Abstract
Key messageThe gene Phvul.010G130600 which codes for a MYB was shown to be tightly associated with seed coat darkening in Phaseolus vulgaris and a single nucleotide deletion in the allele in Wit-rood disrupts a transcription activation region that likely prevents its functioning in this non-darkening genotype.The beige and white background colors of the seed coats of conventional pinto and cranberry beans turn brown through a process known as postharvest darkening (PHD). Seed coat PHD is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. The J gene is an uncharacterized classical genetic locus known to be responsible for PHD in common bean (P. vulgaris) and individuals that are homozygous for its recessive allele have a non-darkening (ND) seed coat phenotype. A previous study identified a major colorimetrically determined QTL for seed coat color on chromosome 10 that was associated with the ND trait. The objectives of this study were to identify a gene associated with seed coat postharvest darkening in common bean and understand its function in promoting seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL associated with the ND trait revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in non-darkening recombinant inbred lines derived from crosses between ND ‘Wit-rood boontje’ and a regular darkening pinto genotype. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) with a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. The deletion in the ‘Wit-rood boontje’ allele of Phvul.010G130600 likely causes a translational frame shift that disrupts the function of a transcriptional activation domain contained in the C-terminus of the R2R3-MYB. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans.
Highlights
Common bean (Phaseolus vulgaris L.) is the most important food legume crop
The current results suggest that the gene Phvul.010G130600, which encodes a R2R3-MYB transcription factor located on chromosome Pv10, close to the sequence-tagged site (STS) marker OL4S500 which was previously found to be linked to J (McClean et al 2002) and is located in the major QTL associated with the ND trait (Erfatpour et al 2018), is responsible for the phenotypes conditioned by the J gene
The after-darkening phenotype and its association with PA levels is consistent with the finding that the Phvul010G130600 gene encodes a protein with high sequence identity to the R2R3-MYB transcription factor encoded by MtPAR, which plays a significant role in PA biosynthesis in Medicago seed coat tissue (Pang et al 2009; Verdier et al 2012; Li et al 2016)
Summary
Common bean (Phaseolus vulgaris L.) is the most important food legume crop. It is grown worldwide for its nutrient-rich green pods or mature seeds (shell beans and dry beans). Dry beans are rich sources of vitamins and minerals, as well as Communicated by Albrecht E. Flavonoids represent one of the largest classes of plant phenolic compounds. More than 9000 individual compounds, characterized by a 15-carbon skeleton, arranged in two aromatic rings connected by a three-carbon bridge (C6–C3–C6) have been identified (Buer et al 2010). Flavonoids are further divided by the nature of the C3 element into major subclasses, including chalcones, flavones, flavonols, flavan 3-ols, isoflavonoids, anthocyanins, and proanthocyanidins (PAs) (Davies and Schwinn 2006)
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