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`

M. Erfatpour and K. P. Pauls Theoretical and Applied Genetics June 2020, vol. 133:1977–1994

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 ‘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.

See: https://link.springer.com/article/10.1007/s00122-020-03571-7

Phvul.010G130600 SNP-based marker and the marker screen of regular, slow (SD) and non-darkening (ND) recombinant inbred lines (RIL), breeding lines and varieties of bean. a PCR binding sites for PCR primers (Table 3) in regular darkening (RD) and non-darkening (ND) genotypes. The SNP is identified with a red box. b PCRs with genomic DNA from a ND genotype like ‘Wit-rood boontje’ did not produce an amplicon. PCRs with genomic DNA from a slow darkening (SD) parent 1533-15 produced a single DNA fragment with a size of 254 bp. c RILs88-101 are recombinant inbred lines from a ND ‘Wit-rood-boontje’ x SD 1533-15 cross. d Burdett, Othello, Windbreaker, Sequoia, PT11-9, Kodiak, Kimberly, La Paz, 16-NDP1, UI 114, and ME105 are Pinto bean varieties and lines. Etna, CBX 1148, C15HR009, Red Rider, OAC Racer, C13HR185, and 8184 (94CTCOOP-8184) are cranberry bean varieties and lines. Labels that are highlighted red, yellow, and blue represent seeds with (regular darkening) RD, SD, and ND phenotypes, respectively (color figure online).