 variant rs8104480 ( P =1.20х10 -3 ) were associated with atherosclerosis in blacks; MIA3 variant rs17465637 ( P =8.00х10 -3 ), DUS4L missense variant rs6957510 ( P =6.4х10 -3 ), BOLL variant rs771018 ( P =6.2х10 -3 ), BUD3 missense variant rs11820589 ( P =2.1х10 -3 ), and COL4A1 variant rs1133219 ( P =1.8х10 -3 ) were associated with atherosclerosis in whites. Conclusion: Genes in GWAS-identified loci may play a role in the development of atherosclerosis at a young age.

scholarly journals Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program

2021 ◽  
Author(s):  
Lance F Merrick ◽  
Adrienne B Burke ◽  
Zhiwu Zhang ◽  
Arron H Carter
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Seedling Emergence ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Coleoptile Length ◽  
Correlated Traits ◽  
Genome Wide ◽  
Reduced Height ◽  
Chromosome 5A

Traits with an unknown genetic architecture make it difficult to create a useful bi-parental mapping population to characterize the genetic basis of the trait due to a combination of complex and pleiotropic effects. Seedling emergence of wheat (Triticum aestivum L.) from deep planting is a vital factor affecting stand establishment and grain yield, has a poorly understood genetic architecture, and is historically correlated with coleoptile length. The creation of bi-parental mapping populations can be overcome by using genome-wide association studies (GWAS). This study aimed to dissect the genetic architecture of seedling emergence while accounting for correlated traits using one multi-trait GWAS model (MT-GWAS) and three single-trait GWAS models (ST-GWAS) with the inclusion of covariates for correlated traits. The ST-GWAS models included one single locus model (MLM), and two multiple loci models (FarmCPU and BLINK). We conducted the GWAS using two populations, the first consisting of 473 varieties from a diverse association mapping panel (DP) phenotyped from 2015-2019, and the other population used as a validation population consisting of 279 breeding lines (BL) phenotyped in 2015 in Lind, WA, with 40,368 markers. We also compared the inclusion of coleoptile length and markers associated with reduced height as covariates in our ST-GWAS models for the DP. ST-GWAS found 107 significant markers across 19 chromosomes, while MT-GWAS found 82 significant markers across 14 chromosomes. MT-GWAS models were able to identify large-effect markers on chromosome 5A. FarmCPU and BLINK models were able to identify many small effect markers, and the inclusion of covariates helped to identify the large effect markers on chromosome 5A. Therefore, by using multi-locus models combined with pleiotropic covariates, breeding programs can uncover the complex nature of traits to help identify candidate genes and the underlying architecture of a trait, such as seedling emergence of deep-sown winter wheat.

scholarly journals Genome-wide Association Studies and Candidate Gene Identification for Leaf Scald and Net Blotch in Barley (Hordeum vulgare L.)

Plant Disease ◽  
2019 ◽  
Vol 103 (5) ◽  
pp. 880-889 ◽  
Author(s):  
Sintayehu D Daba ◽  
Richard Horsley ◽  
Robert Brueggeman ◽  
Shiaoman Chao ◽  
Mohsen Mohammadi
Keyword(s):  
Association Studies ◽  
Defense Responses ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Net Blotch ◽  
Hordeum Vulgare L ◽  
Seedling Resistance ◽  
Leaf Scald ◽  
Genome Wide

We report genomic regions that significantly control resistance to scald, net form (NFNB) and spot form net blotch (SFNB) in barley. Barley genotypes from Ethiopia, ICARDA, and the United States were evaluated in Ethiopia and North Dakota State University (NDSU). Genome-wide association studies (GWAS) were conducted using 23,549 single nucleotide polymorphism (SNP) markers for disease resistance in five environments in Ethiopia. For NFNB and SFNB, we assessed seedling resistance in a glasshouse at NDSU. A large proportion of the Ethiopian landraces and breeding genotypes were resistant to scald and NFNB. Most of genotypes resistant to SFNB were from NDSU. We identified 17, 26, 7, and 1 marker-trait associations (MTAs) for field-scored scald, field-scored net blotch, greenhouse-scored NFNB, and greenhouse-scored SFNB diseases, respectively. Using the genome sequence and the existing literature, we compared the MTAs with previously reported loci and genes for these diseases. For leaf scald, only a few of our MTAs overlap with previous reports. However, the MTAs found for field-scored net blotch as well as NFNB and SFNB mostly overlap with previous reports. We scanned the barley genome for identification of candidate genes within 250 kb of the MTAs, resulting in the identification of 307 barley genes for the 51 MTAs. Some of these genes are related to plant defense responses such as subtilisin-like protease, chalcone synthase, lipoxygenase, and defensin-like proteins.

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