Genome‐Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Moghaddam, Samira Mafi; Mamidi, Sujan; Osorno, Juan M.; Lee, Rian; Brick, Mark A.; Kelly, James D.; Miklas, Phillip N.; Urrea, Carlos A.; Song, Qijian; Cregan, Perry B.; Grimwood, Jane; Schmutz, Jeremy; McClean, Phillip E.

doi:10.3835/plantgenome2016.02.0012

Cited by 121 publications

(175 citation statements)

References 165 publications

(177 reference statements)

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“…Seed weight data (Moghaddam et al, 2016) were included for the correlation analysis. Strong positive correlations were detected in the whole panel between seed weight and total weight ( r = 0.84), shoot weight ( r = 0.83), root weight ( r = 0.69), and chlorophyll content ( r = 0.70) under flooded condition.…”

Section: Resultsmentioning

confidence: 99%

“…Genomic regions associated with seed weight were detected on Pv10 (Moghaddam et al, 2016). This region was also associated with total and shoot weight in flooded condition (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

“…The Middle-American Diversity Panel (MDP; Moghaddam et al, 2016) consists of six market classes including pinto ( n = 95), great northern ( n = 35), pink ( n = 22), small red ( n = 27), black ( n = 45), and navy ( n = 48) beans. This panel captures the diversity of dry bean breeding germplasm in North America since the 1930s and represents nearly all released varieties developed by public sector.…”

Section: Methodsmentioning

confidence: 99%

“…~150 K SNP markers with MAF ≥ 5% were used in this analysis (Moghaddam et al, 2016). Multiple models were tested for each trait under both flooded and non-flooded condition.…”

Section: Methodsmentioning

confidence: 99%

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Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

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Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.

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Section: Resultsmentioning

confidence: 99%

“…Genomic regions associated with seed weight were detected on Pv10 (Moghaddam et al, 2016). This region was also associated with total and shoot weight in flooded condition (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…~150 K SNP markers with MAF ≥ 5% were used in this analysis (Moghaddam et al, 2016). Multiple models were tested for each trait under both flooded and non-flooded condition.…”

Section: Methodsmentioning

confidence: 99%

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Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

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“…This experiment was performed with the Middle American Diversity Panel (MDP, n = 277, Supplemental Table S1), following the field design as described in Moghaddam et al (2016). Briefly, at each location, the experiment was an a-design with two replications.…”

Section: Plant Materials and Field Designmentioning

confidence: 99%

Phenotypic Diversity for Seed Mineral Concentration in North American Dry Bean Germplasm of Middle American Ancestry

et al. 2017

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Dry bean (Phaseolus vulgaris L.) seeds are a major protein, carbohydrate, and mineral source in the human diet of peoples in multiple regions of the world. Seed mineral biofortification is an ongoing objective to improve this important food source. The objective of this research was to assess the seed mineral concentration of five macroelements and eight microelements in a large panel (n = 277) of modern race Durango and race Mesoamerica genotypes to determine if variability existed that could be exploited for targeted seed biofortification. Varieties that derive from these races are found in many diets throughout the world. The panel was grown in replicated trials under typical production conditions in the major bean growing regions of the United States, and a subset of the panel was also grown in replicated trials at three locations under control and terminal drought conditions. Except for K, seed mineral concentrations were higher for race Mesoamerica genotypes. Significantly higher seed concentrations for the majority of the minerals were observed for white‐seeded genotypes and race Durango genotypes with the now preferred indeterminate, upright growth habit. Modern genotypes (since 1997) had equal or increased mineral concentrations compared with older genotypes. Drought affected mineral content differentially, having no effect on the microelement content but increased Co, Fe, and Ni concentrations. The correlation of Ca and Mn concentrations suggests that these elements may share seed deposition mechanisms. The high heritability for seed mineral concentration implies that breeding progress can be achieved by parental selection from this panel.

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Genetic Resources and Breeding Priorities in Phaseolus Beans

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Genome‐Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Cited by 121 publications

References 165 publications

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

Phenotypic Diversity for Seed Mineral Concentration in North American Dry Bean Germplasm of Middle American Ancestry

Genetic Resources and Breeding Priorities in Phaseolus Beans

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