摘要
利用来自美洲黑杨及欧美杨的20023条EST序列,进行EST-SSR标记开发研究。首先对这些EST序列进行序列拼接,然后在非重复序列中发现由二核苷酸至五核苷酸组成的SSR重复序列。共在10816个非重复序列中发现1604个序列含有SSR,占总非重复序列的14.8%。在发现的1918个SSR重复序列中,二核苷酸重复是最丰富的重复类型,占总类型的62.3%。设计合成48对SSR引物,利用6个不同的杨树品种对其进行验证。结果约90%的引物获得扩增产物,58%的引物在6个不同杨树品种中产生多态性分离。另外,还对重复序列的数量及重复类型进行了讨论。
Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The big collection of expressed sequence tags（ESTs） from Populus species is available in public database,and offers an opportunity to identify simple sequence repeats（SSR） in ESTs by data mining. These sequences may provide an estimate of diversity in the expressed portion of the genome and may be useful for comparative mapping,for tagging important traits of interest, and for additional map-based cloning of important genes. We analyzed 20 023 EST sequences from Populus deltoides and P for their potential use in developing SSR markers The EST sequences were clustered into contigs firstly to find dinucleotide, trinucleotide, tetranucleotide and pentanucleotide SSR. Totally, 1 604 contigs with 1 918 SSRs were identified from 10 816 contigs, and accounted for 14.8% of the total number of contigs. Dinucleotide repeats were the most abundant repeat class, and accounted for 62.3 % of all found SSRs. About 90 % primers out of the designed 48 pairs were able to produce an amplification product from 6 poplar cuhivars, among which 58 % exhibited polymorphism for at least one cuhivar among the six tested ones. The number and type of repeats were also discussed. The development of new EST-SSR markers from Populus has potential important implication for genetic analysis and exploitation of genetic resources of Populus and would provide a more direct estimate of functional diversity.
出处
《林业科学》
EI
CAS
CSCD
北大核心
2009年第9期53-59,共7页
Scientia Silvae Sinicae
基金
国家林业局"948"项目(2006-4-80)
作者简介
杨彦伶为通讯作者。
