Discovery for Maize Function Insertion/Deletion(InDel) Polymorphic Marker and Its Implication in Purity Identification of Maize Hybrid Seeds

InDels,as an important source of genetic markers,have been extensively used in linkage map construction and diversity research.Here,we described the discovery of maize InDel markers across the whole genome with bioinformatics and a test of the usefulness of InDel markers in purity identification of maize hybrid seeds.Based on B73 whole genome sequences(version 2) and Mo17 assembled contigs,in silico,more than 40 000 InDels were detected and near 11 400 loci with InDel could be used for specific primer designing.One hundred and forty-three novel polymorphic function InDel markers located close to(1 kb) or in the expressed genes were validated between B73 and Mo17,subsequently,were applied in purity identification of maize hybrid seeds.Thirteen co-dominant InDel markers exhibited the easily visible length polymorphism(50 bp) in respective parents of six hybrids.In combination with a rapid individual kernel DNA extraction,InDels found to be polymorphic between parents were scored in more than 1 400 F1 samples.The results showed that the InDel markers,as an accurate and cost-efficient means,could be suitable for rapid purity identification ofmaize hybrid seeds,although challenges remained.