Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats

被引:67
作者
Pinto, LR
Oliveira, KM
Ulian, EC
Garcia, AAF
de Souza, AP
机构
[1] Univ Estadual Campinas, UNICAMP, Ctr Biol Mol & Engn Genet, BR-13083970 Campinas, SP, Brazil
[2] COPERSUCAR, Ctr Technol, Piracicaba, SP, Brazil
[3] Univ Sao Paulo, Escola Super Agr Luiz Queiroz, Dept Genet, BR-13400970 Piracicaba, SP, Brazil
关键词
sugarcane; polyploid; expressed sequence tags (ESTs); microsatellites (SSRs); genetic mapping;
D O I
10.1139/G04-055
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43 141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F-1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.
引用
收藏
页码:795 / 804
页数:10
相关论文
共 32 条
[1]  
Cardle L, 2000, GENETICS, V156, P847
[2]   Preliminary analysis of expressed sequence tags for sugarcane [J].
Carson, DL ;
Botha, FC .
CROP SCIENCE, 2000, 40 (06) :1769-1779
[3]   A rapid PCR-based method for genetically mapping ESTs [J].
Cato, SA ;
Gardner, RC ;
Kent, J ;
Richardson, TE .
THEORETICAL AND APPLIED GENETICS, 2001, 102 (2-3) :296-306
[4]   Maize simple repetitive DNA sequences: Abundance and allele variation [J].
Chin, ECL ;
Senior, ML ;
Shu, H ;
Smith, JSC .
GENOME, 1996, 39 (05) :866-873
[5]   Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum [J].
Cordeiro, GM ;
Casu, R ;
McIntyre, CL ;
Manners, JM ;
Henry, RJ .
PLANT SCIENCE, 2001, 160 (06) :1115-1123
[6]   Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species [J].
Cordeiro, GM ;
Taylor, GO ;
Henry, RJ .
PLANT SCIENCE, 2000, 155 (02) :161-168
[7]   Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining [J].
Creste, S ;
Neto, AT ;
Figueira, A .
PLANT MOLECULAR BIOLOGY REPORTER, 2001, 19 (04) :299-306
[8]   Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs) [J].
da Silva, JAG .
GENETICS AND MOLECULAR BIOLOGY, 2001, 24 (1-4) :155-159
[9]   RFLP LINKAGE MAP AND GENOME ANALYSIS OF SACCHARUM-SPONTANEUM [J].
DASILVA, JAG ;
SORRELLS, ME ;
BURNQUIST, WL ;
TANKSLEY, SD .
GENOME, 1993, 36 (04) :782-791
[10]   A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar 'R570' [J].
Daugrois, JH ;
Grivet, L ;
Roques, D ;
Hoarau, JY ;
Lombard, H ;
Glaszmann, JC ;
DHont, A .
THEORETICAL AND APPLIED GENETICS, 1996, 92 (08) :1059-1064