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

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 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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Genome-Wide Association Study (GWAS) for Resistance to Sclerotinia sclerotiorum in Common Bean

Genes ◽

10.3390/genes11121496 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1496

Author(s):

Ana Campa ◽

Carmen García-Fernández ◽

Juan José Ferreira

Keyword(s):

Association Study ◽

Common Bean ◽

Genome Wide Association Study ◽

Continuous Distribution ◽

Genome Wide Association ◽

Host Recognition ◽

Gene Pools ◽

Potential Candidate ◽

Genome Wide ◽

A Genome

White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods were used in the GWAS. Response to this fungus showed a continuous distribution, and 28 lines were identified as potential resistance sources, including lines of Andean and Mesoamerican origin, as well as intermediate lines between the two gene pools. Twenty-two significant associations were identified, which were organized into 15 quantitative trait intervals (QTIs) located on chromosomes Pv01, Pv02, Pv03, Pv04, Pv08, and Pv09. Seven of these QTIs were identified for the first time, whereas eight corresponded to chromosome regions previously identified in the WM resistance. In all, 468 genes were annotated in these regions, 61 of which were proposed potential candidate genes for WM resistance, based on their function related to the three main defense stages on the host: recognition (22), signal transduction (8), and defense response (31). Results obtained from this work will contribute to a better understanding of the complex quantitative resistance to WM in common bean and reveal information of significance for future breeding programs.

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