Sequence characterization ofT,Bip, andPhbwdemonstrates the role of MYB-bHLH-WD40 complexes and temperature in common bean seed color pattern formation

Abstract

Seed colors and color patterns are critical for the survival of wild plants and the consumer appeal of crops. In common bean, a major global staple, these patterns are also critical for determining market classes, yet the genetic and environmental control of many pigmentation patterns remains unresolved. In this study, we genetically mapped variation for three important seed pattern loci, T, Bip, and phbw, which co-segregated completely with PvTTG1, PvMYC1, and PvTT8, respectively. Proteins encoded by these genes are predicted to work together in MYB-bHLH-WD40 (MBW) complexes, propagating flavonoid biosynthesis across the seed coat. Whole-genome sequencing of 37 diverse accessions identified putative mutations in each gene, including seven unique parallel mutations in T (PvTTG1) and a non-synonymous SNP in a conserved residue in bipana (PvMYC1). A 612 bp intron deletion in phbw (PvTT8) eliminated motifs conserved since the origins of the Papilionoidea and corresponded to a 20-fold reduction in transcript abundance. Mutations in MBW candidate genes for Z (PvTT2) and Sellatus (WDR) were also identified. In multi-location field trials with seven varieties with partial seed coat patterning, pigmented seed coat area was highly unstable and correlated with temperature, with up to 11-fold differences in pigmented area between the warmest and the coolest environments. In controlled growth chamber conditions, an increase of 4C was sufficient to cause pigmentation on an additional 21% of the seed coat area. Our results shed light on the fundamental activation of flavonoid biosynthesis in common bean and will be instrumental for maximizing consumer appeal in this nutritious staple crop.

An empirical evaluation of simulated gastrointestinal digestion platforms for use in plant breeding, using common bean (Phaseolus vulgarisL.) as a model

“…Adapted from Parker et al. 49 *UC Southwest Gold grown in San Gregorio in 2022 displayed a phenotype similar to UC Southwest Gold grown in Pescadero in 2019 (Figure S1).…”

“…Two recently released common bean varieties (UC Southwest Red and UC Southwest Gold 51,52 ) that tend to exhibit variability in the extent of pigmented seed coat area across field environments within California 49 were used herein. UC Southwest Gold and Red are common bean lines descended from a cross between ‘Zuni Gold’ and UCD 9634 pink bean (and specifically, are the F 7 bulk-harvested progeny of a single F 3 progenitor and an F 9 family from a single F 5 progenitor, respectively 51,52 ).…”

“…Whole beans were imaged (Figure S1) and analyzed to quantify the percent of pigmented seed area in ImageJ as described by Parker et al . 49 In summary, images were taken using a Brother (Nagoya, Japan) DCP-7065DN scanner and then processed using custom macros which were developed in ImageJ (source code available at https://github.com/TravisParker91/Seed-color). The raw data produced from this analysis included the percentage of pigmented area in the scan and the percentage of the image that was seed.…”

“…For example, in common bean, it has been shown that the environment can majorly affect both seed coat coloration/patterning and seed zinc and iron concentrations. 49,50 The main and interaction effects of genotype and environment on bioaccessible nutrient levels through simulated gastrointestinal digestion are yet to be characterized in several populations and germplasm pools of importance for common bean breeding and production.…”

“…For our first aim, we compared four digestive platforms: a shaking water bath, the PS, the HGS with dynamic gastric secretions and emptying (hereafter referenced as the ‘full HGS’ method), and a simplified HGS method. For our second aim, two recently released common bean varieties (UC Southwest Red and UC Southwest Gold 51,52 ) that exhibit variability in seed coat patterning across field environments within California 49 were analyzed using the PS and simplified HGS platforms. These sample types (representing genotype-environment combinations) were used to examine gastrointestinal outcomes from beans with varying pigmentation hue (perceived coloration; red vs. gold) and percentage of pigmented seed coat area.…”