作物学报2018，Vol.44Issue(7)：956-965,10.DOI:10.3724/SP.J.1006.2018.00956
利用SNP芯片构建我国冬油菜参试品种DNA指纹图谱
Construction of DNA Fingerprinting for Brassica napus Varieties Based on SNP Chip
摘要
Abstract
Using the Brassica 60K Infinium SNP (single nucleotide polymorphism) array, a total of 52157 SNP markers were obtained by genotyping 33 annual test varieties in 2015–2016 and 187 varieties in 2016–2017. A total of 5374 high quality SNPs were retained after removing SNPs with AA or BB frequency = 0, main gene frequency ＜ 0.80, secondary gene frequency ＜ 0.05, sample loss rate ＞ 0.50, or SNPs that did not show clearly defined clusters. The mean PIC (polymorphism information content) value of selected 5374 markers was 0.27, SNPs with the PIC value ＞0.25 accounted for 55.94% of total number. Among 5374 SNPs, 5143 corresponded to the A1–A10 and C1–C9 linkage groups, and covered the rapeseed genome. We analyzed 5374 SNPs from 224 samples with softwares like PowerMarker and MEGA, etc. The technical error of the SNP array was 0.36%, when comparing two replicates of eight samples. It was close to the 0.1% technical error announced by Illumina. The NJ(Neighbor-joining) cluster analysis revealed that 97.86% of the tested varieties had a similarity coefficient of less than 93%, 87.88% renewed varieties had a similarity coefficient of greater than 95%, which could be further used as criteria for the varietal specificity and the annual consistency assessment. The 5374 SNP markers screened in this study were highly polymorphic and evenly distributed in the rapeseed genome, and could be used for future variety identification and the construction of DNA fingerprinting.关键词
甘蓝型油菜/DNA指纹图谱/SNP/基因芯片Key words
Brassica napus/DNA fingerprinting/SNP/gene chip引用本文复制引用
赵仁欣,易斌,李森业,郭瑞星,曾新华,文静,马朝芝,沈金雄,涂金星,傅廷栋..利用SNP芯片构建我国冬油菜参试品种DNA指纹图谱[J].作物学报,2018,44(7):956-965,10.基金项目
本研究由国家重点研发计划项目(2017YFD0102000)和中央高校基本科研业务费专项(2662016PY063)资助.This study was supported by the National Key Research and Development Program of China (2017YFD0102000) and the Fundamental Re-search Funds for the Central Universities (2662016PY063). （2017YFD0102000）
