Identification and characterization of presence/absence variation in maize genotype M017

Presence/absence variation (PAV), a major class of genome structure variation, is pervasive in the maize genome. PAVs present in the B73 but absent from the Mo17 genome have been reported in previous studies. Here, the next-generation sequencing was used to identify the PAVs present in Mo17 but absent from B73. A total of 119 PAVs were identified, of which 57 were validated by PCR. Using the intermated B73 x Mo17 segregating population, 57 validated PAVs were mapped into the genetic map. These PAVs were dispersed on the ten chromosomes. Also, several large genetic regions of PAVs were identified. This suggested the possibility that large genetic fragments in Mo17 were absent from the B73 genome. Several PAVs were also found to be related to disease resistance suggesting that presence/absence variations in the genome may play a role in disease resistances in maize. In addition, the majority of the genes within PAV were transcriptionally silenced or expressed at low levels in some tissues, especially for PAVs related to disease resistance. The results of this study not only provided the identities of additional PAVs in maize but also helped understand the functional role of PAVs in this agriculturally important crop.