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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE PEANUT AND CORN RESISTANCE TO DISEASE AND AFLATOXIN CONTAMINATION Title: Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

Authors
item Liang, X -
item Chen, X -
item Hong, Y -
item Liu, H -
item Zhou, G -
item Li, S -
item Guo, Baozhu

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 24, 2009
Publication Date: March 24, 2009
Repository URL: http://www.biomedcentral.com/1471-2229/9/35
Citation: Liang, X., Chen, X., Hong, Y., Liu, H., Zhou, G., Li, S., Guo, B. 2009. Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biology. 9:35.

Interpretive Summary: Peanut is vulnerable to a range of diseases. Lack of sufficient molecular markers hinders current genetic improvement in peanut resistance to diseases. It is needed to develop more molecular markers for potential use in peanut molecular genetic breeding. With the development of peanut EST (expressed sequence tag) projects, a vast amount of available EST sequences has been generated. These data offered an opportunity to identify SSR (simple sequence repeat) in ESTs by data mining. In this study, we investigated 24,238 ESTs for the identification and development of SSR markers. In total, 881 SSRs were identified from 780 SSR-containing unique ESTs. On an average, one SSR was found per 7.3 kb of EST sequence. Based on the 780 SSR-containing ESTs, a total of 290 primer pairs were successfully designed and used for amplification of the polymorphism among 22 cultivated peanuts and 16 accessions of wild species. The results showed that 251 primer pairs yielded amplification products, of which 26 and 221 primer pairs exhibited polymorphism among the cultivated and wild species examined, respectively. Sequence analysis of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the simple sequence repeat regions. This study gives an insight into the frequency, type and distribution of peanut EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated peanut.

Technical Abstract: Lack of sufficient molecular markers hinders current genetic research in peanuts (Arachis hypogaea L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining. In this study, we investigated 24,238 ESTs for the identification and development of SSR markers. In total, 881 SSRs were identified from 780 SSR-containing unique ESTs. On an average, one SSR was found per 7.3 kb of EST sequence with tri-nucleotide motifs (63.9%) being the most abundant followed by di- (32.7%), tetra- (1.7%), hexa- (1.0%) and penta-nucleotide (0.7%) repeat types. The top six motifs included AG/TC (27.7%), AAG/TTC (17.4%), AAT/TTA (11.9%), ACC/TGG (7.72%), ACT/TGA (7.26%) and AT/TA (6.3%). Based on the 780 SSR-containing ESTs, a total of 290 primer pairs were successfully designed and used for validation of the amplification and assessment of the polymorphism among 22 genotypes of cultivated peanuts and 16 accessions of wild species. The results showed that 251 primer pairs yielded amplification products, of which 26 and 221 primer pairs exhibited polymorphism among the cultivated and wild species examined, respectively. Two to four alleles were found in cultivated peanuts, while 3-8 alleles presented in wild species. The apparent broad polymorphism was further confirmed by cloning and sequencing of amplified alleles. Sequence analysis of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the microsatellite regions. In addition, a few single base mutations were observed in the microsatellite flanking regions.

Last Modified: 12/22/2014