ANALYSIS OF MICROSATELLITES IN MAJOR CROPS ASSESSED BY COMPUTATIONAL AND EXPERIMENTAL APPROACHES

¹ Key Laboratory of Crop Germplasm & Biotechnology, MOA, Institute of Crop Germplasm Resource, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Over 85Mb publicly available expressed sequence tags (ESTs) data of four agronomically important crops were used to search for the types and frequencies of simple sequence repeats (SSRs) with motif length of 1-6bp long. The frequency of EST-SSRs was one every 11.81kb in rice, 17.42kb in wheat, 23.80kb in soybean, and 28.32kb in maize, respectively. Trinucleotide repeats were the most abundant SSR types with up to 47 trinucleotide repeat units in 100kb ESTs. Compared with the dicot, the monocots preferred GC-rich tri- and hexa- motifs very much, especially in rice where 23.6 CCG motif occurred in 100kb ESTs. 597 EST-SSR primer pairs were designed for wheat, of which, 478 primer pairs had successful PCR amplifications. The percentage of polymorphism was up to 41.8% among wheat varieties. A total of 65 microsatellite loci are mapped to the framework map, which are distributed on 18 of the 21 chromosomes. 53 EST show significant homology to known function genes, including storage protein, regulatory factors, metabolic enzymes as well as stress-resistant proteins. These EST-SSR markers directly screen variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection as well as comparative genetic analysis.