Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean.

White mold can result in snap bean yield losses of 90 to 100% when field conditions favor the pathogen. A genome-wide association study (GWAS) was conducted to detect loci significantly associated with white mold resistance in a panel of snap bean (Phaseolus vulgaris L.) cultivars. Two populations of snap bean were used in this study. The first population was the BeanCAP (Coordinated Agriculture Project) Snap Bean Diversity Panel (SBDP) (n = 136), and the second population was the Snap Bean Association Panel (SnAP) (n = 378). SBDP was evaluated for white mold reaction in the field in 2012 and 2013, and SnAP was screened in a greenhouse only using the seedling straw test in 2016. Two reference genomes representing the Andean and Middle American centers of domestication were utilized to align the genotyping-by-sequencing (GBS) data. A GWAS was performed using FarmCPU with one principal component after comparing five models. Thirty-four single-nucleotide polymorphisms (SNPs) significantly associated with white mold resistance were detected. Eleven significant SNPs were identified by the seedling straw test, and 23 significant SNPs were identified by field data. Fifteen SNPs were identified within a 100 kb window containing pentatricopeptide repeat (PPR)-encoding genes, and eleven were close to leucine-rich repeat (LRR)-encoding genes, suggesting that these two classes are of outsized importance for snap bean resistance to white mold.

Bridging Sensory Evaluation and Consumer Research for Strategic Leafy Brassica (Brassica oleracea) Improvement.

Plant breeders working with new or underrepresented horticultural crops often have minimal sensory resources available to aid in the breeding and selection of new varieties. Kale (Brassica oleracea var. acephala) is a recently popularized horticultural crop in Western markets, however, plant breeding programs have little knowledge regarding the underlying sensory characteristics motivating this trend. We employed a multilayered, sensory-driven approach to understand the inherent consumer values, sensory attributes, and consumer preferences for kale types currently available on the market and novel genotypes from the Cornell AgriTech vegetable breeding program. Underlying consumer values related to storability, health and wellbeing, and sensory characteristics were identified through Qualitative Multivariate Analysis (QMA). A trained descriptive panel developed a lexicon of 44 sensory attributes common within kale germplasm, 21 of which exhibited significant differences among the 15 tested kale genotypes. Following a consumer test, four clusters of kale consumers were identified with agglomerative hierarchical clustering (AHC) and external preference mapping was used to connect consumer hedonic scores with descriptive data. Consumers demonstrated a preference for familiar kale types (that is, curly types), while new test hybrids scored favorably within flavor and appearance modalities. Preference mapping highlighted the utility of plant breeding in developing products to expand the existing sensory space. This work provides important resources for horticultural crop selection efforts, and it serves as a strategic model for breeding programs working with new or unfamiliar traits. PRACTICAL APPLICATION: Plant breeders are responsible for selecting and improving traits that influence consumer acceptance, including quality traits such as appearance and flavor. Understanding the relative importance of sensory characteristics and the variation of these sensory characteristics can help plant breeders prioritize these traits within their program. We have developed a standardized sensory lexicon for kale and related leafy Brassicas, identified variation for texture and flavor in our breeding program, and gained a better understanding of consumer preferences to guide future breeding efforts.

Effects of Growth Temperature and Postharvest Cooling on Anthocyanin Profiles in Juvenile and Mature Brassica oleracea.

The effects of growth temperatures on anthocyanin content and profile were tested on juvenile cabbage and kale plants. The effects of cold storage time were evaluated on both juvenile and mature plants. The anthocyanin content in juvenile plants ranged from 3.82 mg of cyanidin-3,5-diglucoside equivalent (Cy equiv)/g of dry matter (dm) at 25 °C to 10.00 mg of Cy equiv/g of dm at 16 °C, with up to 76% diacylated anthocyanins. Cold storage of juvenile plants decreased the total amount of anthocyanins but increased the diacylated anthocyanin content by 3-5%. In mature plants, cold storage reduced the total anthocyanin content from 22 to 12.23 mg/g after 5 weeks of storage in red cabbage, while the total anthocyanin content increased after 2 weeks of storage from 2.34 to 3.66 mg of Cy equiv/g of dm in kale without having any effect on acylation in either morphotype. The results obtained in this study will be useful for optimizing anthocyanin production.

Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean.

Since its emergence in 2001, an aphid-transmitted virus disease complex has caused substantial economic losses to snap bean (Phaseolus vulgaris L.) production and processing in the Great Lakes Region of the United States. The general ineffectiveness of chemical control measures for nonpersistently transmitted viruses established an urgent need for the development and deployment of cultivars with resistance to the component viruses. Our objectives were to further characterize the inheritance of resistance to Bean yellow mosaic virus (BYMV), which is conditioned by the By-2 allele, to adapt genotyping-by-sequencing (GBS) to common bean to discover and genotype genome-wide single nucleotide polymorphisms (SNPs) in a set of recombinant inbred lines (RILs) derived from an introgression program, and to enable and validate marker-assisted selection for By-2. We optimized ApeKI for GBS in common bean and retained 7530 high-quality SNPs that segregated in our introgression RILs. A case-control genome-wide association study (GWAS) was used to discover 44 GBS SNPs that were strongly associated with the resistance phenotype and which delimited a 974 kb physical interval on the distal portion of chromosome 2. Seven of these SNPs were converted to single-marker Kompetitive Allele-Specific Polymerase chain reaction (KASP) assays and were demonstrated to be tightly linked to BYMV resistance in an F2 population of 185 individuals. This research enables marker-assisted selection of By-2, provides enhanced resolution for fine mapping, and demonstrates the potential of GBS as a highly efficient, high-throughput genotyping platform for common bean breeding and genetics.

A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean.

Clover yellow vein virus (ClYVV) is capable of causing severe damage to common bean (Phaseolus vulgaris L.) production worldwide. The snap bean market class is particularly vulnerable because infection may lead to distortion and necrosis of the fresh green pods and rejection of the harvest. Three putatively independent recessive genes (cyv, desc, bc-3) have been reported to condition resistance to ClYVV; however, their allelic relationships have not been resolved. We identified, evaluated, and characterized the phenotypic and molecular genetic variation present in 21 informative common bean genotypes for resistance to ClYVV. Allelism testing phenotypes from multiple populations provided clear evidence that the three genes were a series of recessive alleles at the Bc-3 locus that condition unique potyvirus strain- and species-specific resistance spectra. Candidate gene analysis revealed complete association between the recessive resistance alleles and unique patterns of predicted amino acid substitutions in P. vulgaris eukaryotic translation initiation factor 4E (PveIF4E). This led to the discovery and characterization of two novel PveIF4E alleles associated with resistance to ClYVV, PveIF4E (3) , and PveIF4E (4) . We developed KASPar allele-specific SNP genotyping assays and demonstrated their ability to accurately detect and differentiate all of the PveIF4E haplotypes present in the germplasm, allelism testing, and in three separate segregating populations. The results contribute to an enhanced understanding and accessibility of the important potyvirus resistance conditioned by recessive alleles at Bc-3. The KASPar assays should be useful to further enable germplasm exploration, allelic discrimination, and marker-assisted introgression of bc-3 alleles in common bean.