摘要
利用生物信息学方法,从dbEST数据库用SSRHunter软件对4 500条核桃EST序列进行搜索,发现462个SSR分布于399条EST序列中,EST-SSR出现频率10.27%,平均每5.65 kb EST出现一个SSR。核桃二核苷酸重复基元占主导地位,其次为三核苷酸重复基元,分别占总SSR的49.57%和27.27%。核桃二核苷酸EST-SSR的优势类型为AG,其次为AT,分别占二核苷酸SSR的67.25%和28.38%。核桃三核苷酸EST-SSR的优势重复基元为AAG,其次为ACC、AAT、AGG,分别占三核苷酸SSR的25.40%、21.43%、16.67%和11.11%。用Primer Primer 5.0软件设计了11对引物,对核桃属5个样品进行PCR扩增,10对引物有扩增产物,引物有效扩增率90.9%,其中7对引物有多态性,多态性引物占可扩增引物的70%。表明,利用核桃EST序列开发EST-SSR标记是可行的。
4 500 ESTs of walnut from the database of dbEST were screened using SSRHunter software, and 462 SSRs in 399 ESTs were mined out, accounting for 10.27% of the total ESTs, corresponding to one SSR in every 5.65 kb of the ESTs. Dinucleotide and trinucleotide repeats EST-SSRs were dominant, accounting for 49.57% and 27.27% respectively. AG was the most frequent motif in dinucleotide repeats, and the next was AT, accounting for 67.25% and 28.38% in dinucleotide ESTSSRs. AAG is the most frequent motif in trinucleotide repeats, accounting for 25.40% in trinucleotide EST-SSRs, followed by ACC （21.43% ）, AAT （ 16.67% ） and AGG （ 11.11% ）. 11 primer pairs were designed, and 10 of them showed amplifications in 5 samples （Julans L.）, the effective amplification frequency is 90.9%. 7 primer pairs showed polymorphisms, accounting for 70% of amplified primers. The results indicated that it is an available approach to develop EST-SSR markers based on walnut ESTs.
出处
《果树学报》
CAS
CSCD
北大核心
2009年第3期394-398,共5页
Journal of Fruit Science
基金
北京市科技新星项目(2004B21)
西南林学院面上科研基金(编号:110611)
