krn1, a major quantitative trait locus for kernel row number in maize

Kernel row number is a fundamental component of maize (Zea mays) yield and an important target for maize breeding. The revolutionary transition from the two-rowed teosinte to maize with increased kernel row numbers dramatically enhanced yields during domestication. Kernel row number is controlled by many quantitative trait loci (QTLs), however most genes responsible for these QTLs remain uncharacterised and the molecular genetic mechanisms are unknown. Here, we combined map-based cloning and association mapping to identify a major QTL for kernel row number, krn1, which is likely to correspond to an existing gene (ids1/Ts6) encoding an AP2 domain protein homologous to the product of the wheat key domestication gene Q. The increased expression of ids1/Ts6 in two maize mutants increased spikelet pair meristem numbers and then enhanced kernel row numbers. Nucleotide diversity analysis further revealed that ids1/Ts6 and Q were under strong parallel selection in maize and wheat that increased their yields during domestication or improvement. RNA-seq revealed that ids1/Ts6 is involved in multiple pathways regulating spikelet pair meristem development, involving several key genes such as fea3, fea4 and ra3. The cloning of the krn1 gene will pave a new way to efficiently improve maize yield in the near future.