烟草的SNP分析
-
https://agris.fao.org/agris-search/search.do?recordID=KR2009003178
a set of seven informative single-nucleotide polymorphisms
(SNPs) and one insertion-deletion (INDEL) distributed over 24 cultivars that can be used for
tobacco (Nicotiana tabacum L.) cultivar identification.
用7个SNP和一个INDEL 分类了24个品种
SNP frequency of tobacco, 1/8,380 bp, was very low in comparison
with those of other plant species
和其他植物比较 烟草的SNP频率相对较低SNPs are more frequent than
SSRs in animal and plant genomes and the
mutation rate is lower, 10-8 (Kondrashov, 2003;
Nachman and Crowell, 2000) than in SSRs, 10-3
(Brinkmann et al., 1998); therefore, SNPs are
more reliable as molecular markers for organism
identification
SNP 比SSR有优势cultivar determination of dried leaves is very
difficult because the original shape is changed
during the curing process and there are more
than 10,000 cultivars in existence.
用形态学鉴定干的叶子显然很困难 而且市面上有1万多个品种
从TGI获取的原始数据 用PCAP program做了组装
From the original 163,000 sequences, we assembled 31,370 contigs and about 60,000 singlets.Primer Design and PCR Reaction
设计引物 然后扩增
Sequences were analyzed on
an A B I3 7 3 0 x l D N A A naly z er ( A p p lied
Biosystems, Foster City, CA).The sequence
data from each amplicon were analyzed with
sequence analyzing software: CLC Workbench
(CLC Bio, Denmark), Clustal X (Larkin et al.,
2007), and SequencherTM 4 . 8 ( G ene Code
Corporation). The minimum and maximum PCR
p roduct length was 71 6 bp and 2, 047 bp ,
respectively, and the average length was 1,295
bp (Table 3). We removed the first 25 bp from
the sequence and compared only the first 26 bp
to 525 bp region.
找到的SNP
烟草的SNP频率不是很多
