scholarly journals Genome-Wide Association Mapping and Gene Expression Analysis Reveal the Negative Role of OsMYB21 in Regulating Bacterial Blight Resistance in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wu Yang ◽  
Junliang Zhao ◽  
Shaohong Zhang ◽  
Luo Chen ◽  
Tifeng Yang ◽  
...  
Keyword(s):  
Bacterial Blight ◽  
Genome Wide Association ◽  
Effective Control ◽  
Blight Resistance ◽  
Potential Candidate ◽  
Rice Breeding ◽  
Chromosome 11 ◽  
Bacterial Blight Resistance ◽  
Genome Wide ◽  
A Genome

Abstract Background Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases in rice all over the world. Due to the diversity and rapid evolution of Xoo, identification and use of the non-race specific quantitative resistance QTLs has been considered the preferred strategy for effective control of this disease. Although numerous QTLs for BB resistance have been identified, they haven’t been effectively used for improvement of BB resistance in rice due to their small effects and lack of knowledge on the function of genes underlying the QTLs. Results In the present study, a genome-wide association study of BB resistance was performed in a rice core collection from South China. A total of 17 QTLs were identified to be associated with BB resistance. Among them, 13 QTLs were newly identified in the present study and the other 4 QTLs were co-localized with the previously reported QTLs or Xa genes that confer qualitative resistance to Xoo strains. Particularly, the qBBR11–4 on chromosome 11 explained the largest phenotypic variation in this study and was co-localized with the previously identified QTLs for BB and bacterial leaf streak (BLS) resistance against diverse strains in three studies, suggesting its broad-spectrum resistance and potential value in rice breeding. Through combined analysis of differential expression and annotations of the predicted genes within qBBR11–4 between two sets of rice accessions selected based on haplotypes and disease phenotypes, we identified the transcription factor OsMYB21 as the candidate gene for qBBR11–4. The OsMYB21 overexpressing plants exhibited decreased resistance to bacterial blight, accompanied with down-regulation of several defense-related genes compared with the wild-type plants. Conclusion The results suggest that OsMYB21 negatively regulates bacterial blight resistance in rice, and this gene can be a promising target in rice breeding by using the gene editing method. In addition, the potential candidate genes for the 13 novel QTLs for BB resistance were also analyzed in this study, providing a new source for cloning of genes associated with BB resistance and molecular breeding in rice.

scholarly journals Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

2021 ◽  
Author(s):  
Lei Wu ◽  
Yujie Chang ◽  
Lanfen Wang ◽  
Shumin Wang ◽  
Jing Wu
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Drought Resistance ◽  
Survival Rates ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Chromosome 11 ◽  
Genome Wide ◽  
A Genome

Abstract A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3832340 SNPs. The coefficient of variation ranged from 40.90% to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

scholarly journals A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility

2016 ◽  
Vol 149 (3) ◽  
pp. 156-164 ◽  
Author(s):  
Yadav Sapkota ◽  
Ashok Narasimhan ◽  
Mahalakshmi Kumaran ◽  
Badan S. Sehrawat ◽  
Sambasivarao Damaraju
Keyword(s):  
Breast Cancer ◽  
Association Study ◽  
Copy Number ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Frequency Effect ◽  
Potential Candidate ◽  
Disease Etiology ◽  
Genome Wide ◽  
A Genome

Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.

scholarly journals Distribution of Bacterial Blight Resistance Genes in the Main Cultivars and Application of Xa23 in Rice Breeding

2020 ◽  
Vol 11 ◽  
Author(s):  
Shiguang Wang ◽  
Wei Liu ◽  
Dongbai Lu ◽  
Zhanhua Lu ◽  
Xiaofei Wang ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Blight ◽  
Blight Resistance ◽  
Rice Breeding ◽  
Bacterial Blight Resistance

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Gina A. Garzón-Martínez ◽  
Paola Delgadillo-Duran ◽  
Silvio Bastidas ◽  
Leidy P. Moreno ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Genome Wide Association ◽  
Hybrid Population ◽  
Potential Candidate ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Pyramiding of two rice bacterial blight resistance genes, Xa3 and Xa4, and a closely linked cold-tolerance QTL on chromosome 11

2016 ◽  
Vol 129 (10) ◽  
pp. 1861-1871 ◽  
Author(s):  
Yeon-Jae Hur ◽  
Jun-Hyeon Cho ◽  
Hyun-Su Park ◽  
Tae-Hwan Noh ◽  
Dong-Soo Park ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Resistance Genes ◽  
Bacterial Blight ◽  
Blight Resistance ◽  
Chromosome 11 ◽  
Bacterial Blight Resistance ◽  
Rice Bacterial Blight

scholarly journals Genome-wide Association Study of Pulmonary Function in Europeans and Africans from the UK Biobank Identifies Distinct Variants

2022 ◽  
Author(s):  
Musalula Sinkala ◽  
Samar S. M. Elsheikh ◽  
Mamana Mbiyavanga ◽  
Joshua Cullinan ◽  
Nicola Mulder
Keyword(s):  
Pulmonary Function ◽  
Genome Wide Association Study ◽  
Well Being ◽  
Genome Wide Association ◽  
Significant Finding ◽  
Uk Biobank ◽  
Chromosome 11 ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause of death worldwide. FEV1, FVC, and PEF are quantitively used to assess pulmonary function. We conducted a genome-wide association analysis of pulmonary function in 383,471 individuals of European and 5,978 African descent represented in the UK Biobank. Here, we report 817 variants in Europeans and 3 in Africans associated (p-values < 5 x 10-8) with three pulmonary function parameters; FEV1, FVC and PEF. In addition to 377 variants in Europeans previously reported to be associated with phenotypes related to pulmonary function, we identified 330 novel loci, including an ISX intergenic variant rs369476290 on chromosome 22 in Africans and a KDM2A intron variant rs12790261 on chromosome 11 in Europeans. Remarkably, we find no shared variants among Africans and Europeans. Enrichment analyses of variants separately for each ancestry background revealed significant enrichment for terms related to pulmonary phenotypes in Europeans but not Africans. Further analysis of studies of pulmonary phenotypes revealed individuals of European background are disproportionally overrepresented in datasets compared to Africans, with the gap widening over the past five years. Our findings offer a better understanding of the different variants that modify pulmonary function in Africans and Europeans, a significant finding for future GWAS studies and medicine.

scholarly journals Genome-wide association study identifies two new loci associated with anti-NMDAR encephalitis

2021 ◽  
Author(s):  
Anja K Tietz ◽  
Klemens Angstwurm ◽  
Tobias Baumgartner ◽  
Kathrin Doppler ◽  
Katharina Eisenhut ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
Genome Wide Association ◽  
Chromosome 11 ◽  
Genetic Determinants ◽  
Nmdar Encephalitis ◽  
Genome Wide ◽  
A Genome ◽  
Causal Genes

AbstractObjectiveTo investigate the genetic determinants of the most common type of antibody-mediated autoimmune encephalitis, anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis.MethodsWe performed a genome-wide association study in 178 patients with anti-NMDAR encephalitis and 590 healthy controls followed by a colocalization analysis to identify putatively causal genes.ResultsWe identified two independent risk loci harboring genome-wide significant variants (P < 5 × 10−8, OR ≤ 2.2), one on chromosome 15, harboring only the LRRK1 gene, and one on chromosome 11 centered on the ACP2 and NR1H3 genes in a larger region of high linkage-disequilibrium. Colocalization signals with expression quantitative trait loci (eQTL) for different brain regions and immune cell types suggested ACP2, NR1H3, MADD, DDB2, and C11orf49 as putatively causal genes. The best candidate genes in each region are LRRK1, encoding Leucine-Rich Repeat Kinase 1, a protein involved in B-cell development, and NR1H3 liver x receptor alpha, a transcription factor whose activation inhibits inflammatory processes.ConclusionThis study provides evidence for relevant genetic determinants of antibody-mediated autoimmune encephalitides outside the HLA-region. The results suggest that future studies with larger sample sizes will successfully identify additional genetic determinants and contribute to the elucidation of the pathomechanism.

scholarly journals Genome-wide Association Study Identifies 2 New Loci Associated With Anti-NMDAR Encephalitis

2021 ◽  
Vol 8 (6) ◽  
pp. e1085
Author(s):  
Anja K. Tietz ◽  
Klemens Angstwurm ◽  
Tobias Baumgartner ◽  
Kathrin Doppler ◽  
Katharina Eisenhut ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
Genome Wide Association ◽  
Chromosome 11 ◽  
Genetic Determinants ◽  
Nmdar Encephalitis ◽  
Genome Wide ◽  
A Genome ◽  
Causal Genes

Background and ObjectivesTo investigate the genetic determinants of the most common type of antibody-mediated autoimmune encephalitis, anti-NMDA receptor (anti-NMDAR) encephalitis.MethodsWe performed a genome-wide association study in 178 patients with anti-NMDAR encephalitis and 590 healthy controls, followed by a colocalization analysis to identify putatively causal genes.ResultsWe identified 2 independent risk loci harboring genome-wide significant variants (p < 5 × 10−8, OR ≥ 2.2), 1 on chromosome 15, harboring only the LRRK1 gene, and 1 on chromosome 11 centered on the ACP2 and NR1H3 genes in a larger region of high linkage disequilibrium. Colocalization signals with expression quantitative trait loci for different brain regions and immune cell types suggested ACP2, NR1H3, MADD, DDB2, and C11orf49 as putatively causal genes. The best candidate genes in each region are LRRK1, encoding leucine-rich repeat kinase 1, a protein involved in B-cell development, and NR1H3 liver X receptor alpha, a transcription factor whose activation inhibits inflammatory processes.DiscussionThis study provides evidence for relevant genetic determinants of antibody-mediated autoimmune encephalitides outside the human leukocyte antigen (HLA) region. The results suggest that future studies with larger sample sizes will successfully identify additional genetic determinants and contribute to the elucidation of the pathomechanism.

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