QTL mapping of post-processing color retention in two black bean populations

Bornowski, Nolan; Song, Qijian; Kelly, James D.

doi:10.1007/s00122-020-03656-3

Cited by 9 publications

(12 citation statements)

References 27 publications

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“…SL * 10.1, Sa * 10.1, and Sb * 10.1 overlapped with the J-locus associated with postharvest non-darkening (Erfatpour et al, 2018). SL * 8.1, SL * 10.1, and Sa * 10.1 overlapped with QTL for L * and a * of canned black beans identified by Bornowski et al (2020). Two seed coat lightness QTL fall within the ranges of known P. vulgaris color genes.…”

Section: Discussionmentioning

confidence: 90%

“…Following image collection, each image was cropped to center the petri dish and minimize background. To examine the relationship among color, cooking time, and sensory attributes, CIELAB values were obtained using a custom batch macro in ImageJ developed by Bornowski et al (2020) that applies a gamma correction of 0.5, excludes background pixels outside the petri dish, and measures each slice of the LAB stack. CIELAB uses three values to describe color: L ∗ for black (0) to white (100), a ∗ for green (−) to red (+), and b ∗ for blue (−) to yellow (+).…”

Section: Methodsmentioning

confidence: 99%

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QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population

et al. 2021

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Manteca yellow dry beans (Phaseolus vulgaris L.) have many quality traits that appeal to consumers, including fast cooking times, creamy texture, and sweet, buttery flavor. They are native to Chile and consumed in regions of South America and Africa but are largely unfamiliar to United States consumers. While cooking time, flavor, and texture have not been prioritized in United States dry bean breeding programs, genetic variability exists such that these traits could be addressed through breeding. In this study, a recombinant inbred line (RIL) population was developed from a cross between Ervilha (Manteca) and PI527538 (Njano), yellow dry beans with contrasting cooking time and sensory attributes. The population and parents were grown for 2 years in Michigan and evaluated for cooking time and sensory attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Cooking time ranged 19–34 min and exhibited high broad-sense heritability (0.68). Sensory attribute intensities also exhibited variation among RILs, although broad-sense heritability was low, with beany and total flavor exhibiting the highest (0.33 and 0.27). A linkage map of 870 single nucleotide polymorphisms markers across 11 chromosomes was developed for quantitative trait loci (QTL) mapping, which revealed QTL for water uptake (3), cooking time (6), sensory attribute intensities (28), color (13), seed-coat postharvest non-darkening (1), seed weight (5), and seed yield (2) identified from data across 2 years. Co-localization was identified for starchy, sweet, and seed-coat perception on Pv01; for total flavor, beany, earthy, starchy, sweet, bitter, seed-coat perception, cotyledon texture, and color on Pv03; water uptake and color on Pv04; total flavor, vegetative, sweet, and cotyledon texture on Pv07; cooking time, starchy, sweet, and color on Pv08; and water uptake, cooking time, total flavor, beany, starchy, bitter, seed-coat perception, cotyledon texture, color, and seed-coat postharvest non-darkening on Pv10. The QTL identified in this work, in particular CT8.2 and CT10.2, can be used to develop molecular markers to improve seed quality traits in future dry bean varieties. Considering yellow dry beans already excel in quality and convenience, they might be an ideal market class to signal a new focus on consumer-valued traits in the United States.

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Section: Discussionmentioning

confidence: 90%

Section: Methodsmentioning

confidence: 99%

QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population

et al. 2021

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“…All the significant single nucleotide polymorphisms in this study for L* were within the ranges of Sa*.10.1, Sb*.10.1, SL*.10.1, and ND.10.1 (Bassett et al., 2021). Chr10pos42388055 was within the range of L*10.1BB (I) (Bornowski et al., 2020). Chr10pos42388055 was within the range of a*10.1BB (I) (Bornowski et al., 2020)…”

Section: Resultsmentioning

confidence: 99%

“…Chr10pos42388055 was within the range of L*10.1BB (I) (Bornowski et al., 2020). Chr10pos42388055 was within the range of a*10.1BB (I) (Bornowski et al., 2020)…”

Section: Resultsmentioning

confidence: 99%

Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association

et al. 2021

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Common bean (Phaseolus vulgaris L.) is consumed worldwide, with strong regional preferences for seed appearance characteristics. Colors of the seed coat, hilum ring, and corona are all important, along with susceptibility to postharvest darkening, which decreases seed value. This study aimed to characterize a collection of 295 yellow bean genotypes for seed appearance and postharvest darkening, evaluate genotype × environment (G × E) effects and map those traits via genome‐wide association analysis. Yellow bean germplasm were grown for 2 yr in Michigan and Nebraska and seed were evaluated for L*a*b* color values, postharvest darkening, and hilum ring and corona colors. A model to exclude the hilum ring and corona of the seeds, black background, and light reflection was developed by using machine learning, allowing for targeted and efficient L*a*b* value extraction from the seed coat. The G × E effects were significant for the color values, and Michigan‐grown seeds were darker than Nebraska‐grown seeds. Single‐nucleotide polymorphisms (SNPs) were associated with L* and hilum ring color on Pv10 near the J gene involved in mature seed coat color and hilum ring color. A SNP on Pv07 associated with L*, a*, postharvest darkening, and hilum ring and corona colors was near the P gene, the ground factor gene for seed coat color expression. The machine‐learning‐aided model used to extract color values from the seed coat, the wide variability in seed morphology traits, and the associated SNPs provide tools for future breeding and research efforts to meet consumers’ expectations for bean seed appearance.

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“…Hence, in recent years, use of GWAS for mapping economically important QTLs in agricultural crops has increased and P. vulgaris is not behind. Many QTLs having economic importance in common bean have been mapped using a GWAS approach ( Moghaddam et al, 2016 ; Wu et al, 2017 ; Kelly and Bornowski, 2018 ; Kamfwa et al, 2019 ; Bisneta and Gonçalves-Vidigal, 2020 ; Bornowski et al, 2020 ; Gonçalves-Vidigal et al, 2020 ; Mungalu et al, 2020 ). In the present study, significant differences observed in NW Indian bean genotypes led to the identification of SNPs associated with the anthracnose resistance.…”

Section: Discussionmentioning

confidence: 99%

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

et al. 2020

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Common bean ( Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum . The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.

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QTL mapping of post-processing color retention in two black bean populations

Cited by 9 publications

References 27 publications

QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population

QTL Mapping of Seed Quality Traits Including Cooking Time, Flavor, and Texture in a Yellow Dry Bean (Phaseolus vulgaris L.) Population

Seed coat color genetics and genotype × environment effects in yellow beans via machine‐learning and genome‐wide association

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

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