黄瓜杂交种品种鉴定SNP标记的初步分析研究
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摘要
将11个华北型黄瓜杂交种F1代进行基于Illumina HiSeq X10平台的全基因组重测序,测序深度10X。样本基因组DNA采用单株混合提取和混池二代测序。对测序原始数据经过数据质控获得有效读长基础上进行了二次筛选。最终在684 891个SNP变异信息中筛选出381个变异位点,其中的180个为位于核染色体组上的变异(166个SNPs,14个InDels变异)。使用Minimal marker对SNP位点进行三位点组合选择,挑选出可区分参试品种的25个非重复SNP位点,35种三位点组合,涉及基因组1～6号染色体。最后选择10个在5’和3’侧翼序列50bp内无过滤过变异的候选位点,用于PCR扩增验证。得到7个高质量SNP,包括:Chr1_14433374,Chr3_24329128,Chr3_32823086,Chr3_33307511,Chr5_1548305,Chr5_6143567和Chr5_26188907。采用KASP基因分型技术验证,这7个位点的分型结果与二代测序结果吻合。
引文
[1]SANWEN H,RUIQIANG L,etc.The genome of the cucumber,Cucumis sativus L.[J].Nature genetics,2009,41(12):1275-1281.
[2]葛凤伟,张海英,陈青君.黄瓜SSR反应体系的建立[J].华北农学报,2004,19(2):5-9.
[3]The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.[DB/OL].http://hannonlab.cshl.edu/fastx_toolkit/.
[4]LI H,DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler Transform[J].Bioinformatics,2009(25):1754-1760.
[5]ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/075/GCF_000004075.2_ASM407v2/GCF_000004075.2_ASM407v2_genomic.fna.gz.[DB/OL].
[6]National Center for Biotechnology Information.[DB/OL].https://www.ncbi.nlm.nih.gov/genome/?term=Cucumber.
[7]SAM(Sequence Alignment/Map)format is a generic format for storing large nucleotide sequence alignments.[DB/OL].http://samtools.sourceforge.net/index.shtml.
[8]Genome Analysis Toolkit Variant Discovery in HighThroughput Sequencing Data.[DB/OL].https://software.broadinstitute.org/gatk.
[9]Primer 3 Plus,pick primers from a DNA sequence.[DB/OL].http://www.primer3plus.com.
[2]葛凤伟,张海英,陈青君.黄瓜SSR反应体系的建立[J].华北农学报,2004,19(2):5-9.
[3]The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.[DB/OL].http://hannonlab.cshl.edu/fastx_toolkit/.
[4]LI H,DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler Transform[J].Bioinformatics,2009(25):1754-1760.
[5]ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/075/GCF_000004075.2_ASM407v2/GCF_000004075.2_ASM407v2_genomic.fna.gz.[DB/OL].
[6]National Center for Biotechnology Information.[DB/OL].https://www.ncbi.nlm.nih.gov/genome/?term=Cucumber.
[7]SAM(Sequence Alignment/Map)format is a generic format for storing large nucleotide sequence alignments.[DB/OL].http://samtools.sourceforge.net/index.shtml.
[8]Genome Analysis Toolkit Variant Discovery in HighThroughput Sequencing Data.[DB/OL].https://software.broadinstitute.org/gatk.
[9]Primer 3 Plus,pick primers from a DNA sequence.[DB/OL].http://www.primer3plus.com.