Candidate gene (PHA-E) and phytohemagglutinin content in snap bean (Phaseolus vulgaris L.): an association study

Abstract

Snap bean (Phaseolus vulgaris L.) is low in fat and high in nutrients; however, it also contains toxigenic factors such as phytohemagglutinin (PHA), which is poisonous to humans. Here, we aimed to determine the distribution of PHA in natural populations of snap bean by analyzing a candidate gene (PHA-E) related to PHA content. Functional genome-wide single nucleotide polymorphisms (SNPs) were then scanned to identify SNPs related to PHA content. A total of 150 snap bean varieties were examined. PHA content and PHA-E expression levels were determined 10, 14, 18, 22, 26 and 30 days after anthesis. Then, association analyses were carried out to identify causal SNPs in PHA-E via genotyping and association tests. PHA-E expression was positively-correlated with PHA content. Among 59 detected SNPs, the ratio of synonymous to nonsynonymous changes was 1:8. P190 was identified as a novel SNP associated with PHA content. The allele carrying the GG genotype at P190 was detected in 130 varieties, of which 86 had an above-average PHA content, while the allele carrying the AA genotype at P190 was detected in 20 varieties, of which 17 (85%) had a low PHA content. Analyses of the PHA content and gene expression in fresh pods of 150 snap bean cultivars revealed population-level distribution and genetic variation, providing a unique measure for screening of low-level or nontoxic cultivars and aiding future breeding of new cultivars. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1985613.