Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Table 6

Comparisons of different search criteria and software for SSR development.

	References
	Wöhrmann and Weising [6]	Ong et al. [19]	In this study
Software to assemble ESTs	Geneious 5.0 software	SeqMan software	StackPACK v2.2 program
Software to search SSRs	SciROKO	SynaRex tool	MISA
Search criteria	Mono- ≥ 15, di- ≥ 7, tri-, tetra-, penta-, hexa- ≥ 5	Di- ≥ 8, tri- ≥ 6, tetra- ≥ 5	Mono- ≥ 10, di-, tri- ≥ 6, tetra-, penta-, hexa- ≥ 5
No. of ESTs analysised	5659 Moyle et al. [20]	5931 Moyle et al. [20], Ong et al. [19]	5659 Moyle et al. [20]
No. of SSRs identified	581	416	588
No. of SSR motif types	42	5	44
Frequency of SSRs	1/4.1 KB	Not mentioned	1/3.73 KB
SSRs for primerdesign	537	133	588
No. of di-	240	203	381
No. of tri-	251	213	158
No. of (CG)n	2	0	1

Mono-, di-, tri-, tetra-, penta- and hexa- represent mononucleotide repeats, dinucleotide repeats, trinucleotide repeats, tetranucleotide repeats and hexanucleotide repeats, respectively.