Fine mapping of qhir1 influencing in vivo haploid induction in maize

Production of haploids by the in vivo haploid induction method has now become routine for generating new inbred lines in maize. In previous studies, a major quantitative trait locus (QTL) (qhir1) located in bin 1.04 was detected, explaining up to 66 % of the genotypic variance for haploid induction rate (HIR). Our objectives were to (1) fine-map qhir1 and (2) identify closely linked markers useful for marker-assisted breeding of new inducers. For this purpose, we screened a mapping population of 14,375 F-2 plants produced from a cross between haploid inducer UH400 and non-inducer line 1680 to identify recombinants. Based on sequence information from the B73 reference genome, markers polymorphic between the two parents were developed to conduct fine mapping with these recombinants. A progeny test mapping strategy was applied to accurately determine the HIR of the 14 recombinants identified. Furthermore, F-3 progeny of recombinant F-2 plants were genotyped and in parallel evaluated for HIR. We corroborated earlier studies in that qhir1 has both a significantly positive effect on HIR but also a strong selective disadvantage, as indicated by significant segregation distortion. Altogether, we were able to narrow down the qhir1 locus to a 243 kb region flanked by markers X291 and X263.