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United States Department of Agriculture

Agricultural Research Service

Title: EST-based Microsatellite Marker Data Mining and Characterizing

item Chen, X
item Culbreath, A
item Hong, Y
item Liang, X
item Lin, K
item Guo, Baozhu

Submitted to: American Peanut Research and Education Society Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 7/1/2007
Publication Date: 7/14/2007
Citation: Chen, X.P., Culbreath, A.K., Hong, Y., Liang, X.Q., Lin, K., Guo, B. 2007. EST-based microsatellite marker data mining and characterizing [abstract]. Proceedings of the American Peanut Research and Education Society Meeting, July 10-13, 2007, Birmingham, Alabama. p. 41-42.

Interpretive Summary:

Technical Abstract: Peanut (Arachis hypogaea L.) is an important crop for oil production. In the recent years, molecular marker technologies have been widely applied to genetic diversity analysis, genetic mapping, molecular marker-assisted breeding, gene tagging and QTLs analysis. However, it is expensive, labor-intensive and time-consuming to develop molecular markers from genomic DNA libraries. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data can be mined for simple sequence repeats (SSR) and their development is inexpensive. The EST-SSRs derived from transcripts represent transcribed genes and a putative function of EST-SSR can be deduced by a homology search. A Perl script known as MIcroSAtellite (MISA) was used to mine microsatellites in available peanut ESTs. A total of 3,581 bi- to hexa-motif SSRs were identified from 3,217 SSR-containing sequences. On an average, at least one SSR was found per 7.2 kb of EST sequence. The number of the tri-nucleotide motif was the most abundant type of SSRs with 1925 (53.7%), followed by bi- (1540, 43%), tetra- (67, 1.9%), penta- (31, 0.9%) and hexa-nucleotide (18, 0.5%) motifs. The top 8 repeat motifs, frequency of which considering sequence complementary is more than 100, included AG/CT, AAT/ATT, AAG/CTT, AT/AT, AC/GT, ACT/ATG, ACC/GGT and AGT/ACTA. A set of 312 pairs of primers were synthesized and used to examine 38 peanut genotypes of wild and cultivated peanuts. The results show that more pairs of primers were found to have polymorphism in wild species than in cultivated peanuts. The PCR polymorphic bands will be characterized further via cloning and sequencing. The results show that insertions/deletions occur in SSR sites among alleles of wild species and cultivated peanuts.

Last Modified: 08/17/2017
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