牛场辣椒的全基因组SNP标记分析

Analysis of SNP Molecular Markers in the Whole Genome of Niuchang Pepper

本试验以牛场辣椒为研究对象,利用Illumina HiSeq 2000平台进行全基因组重测序,通过生物信息学软件分析测序质量、SNP在染色体和基因组上的分布规律和特征。结果表明,本研究获得了783349390条clean reads,基因组覆盖率98.23%,测序深度36.35×;12条染色体上共获得9141358个SNP,10号染色体上的纯合SNP最多,9号染色体上的纯合SNP最少;不同染色体上SNP密度分布不同;SNP分布在基因组上5个位置且数量不同,基因间(94.68%)>基因内(3.64%)>基因上游(0.9%)>基因下游(0.74%)>基因上游/下游;基因内SNP数量依次为内含子(281002)>外显子(51242)>剪接位点(288);外显子上有4种类型的SNP变异且数量不同,非同义突变(31265)>同义突变(19079)>终止子获得(710)>终止子缺失(188);发生转换的SNP数量是颠换的1.99倍。牛场辣椒SNP的出现频率为1个/366 bp,其中外显子上的51242个SNP具有开发成功能标记的潜力,外显子上SNP产生的710处终止子获得对基因功能研究具有重要意义。

The aims of this article were to analyse SNP markers in the whole genome of Niuchang pepper and provide powerful tool for gene function research and molecular breeding of pepper.The whole genome of Niuchang pepper was sequenced by illumina HiSeq 2000 paltform.The quality of sequencing and the distribution of SNP on chromosome and genome were analyzed by bioinformatics software.The results showed that 783349390 clean reads were obtained,with 98.23%genome coverage and 36.35×sequencing depth.9141358 SNPs were distributed on 12 chromosomes.The homozygous SNP was the most on chromosome 10 and the least on chromosome 9.The SNP density was different on each chromosome.SNPs were distributed in 5 positions of the genome.The number of SNPs followed the order of intergenic(94.68%)>intragenic(3.64%)>upstream of gene(0.9%)>downstream of gene(0.74%)>upstream/downstream of gene.For the intragenic region,the number of SNPs followed the order of intron(281002)>exon(51242)>splice site(288).There were four types of SNP mutations in exon,and the number was different:non synonymous mutation(31265)>synonymous mutation(19079)>terminator acquisition(710)>terminator deletion(188).The number of SNPs converted was 1.99 times that of transversion.The frequency of SNPs was 1/366 bp in exon,of which 51242 SNPs had the potential to develop functional markers.The 710 stop gain SNPs in exon were of great significance for the study of gene function.