| As a special germplasm resource,popcorn is characterized with hardness of kernel,quick dehydration and precocity which are focused by modern breeding.Through the second generation sequencing technology,this study did genome sequencing for two maize inbreds N04 and Dan232,popcorn inbred N04 with small grain and the dent corn inbred Dan 232 with large grains.The data-analyzing pipeline for genome sequencing data included data quality assessment,comparison to the reference genome,acquiring variation information of SNP and InDel,annotation of variation,extracting the variation gene and gene clustering.Some perl programs were made to achieve personalized management when software was unavailable.Large quantities important differences reveled analysis through this laid reliable data basis for the development of molecular marking and key gene mining.The main results were as follows:1.Sequencing data for the popcorn inbred line N04 was 46 Gb,.The sequencing depth was 19.2X;dent corn inbred lines Dan 232 sequencing data sequencing depth was 28.8 Gb.Total data of the two inbreds was 115 Gb,the average sequencing depth was 25 X.2.When compared with B73 reference genome data,the genome date for the popcorn inbred lines N04 received 0.99 million reads,about 41.32 Gb,with coverage of 89.82%.The data analysis obtained4.5 million SNPs,which included 3.61 million genes,with 0.92 million located in the intron,0.18 million located in coding regions causing amino acid change;0.3 million and 0.42 million InDel with located in between genes,0.15 on the intron and 0.02 million on the coding region.3.Compared with B73 reference genome data,genome data for the dent corn inbred lines Dan232 received 1.48 million reads,about 62.41 Gb,with coverage of 90.54%.The data analysis obtained 5million SNP,of which 4.01 million genes,0.98 located in the intron,0.190 coding regions causing amino acid change;and 0.51 InDel at the same time,with 0.36 located in between genes,0.17 on the intron,0.024 million on the coding region.4.Through the conjoint analysis of different loci from the comparison with B73,the variation information of popcorn inbred lines N04 and dent corn inbred Dan232 was achieved,including 0.95 million SNPs,0.44 million Insertion,0.49 million Deletion.These mutation sites had the advantages of high accuracy and high density,homogeneous distribution,thus could be used as molecular markers.The same two inbreds were used to built near isogenic line and recombinant inbred lines in our precious research,from which 12 QTL for 100-grain weight and 10 reveled explosive QTL for popping expansion were located.Through bioinformatics methods,variation information analysis reached that 30000 SNP and 4000 InDel would cause non-synonymous mutation in the QTL intervals of 100-grain weight,and 5980 relative genes were obtained;18000 SNPs and 2300 InDels would cause non-synonymous mutation in the QTL intervals for popping expansion,and 3162 relative genes;This results could provid a large amount of reliable information for fine QTL mapping in further research.5.Combining with the genome information submitted online and downloading Mexico burst Pomreso corn and normal corn inbreds Zheng 58 and Chang 7-2,Mo17.Through bioinformatics analysis method,10837 difference genes were related between the popcorn germplasms and the dent corn inbreds.Among the 308 unique difference genes in popcorn.54 genes were found in cellular protein metabolism,36 genes were found in protein phosphorylation,and 126 genes were found in metabolism process.190 genes might be used to revel the popcorn specificity.Gene difference and specificity excavation of popcorn and dent corn inbred lines had important reference value for further study on the function of these genes,selection and breeding implementation of assisted molecular marker.6.Based on the EST and protein data of the two inbred lines in our previous research,136 differential genes from the EST data and 1397 differential genes from the protein data were obtained.After analyzing the data,the study found that 25 differential genes were shared by distinct protein and EST;318 differential genes were shared by distinct protein,and the difference between the popcorn and dent corn germplasms;4 differential genes were shared by all of them. |
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