Genome‐wide association study of variation in cooking time among common bean (<scp><i>Phaseolus vulgaris</i></scp> L.) accessions using Diversity Arrays Technology markers

Wahome, Samuel; Githiri, Mwangi; Kinyanjui, Peter K.; Toili, Mary Esther Muyoka; Angenon, Geert

doi:10.1002/leg3.184

Cited by 5 publications

(4 citation statements)

References 26 publications

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“…The genetic control of water uptake during soaking and cooking time has been investigated via diversity panels using genome‐wide association studies (GWAS) and biparental populations using quantitative trait locus (QTL) mapping (Bassett, Kamfwa, et al., 2021; Bassett, Katuuramu, et al., 2021; Berry et al., 2020; Cichy et al., 2015; Diaz et al., 2021; Garcia et al., 2011). These studies found genomic regions associated with water uptake and cooking time on every chromosome and identified candidate genes within these QTLs associated with cooking time (Berry et al., 2020; Martinez‐Manríque et al., 2011; Sadohara et al., 2022; Wahome et al., 2023). The candidate genes identified include enzymes that modify pectin solubility such as galacturan 1,4‐alpha‐galacturonidase, pectinesterase/pectin methylesterase, polygalacturonase, and pectate lyase, as well as enzymes that indirectly impact cell wall solubility such as peroxidase (synthesizes condensed tannins) and phytase (removes phytic acid).…”

Section: Introductionmentioning

confidence: 99%

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

Jeffery,

Mudukuti,

Buell

et al. 2023

The Plant Genome

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Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast‐cooking and slow‐cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant‐seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast‐ and slow‐cooking beans due to soaking. Candidate genes identified in the slow‐cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall‐strengthening enzymes in the slow‐cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.

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Section: Introductionmentioning

confidence: 99%

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

Jeffery,

Mudukuti,

Buell

et al. 2023

The Plant Genome

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“…Phvul.008G019500 (MEI2-like 4) associated with a SNP at 1,633,220 bp in G19833 was a candidate for L* pod interior and a* pod exterior, and previously was identified as a candidate for flower, pod, and seed development [35,63]. Phvul.010G032700 (Sec23/Sec24 protein transport family protein) at 4,552,800-4,753,654 bp was a candidate for a*, b*, and C* pod exterior in G19833 and it was previously identified as being involved in the photosynthetic process as a response to water deficiency [63][64][65] (Table S1).…”

Section: Candidate Genes From Other Studiesmentioning

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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“…In a previous study consisting of 206 common bean accessions of the Andean Diversity Panel (ADP), several significant single nucleotide polymorphisms (SNPs) associated with CT were reported on Pv02, Pv03 and Pv06, respectively (Cichy et al, 2015). Additional evaluation of 430 accessions of the ADP resulted in identification of additional significant SNPs on Pv03, Pv04, Pv06, Pv07, Pv08 and Pv11 (Bassett et al, 2020), and on Pv10 using 220 accessions freshly harvested and stored for 4 months at 35 C and 50% RH for accelerating aging (Wanjohi et al, 2023). In another study, 10 QTLs were identified for CT in TZ-27 (slow cooking) and TZ-37 (fast cooking) recombinant inbred line (RIL) population on chromosomes Pv01, Pv02, Pv03, Pv05, Pv06, Pv10 and Pv11, and three QTLs, namely, CT3.1 on Pv03, CT6.1 on Pv06 and CT11.2 on Pv11, were stable across multiple environments (Berry et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Assessment of genotypic variability and genome‐wide association analysis of cooking time and canning quality traits in common bean (Phaseolus vulgaris L.)

Kesiime,

Nkalubo,

Ochwo Ssemakula

et al. 2024

Plant Breeding

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Developing improved common bean varieties with short cooking time (CT) and good canning quality traits (CQTs) is very key for accelerating bean consumption among the urban and middle‐class population. The objective of this study was to assess the genotypic variability and identify single nucleotide polymorphism (SNP) markers associated with CT and CQTs in common bean. A total of 250 common bean accessions were evaluated under field conditions for two seasons using alpha lattice design with two replications. Three months post‐harvest, the dry bean grains were evaluated for CT and CQTs. Significant variation was observed among the 250 common bean accessions tested for both traits. CT ranged from 51 to 215 min, with 11 genotypes cooking in less than 60 min. The percentage total CQTs' score ranged from 41% to 84% with 31 genotypes scoring 76% and above. Forty‐seven significant GWAS signals were detected for CT on chromosomes Pv01, Pv04, Pv05 and Pv11 and CQTs on Pv01, Pv02, Pv03, Pv04, Pv05, Pv06, Pv07, Pv08, Pv10 and Pv11, respectively. Positional candidate genes including Phvul.005G161200 on chromosome Pv05, Phvul.007G2803001 and Phvul.007G280700 on chromosome Pv07 were associated with seed coat colour retention of the canned beans. Besides their usefulness in breeding research, the identified bean genotypes with shorter CT and good CQTs could enhance bean consumption and processing industries.

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Genome‐wide association study of variation in cooking time among common bean (Phaseolus vulgaris L.) accessions using Diversity Arrays Technology markers

Cited by 5 publications

References 26 publications

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

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

Assessment of genotypic variability and genome‐wide association analysis of cooking time and canning quality traits in common bean (Phaseolus vulgaris L.)

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