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

Crop Science ◽  
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

scholarly journals Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150506 ◽  
Author(s):  
Juliana Morini Küpper Cardoso Perseguini ◽  
Paula Rodrigues Oblessuc ◽  
João Ricardo Bachega Feijó Rosa ◽  
Kleber Alves Gomes ◽  
Alisson Fernando Chiorato ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Leaf Spot ◽  
Association Studies ◽  
Angular Leaf Spot ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Phaseolus Vulgaris L ◽  
Genome Wide

scholarly journals Quantile regression for genome-wide association study of flowering time-related traits in common bean

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190303 ◽  
Author(s):  
Moysés Nascimento ◽  
Ana Carolina Campana Nascimento ◽  
Fabyano Fonseca e Silva ◽  
Leiri Daiane Barili ◽  
Naine Martins do Vale ◽  
...  
Keyword(s):  
Quantile Regression ◽  
Association Study ◽  
Common Bean ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals New genomic regions for resistance to anthracnose (Colletotrichum lindemuthianum) through GBS-based genome-wide association study in common bean (Phaseolus vulgaris)

2021 ◽  
Vol 12 (1) ◽  
pp. 020-040
Author(s):  
Mariana Vaz Bisneta ◽  
Maria Celeste Gonçalves-Vidigal ◽  
Pedro Soares Vidigal Filho ◽  
Júlio Cesar Ferreira Elias ◽  
Giseli Valentini ◽  
...  
Keyword(s):  
Association Study ◽  
Common Bean ◽  
Genome Wide Association Study ◽  
Crop Improvement ◽  
Gene Pyramiding ◽  
Colletotrichum Lindemuthianum ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Genomic Regions

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.

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

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

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

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.

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

Genes ◽  
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.

scholarly journals Genome-Wide Association Study of Seed Folate Content in Common Bean

2021 ◽  
Vol 12 ◽  
Author(s):  
C. Joe Martin ◽  
Davoud Torkamaneh ◽  
Muhammad Arif ◽  
Karl Peter Pauls
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Association Study ◽  
Common Bean ◽  
Genome Wide Association Study ◽  
Folate Deficiency ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Essential Components

Plant-derived folates (Vitamin B9) are essential components of the human diet. They provide one-carbon units that are required for the synthesis of nucleic acids and proteins, and folate deficiency is associated with numerous adverse health conditions. The development of high-folate cultivars of common bean (Phaseolus vulgaris L.) and other staple crops is an important tool to combat folate deficiency. A population of 96 P. vulgaris accessions, representing major North American market classes, was grown in 2 years in Ontario, Canada. The population was genotyped for 5,361 molecular markers with an Illumina Infinium platform. Total folate was extracted from mature seeds using the tri-enzyme extraction method and quantified based on a microbiological assay with Lactobacillus rhamnosus. Significant genetic diversity for folate content was observed among the population in both years of study, and folate content had a range 113–222 μg per 100 g of seeds. Quantitative trait loci (QTL) for seed folate content were identified based on a genome-wide association study (GWAS). Six QTL were identified on Chr. 4, 6, 8, and 11, with three in each year of field trials. Both QTL on Chr. 11 occurred in genomic regions that were syntenic to seed folate QTL detected in previous work with P. vulgaris, Z. mays, and O. sativa. Candidate genes were identified for these QTL that might be targets for the development of molecular markers for selecting P. vulgaris cultivars with improved seed folate content. This work reports the largest survey of genetic diversity for seed folate content in P. vulgaris and identified several genotypes, including SCN4, Bat 93, OAC Redstar, and Pompadour 1014, that would be useful for breeding beans with higher than average folate levels.

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