Single cell sequencing technology emerged recently,enabling high-throughput analyses of the cell lineage trees of higher organisms.In plants,single-cell sequencing is still challenging because the cell wall hinders the isolation and lysis of the nuclear contents.We have developed a simple method to isolate and sequence the whole genome of each of the four microspores from a plant tetrad which was used to study the meiotic recombination mechanism of maize male gametes (Li et al,2015).Recently,we made further efforts to improve the method for isolating the three nuclei from one mature pollen grain of maize for whole-genome sequencing.This technique was used to study the haploid induction mechanism in maize.Production of maternal haploids via intra-specific genotypes as the haploid inducer is routine and highly efficient in maize.However,the underlying mechanism of haploid induction (HI) is unclear.We found that the aneuploidy caused by chromosome fragmentation occurring post meiosis in the gametophyte may affect embryogenesis and be the underlying cause of HI.