Unveiling the characteristics of popcorn by genome re-sequencing and integrating the ESTs and proteome data

Popcorn (Zea mays everta Sturt.) can explode popcorn flake for snack food when heated. In this study, a popcorn inbred line, N04 with small grain weight, and a dent corn Dan232 with large grain weight were re-sequenced and compared with the B73 reference genome, respectively. The genome variation information between N04 and Dan232 was obtained, including 0.95 million SNPS, 0.44 million INS and 0.49 million DEL. Combining the genome of Mexican landrace Palomero and dent maize inbred lines Zheng58, Chang7-2 and Mo17, 10,837 genes with sequence variation were identified between popcorn and dent corn. There were 308 unique genes found in the popcorn genome, which were mainly involved in metabolic processes, phosphorus metabolism, protein modification and other biological processes. A total of 318 differential genes were obtained by analyzing proteome and genomic data of kernel development of N04 and Dan232. And only 4 differential expression genes were found among ESTs, genome and proteome data simultaneously, which encode auxin-binding protein, amylase, pyruvate phosphate kinase and glucose phosphate adenylyltransferase, respectively. These results uncover the genome characteristics of popcorn, which will provide important information for studying the molecular mechanism of popping characteristics.