Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

La Rota, Mauricio; Kantety, Ramesh V; Yu, Ju-Kyung; Sorrells, Mark E

doi:10.1186/1471-2164-6-23

Table 1 Frequency table of perfect and imperfect microsatellites grouped by type of repeat in the non-redundant rice genome (IRGSPnr), rice gene index (Osgi), barley gene index (Hvgi) and wheat's gene index (Tagi) under nine different constraints for minimum SSR length, starting at a minimum of 12 bp. 'n' is SSR count, 'f' is relative proportion (fraction). 'U.f' is unigene fraction: the percentage of unigenes from that species containing at least one SSR.

From: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

Dataset	SSRLength	> = 12		> = 14		> = 15		> = 16		> = 18		> = 20		> = 24		> = 30		> = 40
	SSR type	n	f	n	f	n	f	n	f	n	f	n	f	n	f	n	f	n	f
Osgi	dinucleotide	1751	0.07	1206	0.09	950	0.07	950	0.14	673	0.12	507	0.16	366	0.25	237	0.45	136	0.67
	trinucleotide	17342	0.67	8921	0.63	8921	0.65	4272	0.62	4272	0.75	1993	0.62	912	0.61	242	0.46	56	0.28
	tetranucleotide	4039	0.16	1242	0.09	1242	0.09	1242	0.18	275	0.05	275	0.09	84	0.06	18	0.03	9	0.04
	pentanucleotide	2706	0.10	2706	0.19	2706	0.20	458	0.07	458	0.08	458	0.14	124	0.08	33	0.06	2	0.01
	Total SSR	25838		14075		13819		6922		5678		3233		1486		530		203
	U.f		50%		27%		27%		13%		11%		6%		3%		1%		0.4%
Hvgi	dinucleotide	1304	0.07	916	0.10	706	0.08	706	0.15	508	0.15	387	0.17	237	0.25	162	0.48	96	0.67
	trinucleotide	9176	0.52	4326	0.45	4326	0.46	1990	0.43	1990	0.57	971	0.42	464	0.48	115	0.34	34	0.24
	tetranucleotide	4122	0.23	1359	0.14	1359	0.15	1359	0.29	379	0.11	379	0.16	103	0.11	10	0.03	4	0.03
	pentanucleotide	2976	0.17	2976	0.31	2976	0.32	594	0.13	594	0.17	594	0.25	157	0.16	53	0.16	10	0.07
	Total SSR	17578		9577		9367		4649		3471		2331		961		340		144
	U.f		36%		20%		19%		10%		7%		5%		2%		1%		0.3%
Tagi	dinucleotide	2606	0.08	1890	0.11	1526	0.09	1526	0.18	1122	0.18	890	0.22	668	0.32	478	0.54	317	0.70
	trinucleotide	18650	0.55	8671	0.50	8671	0.51	3847	0.46	3847	0.61	1840	0.45	989	0.48	343	0.39	124	0.27
	tetranucleotide	8189	0.24	2253	0.13	2253	0.13	2253	0.27	572	0.09	572	0.14	181	0.09	26	0.03	8	0.02
	pentanucleotide	4570	0.13	4570	0.26	4570	0.27	773	0.09	773	0.12	773	0.19	243	0.12	33	0.04	5	0.01
	Total SSR	34015		17384		17020		8399		6314		4075		2081		880		454
	U.f		31%		16%		16%		8%		6%		4%		2%		1%		0.4%
IRGSPnr	dinucleotide	32202	0.17	23056	0.21	18541	0.17	18541	0.33	14081	0.34	11286	0.39	8516	0.53	6307	0.72	4284	0.81
	trinucleotide	78832	0.41	38759	0.35	38759	0.36	17615	0.31	17615	0.43	8392	0.29	4431	0.28	1400	0.16	582	0.11
	tetranucleotide	48836	0.25	15030	0.14	15030	0.14	15030	0.26	3789	0.09	3789	0.13	1636	0.10	625	0.07	378	0.07
	pentanucleotide	34102	0.18	34102	0.31	34102	0.32	5591	0.10	5591	0.14	5591	0.19	1401	0.09	385	0.04	54	0.01
	Total SSR	193972		110947		106432		56777		41076		29058		15984		8717		5298

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