Multiple Genomic Regions Govern Tolerance to Sulfentrazone in Snap Bean (Phaseolus Vulgaris L.)

Saballos, Ana; Soler‐Garzón, Alvaro; Brooks, Matthew; Hart, Jonathan J.; Lipka, Alexander E.; Miklas, Philip; Peachey, Ronald Edward; Tranel, Patrick J.; Williams, Martin M.

doi:10.3389/fagro.2022.869770

Cited by 9 publications

(13 citation statements)

References 85 publications

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“…They differ in several traits including growth habit (i.e., bush and pole), market type (i.e., fresh and processing), pod sieve class (i.e., two to six, and flat), and seed size (i.e., 8 to 58 g per 100-seed). Cultivars used in the present work are a subset ( n = 277) of the SNAP panel that also was tested for tolerance to sulfentrazone (Saballos et al 2022).…”

Section: Methodsmentioning

confidence: 99%

“…diversity panel ( n > 120) confirmed that several herbicides used in grain-type soybean were just as safe on edamame grown throughout the United States, facilitating herbicide registrations on the minor crop (Williams and Nelson 2014). Moreover, evaluating herbicide tolerance in a diversity panel with associated genomic data may identify genomic regions related to herbicide tolerance, which could be useful in crop improvement (Saballos et al 2022). Therefore, the objective of this research was to quantify the extent to which pyroxasulfone tolerance exists in a diverse snap bean panel.…”

Section: Introductionmentioning

confidence: 99%

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Snap bean response to pyroxasulfone in a diversity panel

2023

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If available for use on snap bean, pyroxasulfone would provide valuable preemergence control of troublesome weed species that currently contaminate the crop post-harvest. The extent to which snap bean tolerates pyroxasulfone is poorly documented. The objective of this research was to quantify the extent to which pyroxasulfone tolerance exists in a large collection of snap bean cultivars. A snap bean diversity panel of 277 entries was screened for tolerance to sulfentrazone at a rate of 420 g ai ha-1 in a field trial in 2019 and 2020 near Urbana, IL. Snap bean cultivars exhibited variation in tolerance to pyroxasulfone. While a handful of cultivars were tolerant across variable environments, most cultivars were sensitive in the year that had 30% more water supply (rainfall plus sprinkler irrigation) within three weeks of planting. Low estimates of broad-sense heritability reflect a large influence of the environment on seedling emergence and growth. With a few exceptions, currently the margin of crop safety across diverse germplasm is insufficient for registration of pyroxasulfone on snap bean.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Snap bean response to pyroxasulfone in a diversity panel

2023

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“…SNPs with 40% or more missing values were eliminated. The methods of alignment and imputation are otherwise identical to those described by Saballos et al (2022) [ 25 ]. Because the SBDP is a subpopulation of the SnAP, a subset of the GBS data extracted from the original resource (SnAP) was used for all association studies using the SBDP.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean

Arkwazee

Wallace

Hart³

et al. 2022

Genes

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White mold can result in snap bean yield losses of 90 to 100% when field conditions favor the pathogen. A genome-wide association study (GWAS) was conducted to detect loci significantly associated with white mold resistance in a panel of snap bean (Phaseolus vulgaris L.) cultivars. Two populations of snap bean were used in this study. The first population was the BeanCAP (Coordinated Agriculture Project) Snap Bean Diversity Panel (SBDP) (n = 136), and the second population was the Snap Bean Association Panel (SnAP) (n = 378). SBDP was evaluated for white mold reaction in the field in 2012 and 2013, and SnAP was screened in a greenhouse only using the seedling straw test in 2016. Two reference genomes representing the Andean and Middle American centers of domestication were utilized to align the genotyping-by-sequencing (GBS) data. A GWAS was performed using FarmCPU with one principal component after comparing five models. Thirty-four single-nucleotide polymorphisms (SNPs) significantly associated with white mold resistance were detected. Eleven significant SNPs were identified by the seedling straw test, and 23 significant SNPs were identified by field data. Fifteen SNPs were identified within a 100 kb window containing pentatricopeptide repeat (PPR)-encoding genes, and eleven were close to leucine-rich repeat (LRR)-encoding genes, suggesting that these two classes are of outsized importance for snap bean resistance to white mold.

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“…The panel includes accessions with determinate bush (CIAT classification type I) growth habits, but a few were half-runners (type III), and another subset had an indeterminate (type IV) climbing growth habit. The accessions represent different market classes, such as Blue Lake, European small sieves, Refugee and Romano beans, and yellow (wax) beans of American or European origin [23].…”

Section: Plant Materialsmentioning

confidence: 99%

“…HapMap files of the SnAP aligned to the two reference genomes were produced by Alvaro Soler Garzon of the Miklas Lab, USDA-ARS, Prosser, WA. Alignment and imputation methods are described by Saballos et al [23]. After 0.01 minor allele frequency (MAF) filtering, 25,472 SNPs were generated with G19833 (v2.1), and 34,442 SNPs were generated with 5-593 (v1.1) reference genomes.…”

Section: Data Acquisitionmentioning

confidence: 99%

Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color

Celebioglu,

Hart,

Porch

et al. 2023

Genes

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Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

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Multiple Genomic Regions Govern Tolerance to Sulfentrazone in Snap Bean (Phaseolus Vulgaris L.)

Cited by 9 publications

References 85 publications

Snap bean response to pyroxasulfone in a diversity panel

Snap bean response to pyroxasulfone in a diversity panel

Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean

Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color

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