A R2R3-MYB gene-based marker for the non-darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from ‘Wit-rood boontje’

Abstract

Key message The 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. Abstract 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 'Witrood 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.Communicated by Albrecht E. Melchinger. Electronic supplementary materialThe online version of this article (https ://doi.org/10.1007/s0012 2-020-03571 -7) contains supplementary material, which is available to authorized users.

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

“…This phenomenon has been most studied in pinto and cranberry beans but can be observed in other market classes. Lighter seed coats are perceived by consumers as indications of freshness or quality, so seeds exhibiting postharvest darkening have reduced market value ( Nasar-Abbas et al, 2009 ; Erfatpour and Pauls, 2020 ). The J locus was previously identified on Pv10, and genotypes that are homozygous recessive at J do not exhibit postharvest darkening ( Bassett, 2007 ; Elsadr et al, 2011 ; Erfatpour et al, 2018 ).…”

Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

“…MBW complex has been studied including R2R3-MYB, bHLH, and WD40 complex [ 59 ]. In Phaseolus vulgaris (Common bean), an R2R3 MYB was associated with seed coat darkening and involved in PAs oxidation and accumulation in the seed coat [ 79 ]. LACCASE family in Arabidopsis was involved in oxidative lignin polymerization and it was downstream of MYB46 and MYB58 [ 54 ].…”

The Effect of Processing on Bioactive Compounds and Nutritional Qualities of Pulses in Meeting the Sustainable Development Goal 2

“…Bassett et al (2002) showed that the J gene was the genetic locus initiating the postharvest darkening in common beans while those with the recessive allele jj had no problems of postharvest darkening. On this note, Erfatpour and Pauls (2020) developed an R2R3-MYB gene-based marker obtained from "Wit-rood boontje" to aid bean breeders in the selection of non-darkening dry beans carrying the recessive jj genes in early generations as opposed to waiting to screen the phenotypic segregation. R2R3-MYB genes are known to regulate biosynthesis of proanthocyanidin (Erfatpour and Pauls, 2020).…”

“…On this note, Erfatpour and Pauls (2020) developed an R2R3-MYB gene-based marker obtained from "Wit-rood boontje" to aid bean breeders in the selection of non-darkening dry beans carrying the recessive jj genes in early generations as opposed to waiting to screen the phenotypic segregation. R2R3-MYB genes are known to regulate biosynthesis of proanthocyanidin (Erfatpour and Pauls, 2020).…”