Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

Table 1 Composition and length distribution of major SSR types in the apple genome

Repeat unit	Repeat type	Repeat length (bp)				Total	Frequency (%)
		<30	30-40	40-50	>50
Dimer	AC/CA	1883	357	106	73	2419	8.48
	AG/GA	5115	2090	953	595	8753	30.67
	AT/TA	6035	1968	854	495	9352	32.77
	CG	1	0	0	0	1	0.00
	Total	13033	4415	1913	1163	20524	71.92
Trimer	AAT/ATA/TAA	591	97	41	44	773	2.71
	AAC/ACA/CAA	1342	44	7	3	1396	4.89
	AAG/AGA/GAA	643	66	20	44	773	2.71
	Others	520	31	4	6	561	1.97
	Total	3096	238	72	97	3503	12.27
Tetramer	AAAT/TAAA/ATAA/AATA	631	10	0	1	642	2.25
	AATT/ATTA/TTAA/TAAT	93	0	0	0	93	0.33
	AAAG/AAGA/AGAA/GAAA	109	10	2	2	123	0.43
	TACA/ACAT/CATA/ATAC	404	76	15	8	503	1.76
	GTTT/TGTT/TTGT/TTTG	90	1	1	0	92	0.32
	AGGG/GAGG/GGAG/GGGA	91	4	0	0	95	0.33
	Others	222	17	5	1	245	0.86
	Total	1640	118	23	12	1793	6.28
Pentamer	AAAAT/AAATA/AATAA/ATAAA/TAAAA	494	2	0	0	496	1.74
	GTTTT/TGTTT/TTGTT/TTTGT/TTTTG	154	1	0	0	155	0.54
	AATTT/ATTTA/TTTAA/TTAAT/TAATT	94	1	0	0	95	0.33
	AAAAG/AAAGA/AAGAA/AGAAA/GAAAA	115	0	0	0	115	0.40
	AAGCC/AGCCA/GCCAA/CCAAG/CAAGC	170	0	0	0	170	0.60
	CCCTG/CCTGC/CTGCC/TGCCC/GCCCT	121	7	0	1	129	0.45
	Others	747	15	1	1	764	2.68
	Total	1895	26	1	2	1924	6.74
Hexamer	AAAAAT/AAAATA/AAATAA/AATAAA/ATAAAA/TAAAAA	106	2	2	0	110	0.39
	AAAAAG/AAAAGA/AAAGAA/AAGAAA/AGAAAA/GAAAAA	38	1	0	0	39	0.14
	AAAAAC/AAAACA/AAACAA/AACAAA/ACAAAA/CAAAAA	34	0	0	0	34	0.12
	CCCTCT/CCTCTC/CTCTCC/TCTCCC/CTCCCT/TCCCTC	33	2	2	0	37	0.13
	ATACAT/TACATA/ACATAT/CATATA/ATATAC/TATACA	40	6	0	1	47	0.16
	AGAGTG/GAGTGA/AGTGAG/GTGAGA/TGAGAG/GAGAGT	21	1	0	0	22	0.08
	CCTCTC/CTCTCC/TCTCCC/CTCCCT/TCCCTC/CCCTCT	35	3	1	0	39	0.14
	Others	434	23	7	1	465	1.63
	Total	741	38	12	2	793	2.78

SSRs with at least 20 bp in length and more than 3 repeats were recorded. SSR motifs represent variants of both strands of the DNA sequence (e.g., AC/CA includes the reverse complements GT and TG).

ISSN: 1471-2164