Common bean PvIND locus bisulfite sequencing reads

Fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris L.), the principal global grain legume staple, two main production categories are distinguished by fiber deposition in pods: a) dry beans, with fibrous, stringy pods; and b) stringless snap/green beans, with reduced fiber deposition, which frequently revert to the ancestral stringy state. Here, we identify genetic and developmental patterns associated with pod fiber deposition.

Transcriptional, anatomical, epigenetic, and genetic regulation of pod strings were explored through RNA-seq, RT-qPCR, fluorescence microscopy, bisulfite sequencing, and whole-genome sequencing.

Overexpression of the INDEHISCENT (“PvIND”) ortholog was observed in stringless types compared to isogenic stringy lines, associated with overspecification of weak dehiscence zone cells throughout the pod vascular sheath. No differences in DNA methylation were correlated with this phenotype. Non-stringy varieties showed a tandemly direct duplicated PvIND and a Ty1-copia retrotransposon inserted between the two repeats. These sequence features are lost during pod reversion and are predictive of pod phenotype in diverse materials, supporting their role in PvIND overexpression and reversible string phenotype.

Our results give insight into reversible gain-of-function mutations and possible genetic solutions to the reversion problem, of considerable economic value for green bean production.

Methods
Genomic DNA was extracted using a modified CTAB protocol. Bisulfite treatment was conducted with the EZ DNA Methylation-Lightning Kit. Primers were designed with Zymo Bisulfite Primer Seeker 12S, PCR products were checked on a gel, cleaned with a QIAquick PCR Purification Kit, and genotyped by Sanger sequencing at the UC Davis DNA sequencing facility.