Fine mapping of a kernel length-related gene with potential value for maize breeding

Key message A key candidate gene for maize kernel length was fine mapped to an interval of 942 kb; the locus significantly increases kernel length (KL) and hundred-kernel weight (HKW). Kernel size is a major determinant of yield in cereals. Kernel length, one of the determining factors of kernel size, is a target trait for both domestication and artificial breeding. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for kernel length in maize. In this project, a novel major QTL, named qKL9 , controlling maize kernel length was identified. We verified the authenticity and stability of qKL9 via BC 2 F 2 and BC 3 F 1 populations, respectively, and ultimately mapped qKL9 to an ~ 942-kb genomic interval by testing the progenies of recombination events derived from BC 3 F 2 and BC 4 F 2 populations in multiple environments. Additionally, one new line (Mc qKL9−A ) containing the ~ 942-kb segment was screened from the BC 4 F 2 population. Combining transcriptome analysis between Mc qKL9−A and Mc at 6, 9 and 14 days after pollination and candidate regional association mapping, Zm00001d046723 was preliminarily identified as the key candidate gene for qKL9 . Importantly, the replacement in the Mc line of the Mc’s alleles by the V671’s alleles in the qKL9 region improved the performances of single-cross hybrids obtained with elite lines, illustrating the potential value of this QTL for the genetic improvement in maize kernel-related traits. These findings facilitate molecular breeding for kernel size and cloning of the gene underlying qKL9 , shedding light on the genetic basis of kernel size in maize.