scholarly journals Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

2022 ◽  
Author(s):  
Joris A. Alkemade ◽  
Nelson Nazzicari ◽  
Monika M. Messmer ◽  
Paolo Annicchiarico ◽  
Barbara Ferrari ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
White Lupin ◽  
Grain Legume ◽  
Anthracnose Resistance ◽  
Anthracnose Disease ◽  
Genome Wide ◽  
A Genome

Abstract Key message GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. Abstract White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

scholarly journals A genome-wide association study reveals a novel candidate gene for sperm motility in pigs

2014 ◽  
Vol 151 (3-4) ◽  
pp. 201-207 ◽  
Author(s):  
D.B. Diniz ◽  
M.S. Lopes ◽  
M.L.W.J. Broekhuijse ◽  
P.S. Lopes ◽  
B. Harlizius ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Sperm Motility ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengfu Zhou ◽  
Huiyue Guan ◽  
Congcong Liu ◽  
Ziwei Zhang ◽  
Shenghui Geng ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Regulatory Elements ◽  
Genome Wide Association ◽  
Genetic Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. Results Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. Conclusions To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

scholarly journals Genome-Wide Association Study and Subsequent Exclusion of ATCAY as a Candidate Gene Involved in Equine Neuroaxonal Dystrophy Using Two Animal Models

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 82 ◽  
Author(s):  
Erin N Hales ◽  
Christina Esparza ◽  
Sichong Peng ◽  
Anna R Dahlgren ◽  
Janel M Peterson ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Neurodegenerative Disorder ◽  
Genome Wide Association ◽  
Neuroaxonal Dystrophy ◽  
Tocopheryl Acetate ◽  
Unknown Etiology ◽  
Genome Wide ◽  
A Genome

Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (eNAD/EDM) is an inherited neurodegenerative disorder of unknown etiology. Clinical signs of neurological deficits develop within the first year of life in vitamin E (vitE) deficient horses. A genome-wide association study (GWAS) was carried out using 670,000 SNP markers in 27 case and 42 control Quarter Horses. Two markers, encompassing a 2.5 Mb region on ECA7, were associated with the phenotype (p = 2.05 × 10-7 and 4.72 × 10-6). Within this region, caytaxin (ATCAY) was identified as a candidate gene due to its known role in Cayman Ataxia and ataxic/dystonic phenotypes in mouse models. Whole-genome sequence data in four eNAD/EDM and five unaffected horses identified 199 associated variants within the ECA7 region. MassARRAY® genotyping was performed on these variants within the GWAS population. The three variants within ATCAY were not concordant with the disease phenotype. No difference in expression or alternative splicing was identified using qRT-PCR in brainstem across the ATCAY transcript. Atcayji-hes mice were then used to conduct functional analysis in a second animal model. Histologic lesions were not identified in the central nervous system of Atcayji-hes mice. Additionally, supplementation of homozygous Atcayji-hes mice with 600 IU/day of dl-α-tocopheryl acetate (vitE) during gestation, lactation, and adulthood did not improve the phenotype. ATCAY has therefore been excluded as a candidate gene for eNAD/EDM.

scholarly journals CDH12 as a Candidate Gene for Kidney Injury in Posterior Urethral Valve Cases: A Genome-wide Association Study Among Patients with Obstructive Uropathies

2021 ◽  
Vol 28 ◽  
pp. 26-35
Author(s):  
Loes F.M. van der Zanden ◽  
Iris A.L.M. van Rooij ◽  
Josine S.L.T. Quaedackers ◽  
Rien J.M. Nijman ◽  
Martijn Steffens ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Kidney Injury ◽  
Posterior Urethral Valve ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Urethral Valve

scholarly journals A genome-wide association study of heparin-induced thrombocyto - penia using an electronic medical record

2015 ◽  
Vol 113 (04) ◽  
pp. 772-781 ◽  
Author(s):  
Jason H. Karnes ◽  
Robert M. Cronin ◽  
Jerome Rollin ◽  
Alexander Teumer ◽  
Claire Pouplard ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Candidate Gene Study ◽  
Platelet Factor ◽  
Genome Wide ◽  
A Genome ◽  
Gene Study

SummaryHeparin-induced thrombocytopenia (HIT) is an unpredictable, potentially catastrophic adverse effect of heparin treatment resulting from an immune response to platelet factor 4 (PF4)/heparin complexes. No genome-wide evaluations have been performed to identify potential genetic influences on HIT. Here, we performed a genome-wide association study (GWAS) and candidate gene study using HIT cases and controls identified using electronic medical records (EMRs) coupled to a DNA biobank and attempted to replicate GWAS associations in an independent cohort. We subsequently investigated influences of GWAS-associated single nucleotide polymorphisms (SNPs) on PF4/heparin antibodies in non-heparin treated individuals. In a recessive model, we observed significant SNP associations (odds ratio [OR] 18.52; 95% confidence interval [CI] 6.33-54.23; p=3.18×10-9) with HIT near the T-Cell Death-Associated Gene 8 (TDAG8). These SNPs are in linkage disequilibrium with a missense TDAG8 SNP. TDAG8 SNPs trended toward an association with HIT in replication analysis (OR 5.71; 0.47-69.22; p=0.17), and the missense SNP was associated with PF4/heparin antibody levels and positive PF4/heparin antibodies in non-heparin treated patients (OR 3.09; 1.14-8.13; p=0.02). In the candidate gene study, SNPs at HLA-DRA were nominally associated with HIT (OR 0.25; 0.15-0.44; p=2.06×10-6). Further study of TDAG8 and HLA-DRA SNPs is warranted to assess their influence on the risk of developing HIT.

scholarly journals Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Xin ◽  
Jingguo Wang ◽  
Jia Li ◽  
Hongwei Zhao ◽  
Hualong Liu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Negative Impact ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Genome Wide ◽  
A Genome

Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.

scholarly journals Novel Genomic Regions of Fusarium Wilt Resistance in Bottle Gourd [Lagenaria siceraria (Mol.) Standl.] Discovered in Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanwei Li ◽  
Ying Wang ◽  
Xinyi Wu ◽  
Jian Wang ◽  
Xiaohua Wu ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Bottle Gourd ◽  
Genome Wide Association ◽  
Pcr Analysis ◽  
Functional Markers ◽  
Potential Candidate ◽  
Genome Wide ◽  
A Genome

Fusarium wilt (FW) is a typical soil-borne disease that seriously affects the yield and fruit quality of bottle gourd. Thus, to improve resistance to FW in bottle gourd, the genetic mechanism underlying FW resistance needs to be explored. In this study, we performed a genome-wide association study (GWAS) based on 5,330 single-nucleotide polymorphisms (SNPs) and 89 bottle gourd accessions. The GWAS results revealed a total of 10 SNPs (P ≤ 0.01, −log10P ≥ 2.0) significantly associated with FW resistance that were detected in at least two environments (2019DI, 2020DI, and the average across the 2 years); these SNPs were located on chromosomes 1, 2, 3, 4, 8, and 9. Linkage disequilibrium (LD) block structure analysis predicted three potential candidate genes for FW resistance. Genes HG_GLEAN_10001030 and HG_GLEAN_10001042 were within the range of the mean LD block of the marker BGReSe_14202; gene HG_GLEAN_10011803 was 280 kb upstream of the marker BGReSe_00818. Real-time quantitative PCR (qRT-PCR) analysis showed that HG_GLEAN_10011803 was significantly up-regulated in FW-infected plants of YD-4, Yin-10, and Hanbi; HG_GLEAN_10001030 and HG_GLEAN_10001042 were specifically up-regulated in FW-infected plants of YD-4. Therefore, gene HG_GLEAN_10011803 is likely the major effect candidate gene for resistance against FW in bottle gourd. This work provides scientific evidence for the exploration of candidate gene and development of functional markers in FW-resistant bottle gourd breeding programs.

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