Rice Genetics IV - IRRI books - International Rice Research Institute

periments tended to detect only the longer SSR motifs (corresponding to class Imicrosatellites) because of the hybridization conditions used. Estimates from thisearly work predicted that there were from 5,500 to 10,000 microsatellite loci in rice,or one every 40–80 kb. Using a computational approach, Temnykh et al (2001) examined47,430 kb of BAC end sequence, or about 0.11 genome equivalent, the largestsingle source of rice sequence information available at the time of the study. Extrapolatingfrom the frequency of di-, tri-, and tetra-nucleotide SSRs observed in this singlepassBAC end sequence, it was predicted that the rice genome contained approximately11,000 class I and an additional 22,000 class II microsatellites, or a total ofapproximately 33,000 di-tetranucleotide SSRs. These numbers are extrapolations ofthe observed frequencies summarized in Table 1. Two other independent sources ofrice sequence were also examined by Temnykh et al (2001), namely, 27 fully sequencedBAC and PAC clones and 12,000 nonredundant sequenced cDNAs (expressedsequence tags, ESTs). This provided about 4,000 kb of continuous genomic sequenceand 6,000 kb of ESTs. Estimates of total microsatellite frequencies in these sequenceswere approximately three times those based on BAC end sequences (Fig. 2), with oneclass I SSR observed every 15 kb and one class II SSR every 6 kb in the totallysequenced PACs and BACs, suggesting a total of approximately 28,340 class I and70,530 class II SSRs, or about 100,000 SSR motifs in the rice genome (Table 1). Asadditional sequence information becomes available for rice, the accuracy of theseestimates will improve.Table 1. Observed number of microsatellites with di-, tri-, and tetra-nucleotide repeats in threesources of DNA sequence data: (A) BAC ends, (B) fully sequenced PAC and BAC clones, and(C) ESTs.SSR category Category I Category II All SSRs(n≥ 20 nt) (12< n 12 ntA) 74,127 BAC ends (47,430 kb)di 690 (1/69 kb) 969 (1/49 kb) 1,659 (1/29 kb)tri 210 (1/226 kb) 1,035 (1/46 kb) 1,245 (1/38 kb)tetra 289 (1/164 kb) 410 (1/115 kb) 699 (1/68 kb)Total (observed) 1,189 (1/40 kb) 2,414 (1/20 kb) 3,603 (1/16 kb)Predicted total in rice genome 10,780 21,885 32,665B) 27 PACs and BACs (4,036 kb)di 132 (1/30.5 kb) 173 (1/23 kb) 305 (1/13 kb)tri 97 (1/41.6 kb) 382 (1/11 kb) 479 (1/8 kb)tetra 37 (1/109 kb) 107 (1/38 kb) 144 (1/28 kb)Total (observed) 266 (1/15 kb) 662 (1/6 kb) 928 (1/4 kb)Predicted total in rice genome 28,340 70,530 98,870C) 12,532 ESTs (approx. 6,000 kb)di 74 (1/81 kb) 159 (1/38 kb) 233 (1/26 kb)tri 235 (1/26 kb) 1,159 (1/5 kb) 1,394 (1/4 kb)tetra 32 (1/188 kb) No data 32Total (observed) 341 (1/18 kb) 1,318 (1/5 kb) 1,659 (1/3 kb)Predicted total in rice genome 24,440 94,460 118,900120 McCouch et al