Identification of a candidate gene underlying qKRN5b for kernel row number in Zea mays L.

key messageA quantitative trait locus for kernel row number, qKRN5, was dissected into two tightly linked loci, qKRN5a and qKRN5b. Fine mapping, comparative analysis of nucleotide sequences and gene expression established the endonuclease/exonuclease/phosphatase family protein-encoding gene Zm00001d013603 as a causal gene of qKRN5b. Maize grain yield is determined by agronomically important traits that are controlled by interactions among and between genes and environmental factors. Considerable efforts have been made to identify major quantitative trait loci (QTLs) for yield-related traits; however, few were previously isolated and characterized in maize. In this study, we divided a QTL for kernel row number (KRN), qKRN5, into two tightly linked loci, qKRN5a and qKRN5b, using advanced backcross populations derived from near-isogenic lines. KRN was greater in individuals that were homozygous for the NX531 allele, which showed coupling-phase linkage. The major QTL qKRN5b had an additive effect of approximately one kernel row. Furthermore, fine mapping narrowed qKRN5b within a 147.2-kb region. The upstream sequence Zm00001d013603 and its expression in the ear inflorescence showed obvious differences between qKRN5b near-isogenic lines. In situ hybridization located Zm00001d013603 on the primordia of the spikelet pair meristems and spikelet meristems, but not in the inflorescence meristem, which indicates a role in regulating the initiation of reproductive axillary meristems of ear inflorescences. Expression analysis and nucleotide sequence alignment revealed that Zm00001d013603, which encodes an endonuclease/exonuclease/phosphatase family protein that hydrolyzes phosphatidyl inositol diphosphates, is the causal gene of qKRN5b. These results provide insight into the genetic basis of KRN and have potential value for enhancing maize grain yield.