Zea mays subsp. mays Genome sequencing

In vivo haploid induction (HI) triggered by pollination with special intra-specific genotypes, called inducers, is unique to Zea mays L. within the plant kingdom and has revolutionized maize breeding during the last decade. However, the molecular mechanisms underlying HI in maize are still unclear. To investigate the genetic basis of HI, we developed a new approach for genome-wide association studies (GWAS), termed conditional haplotype extension (CHE) test, to cope with the problem of almost perfect confounding between population structure and trait expression encountered in this study. We identified a 3.97 Mb genomic segment, originating from the original ancestor (Stock 6) of all inducers, which is required for HI in maize. To further locate candidate genes for HI in the detected region, we searched for mutated coding sequences by comparing resequencing data of inducer CAU5 with sequences of 14 non-inducers important in global maize breeding.