Table 8. SSR markers for the genotyping of organelle genomes.
| Chloroplast (this study1) | ||||||||
| Name | Target region | SSR From | To | Size | Program | F/R | BStag | Sequence |
| CSS03 | ndhE-ndhG | 122,864 | 122,878 | 292 | 54/28 | F | F9GTC | ctagtatgaggacgtcTCATTAACCAACTCCGTACCA |
| R | - | gtttcttGGCGCGTCAATAACAAATCT | ||||||
| CSS04 | ndhD-psaC | 121,941 | 121,955 | 211 | 56/28 | F | F9GCC | ctagtattaggacgccGTGGTAAAGACAAGATACACTTGG |
| R | - | gtttcttATGGCATGAAACAACCCGA | ||||||
| CSL01 | psbA-trnK | 1,743 | 1,775 | 355 | 60/28 | F | F9GAC | ctagtatcaggacgacCAGTGCTAGTTATCCAGTTACAGA |
| R | - | gtttcttCGGGCAACCCATTCTTATTATT | ||||||
| CSL09 | rpl16-rps3 | 86,713 | 86,730 | 276 | 54/32 | F | F9TAC | ctagtatcaggactacCGCACACTAAGCATAGCAAT |
| R | - | gtttcttCCTCTACAAACCATTGGAGCTA | ||||||
| Chloroplast (Weising and Gardner, 19912) | ||||||||
| Name | Target region | SSR From | To | Size | Program | BStag | Sequence | |
| ccmp2.2 | 5' to trnS | 8,609 | 189 | 54/28 | F | F9GAC | ctagtatcaggacgacATCGTACCGAGGGTTCGAAT | |
| R | - | GATCCAGGGCGTAATCCCG *) | ||||||
| ccmp6.2 | ORF77-ORF82 intergenic | 45,119 | 103 | 60/28 | F | F9GCC | ctagtattaggacgccCGATGCATATGTAGAAAGCC | |
| R | - | CATTACGTGCGACTATCTCT | ||||||
| ccmp7.2 | atp-B-rbcL intergenic | 57,339 | 133 | 52/36 | F | F9CCG | ctagtattaggacccgACATCATTATTGTATACTCTTTC | |
| R | - | CAACAGATAAAACTGTCAAG | ||||||
| ccmp10.2 | rpl2-rps19 intergenic | 86,694 | 103 | 54/32 | F | F9AGG | ctagtattaggacaggTTTTTTTTTAGTGAACGTGTCA | |
| R | - | TTCGCCGCCGTACTAAATAG | ||||||
| Mitochondria (Froelicher, et al. 20113) | ||||||||
| Name | Target region | SSR From | To | Size | Program | BStag | Sequence | |
| rrn5/rrn18-1 | rrn5-rrn18 | 161,129 | 161,383 | 273 | 56/28 | F | F9GTC | ctagtatgaggacgtcGGGTGAAGTCGTAACAAGGT |
| R | - | GAGGTCGGAATGGGATCGGG | ||||||
| nad2/4-3 | nad2-nad4-3 | 330,666 | 331,566 | 239 | 52/28 | F | F9CCG | ctagtattaggacccgGACCTTCACCTCAAATCA |
| R | - | TTCAGATAACACGCACC | ||||||
| nad7/1-2 | nad7-nad1-2 | 132,914 | 133,077 | 163 | 52/28 | F | F9AGG | ctagtattaggacaggGGAACATAGCATAGGG |
| R | - | TTTGATATAGGCTCGCT | ||||||
1 SSR markers developed in this study with reference to the sweet orange chloroplast genome (DQ864733).
2 SSR markers for chloroplast genomes by Weising and Gardner, 1991. The underlined nucleotides represent the modifications from their original sequences.
*) Forward and reverse primers were swapped from the original report.
3 DNA markers for genotyping mitochondrial genomes by Froelicher et al 2011.
All these DNA markers were designed for the single tube post labeling protocol with BStag. F/R: Forward/reverse primers.