Genomic and Genetic Insights into Mendel’s Pea Genes

Abstract

ABSTRACTPea,Pisum sativum, is an excellent model system through which Gregor Mendel established the foundational principles of inheritance. Surprisingly, till today, the molecular nature of the genetic differences underlying the seven pairs of contrasting traits that Mendel studied in detail remains partially understood. Here, we present a genomic and phenotypic variation map, coupled with haplotype-phenotype association analyses across a wide range of traits in a globalPisumdiversity panel. We focus on a genomics-enabled genetic dissection of each of the seven traits Mendel studied, revealing many previously undescribed alleles for the four characterized genes,R,Le,IandA, and elucidating the gene identities and mutations for the remaining three uncharacterized traits. Notably, we identify: (1) a ca. 100kb deletion upstream of theChlorophyll synthase(ChlG) gene, which generates aberrant transcripts and confers the yellow pod phenotype ofgpmutants; (2) an in-frame premature stop codon mutation in a Dodeca-CLE41/44 signalling peptide which explains the parchmentless mutant phenotype corresponding top; and (3) a 5bp in-frame deletion in aCIK-likereceptor kinase gene corresponding to the fasciated stem phenotypefa, which Mendel described in terms of flower position, and we postulate the existence of aModifier of fa(Mfa) locus that masks this meristem defect. Mendel noted the pleiotropy of theamutation, including inhibition of axil ring anthocyanin pigmentation, a trait we found to be controlled by allelic variants of the geneDwithin anR2R3-MYBgene cluster. Furthermore, we characterize and validate natural variation of a quantitative genetic locus governing both pod width and seed weight, characters that Mendel deemed were not sufficiently demarcated for his analyses. This study establishes a cornerstone for fundamental research, education in biology and genetics, and pea breeding practices.