Identifying QTL and candidate genes for prolificacy in maize

Abstract

In maize, prolificacy, the number of ears per plant, is a trait of interest to maize breeders for breeding high grain-yielding cultivars or specialty corn, as well as being a model trait for decoding the molecular mechanism of maize evolution. Its genetic basis remains largely unknown. We identified a stable quantitative trait locus, qEN7, for ear number on chromosome 7 in both F2 and F2:3 populations derived from a single cross between the nonprolific inbred line Mo17 and the prolific inbred line LAN404 derived from the landrace PI217404. qEN7 explained 10.7%–11.9% of phenotypic variation, and the LAN404 allele at this locus was associated with an increase of around one ear per plant. qEN7 was confined by fine-mapping to a 0.56-Mb region containing eight annotated genes. Analysis of selection, gene expression patterns in various maize tissues, and sequence polymorphisms between the two parental lines suggested that Zm00001d020683, which encodes a putative INDETERMINATE DOMAIN (IDD) transcription factor, is the most likely candidate gene underlying qEN7. Zm00001d020683 is expressed mainly in the vegetative meristem, immature ears, and internodes and has undergone selection during maize improvement. The identification of qEN7 and the prediction of its candidate gene sheds some light on the evolution of maize ear number and provides a novel resource for breeding of multi-ear maize cultivars.