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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #340884

Title: Analysis of SSR information in EST resources of sugarcane

item YAN, XUEBING - Collaborator
item QUE, YOUXIONG - Collaborator
item XU, LIPING - Collaborator
item GUO, JINLONG - Collaborator
item CHEN, RUKAI - Collaborator
item Pan, Yong-Bao

Submitted to: Chinese Journal of Tropical Crops
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/14/2010
Publication Date: 12/31/2010
Citation: Yan, X., Que, Y., Xu, L., Guo, J., Chen, R., Pan, Y.-B. 2010. Analysis of SSR information in EST resources of sugarcane. Chinese Journal of Tropical Crops. 31(9):1497-1501.

Interpretive Summary: The genomic DNA of living organisms are made up of two portions. One portion is expressed leading to products, while another portion is not expressed. Expressed DNA sequence tags (ESTs) from the first portion often contain single- or low-copies of conserved core nucleotide sequences that allow the development of simple sequence repeats (SSRs) DNA markers. In this study, a total of 262,113 sugarcane ESTs were downloaded from the GenBank database. Analysis of these sequences identified 62,565 non-redundant genes (Unigenes) with a total length of about 50,058.89 kilo-base pairs and 9,482 SSRs. The frequency of SSR detection was 15.15%, one SSR in 5.28 kilo-base pairs. The dominant SSR types were dinucleotide and tronucleotide, accounting for 21.22% and 8.18%, respectively. The polymorphism of SSRs was also assessed. The information lays the foundation for the exploitation of EST-SSR tags and related molecular biology research in sugarcane.

Technical Abstract: Expressed sequence tags ( ESTs) offer the opportunity to exploit single, low -copy, conserved sequence motifs for the development of simple sequence repeats ( SSRs). The total of 262 113 ESTs of sugarcane (Saccharum officinarum) in the database of NCBI were downloaded and analyzed, which resulted in 62 565 non-redundant Unigenes with total length about 50 058.89 kb. 9 482 SSRs from these sequences were acquired. The frequency of SSR in the unigene was 15.15%. One piece of SSR arised in 5.28 kb averagely. Trinucleotide repeats were the main type, accounting for 45.92% of the total SSRs. The dominant repeat types were dinucleotide and trinucleotide, accounting for 21.22% and 8.18% respectively. The polymorphism of SSRs was assessed. The searching and analysis of SSRs lays foundations for the exploitation of sugarcane EST-SSR tags and the related research of molecular biology.