Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean

The most effective strategy to manage bean anthracnose (ANT), caused by Colletotrichum lindemuthianum, is the use of resistant cultivars. This study aimed to evaluate resistance reactions of common bean accessions to C. lindemuthianum races 2, 9 and 1545, and to perform genome-wide association study (GWAS). Hence, 89 accessions were phenotyped and genotyped through genotyping by sequencing (GBS). As a result, 48 accessions resistant to all evaluated races were identified. Moreover, single-nucleotide polymorphisms (SNP) significantly associated with resistance were identified in new regions of chromosomes Pv03, Pv05 and Pv06, and also at the beginning of Pv04 and end of Pv11, where other resistance genes have been previously found. In reference genome these regions contain model genes encoding resistance proteins as kinases, leucine-rich repeats, receptor-like protein, copper transport protein, pentatricopeptide repeats, calcium-dependent protein kinases, and ethylene-responsive transcription factors. The genomic regions associated to ANT resistance found in this study should be validated for further use in marker assisted selection and gene pyramiding. Together with new sources of ANT resistance our findings show promise for further crop improvement.

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Genome‐Wide Association Study of Agronomic Traits in Common Bean

The Plant Genome ◽

10.3835/plantgenome2014.09.0059 ◽

2015 ◽

Vol 8 (2) ◽

Cited By ~ 38

Author(s):

Kelvin Kamfwa ◽

Karen A. Cichy ◽

James D. Kelly

Keyword(s):

Association Study ◽

Common Bean ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Genome Wide

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Genome‐wide association study of resistance to anthracnose and angular leaf spot in Brazilian Mesoamerican and Andean common bean cultivars

Crop Science ◽

10.1002/csc2.20308 ◽

2020 ◽

Vol 60 (6) ◽

pp. 2931-2950

Author(s):

Pedro S. Vidigal Filho ◽

Maria Celeste Gonçalves‐Vidigal ◽

Mariana Vaz Bisneta ◽

Vanet B. Souza ◽

Thiago A.S. Gilio ◽

...

Keyword(s):

Association Study ◽

Common Bean ◽

Leaf Spot ◽

Genome Wide Association Study ◽

Angular Leaf Spot ◽

Genome Wide Association ◽

Genome Wide

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Genome wide association study discovers genomic regions involved in resistance to soybean cyst nematode (Heterodera glycines) in common bean

PLoS ONE ◽

10.1371/journal.pone.0212140 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0212140 ◽

Cited By ~ 1

Author(s):

Shalu Jain ◽

Susilo Poromarto ◽

Juan M. Osorno ◽

Phillip E. McClean ◽

Berlin D. Nelson

Keyword(s):

Association Study ◽

Common Bean ◽

Soybean Cyst Nematode ◽

Genome Wide Association Study ◽

Heterodera Glycines ◽

Cyst Nematode ◽

Genome Wide Association ◽

Genome Wide ◽

Genomic Regions

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Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03859-2 ◽

2021 ◽

Author(s):

Jessica Delfini ◽

Vânia Moda-Cirino ◽

José dos Santos Neto ◽

Douglas Mariani Zeffa ◽

Alison Fernando Nogueira ◽

...

Keyword(s):

Association Study ◽

Common Bean ◽

Mineral Content ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Diversity Panel ◽

Genome Wide

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Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Core Collection

Frontiers in Plant Science ◽

10.3389/fpls.2021.624156 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ainong Shi ◽

Paul Gepts ◽

Qijian Song ◽

Haizheng Xiong ◽

Thomas E. Michaels ◽

...

Keyword(s):

Association Study ◽

Common Bean ◽

Soybean Cyst Nematode ◽

Core Collection ◽

Genome Wide Association Study ◽

Snp Markers ◽

Cyst Nematode ◽

Genome Wide Association ◽

Genome Wide ◽

Scn Resistance

Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.

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Novel insights into the common heritable liability to addiction: a multivariate genome-wide association study

10.1101/2021.11.19.21266548 ◽

2021 ◽

Author(s):

Tabea Schoeler ◽

Jessie Baldwin ◽

Andrea Allegrini ◽

Wikus Barkhuizen ◽

Andrew McQuillin ◽

...

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genetic Correlations ◽

Brain Regions ◽

Genome Wide Association ◽

Drug Reinforcement ◽

Heroin Use ◽

Genome Wide ◽

The Common

Addiction to nicotine, alcohol and cannabis commonly co-occurs, which is thought to partly stem from a common heritable liability. To elucidate its genetic architecture, we modelled the common liability to addiction, inferred from genetic correlations among six measures of dependence and frequency of use of nicotine, alcohol and cannabis. Forty-two genetic variants were identified in the multivariate genome-wide association study on the common liability to addiction, of which 67% were novel and not associated with the six phenotypes. Mapped genes highlighted the role of dopamine (e.g., dopamine D2 gene), and showed enrichment for a several components of the central nervous systems (e.g., mesocorticolimbic brain regions) and molecular pathways (dopaminergic, glutamatergic, GABAergic) that are thought to modulate drug reinforcement. Genetic correlations with other traits were most prominent for reward-related behaviours (e.g., risk-taking, cocaine and heroin use) and mood (e.g., depression, insomnia). These genome-wide results triangulate and expand previous preclinical and human studies focusing on the neurobiological substrates of addiction, and help to elucidate the common genetic architecture underlying addiction.

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