Molecular Breeding for Phosphorus-efficient Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 75

Pup1 -marker sequences

Table 5.2.

Physical location (bp)

Primer sequence (5 − 3 )

Marker name Pup1 gene model Marker type Kasalath AB458444.1 Nipponbare chromosome 12 Band size (bp) K/N

K1 OsPupK01-1 co-dominant 96175 − 96299 15315156 − 15315277 125 / 122 F: AGTCTGGATGGACAACTCTGCCTG

R: TGCTAGCTCATTGCCGTTACGTCG

K5 OsPupK05-1 co-dominant 116430 − 116701 15336063 − 15336342 272 / 280 F: ATTCAGACATCGACGGCGAC

R: TCCTCGTAAACATGGCTTGC

K20 − 1 169881 − 170120 15410254 − 15410496

OsPupK20-2 co-dominant 240 / 243 F: TCAGGTGATGGGAATCATTG

R: TGTTCCAACCAAACAACCTG

K20 − 1 MSE OsPupK20-2 CAPS 201 / 243

( Mse1 )

K20 − 2 OsPupK20-2 co-dominant 169290 − 170607 15409652 − 15410981 982 / 995 F: TCAAAAATTTCTTCAGGTATGTACTCC

R: TTGGGTGATCAGCTTTCAGA

K20 − 2 BSP OsPupK20-2 CAPS K: 231 + 349 + 402

( Bsp1286I ) N: 413 + 582

K29 − 1 OsPupK29-1 co-dominant 205067 − 205287 15431572 − 15431786 212 / 206 F: ATGGCCAACGGGGTAGAG

R: GTCCAGGTAACCACGAGGAA

K29 − 2 OsPupK29-1 co-dominant 204398 − 204616 15430672 − 15430883 291 / 212 F: CCCGTCTGCGTTCTACCTTA

R: CTCCCGTCAAGCACAAATCT

K29 − 3 OsPupK29-1 co-dominant 202698 − 202933 15419578 − 15419825 236 / 248 F: TTCGTCCAGATGCTGCTATG

R: TCTTCGGTGTAATTGGCACA

K41 OsPupK41-1 dominant 262050 − 262431 absent 382 / − F: TGATGAATCCATAGGACAGCGT

R: TCAGGTGGTGCTTCGTTGGTA

K42 OsPupK42-1 dominant 267154 − 268071 absent 918 / − F: CCCGAGAGTTCATCAGAAGGA

R: AGTGAGTGGCGTTTGCGAT

K43 OsPupK43-1 dominant 268590 − 269501 absent 912 / − F: AGGAGGATGAGCCTGAAGAGA

R: TCGCACTAACAGCAGCAGATT

K45 OsPupK45-1 dominant 274072 − 274344 absent 276 / − F: GCGGAAGAAGAGGATAACGA

R: TCTAGGCTTCGTTTGGCAAG

K46 − 1 OsPupK46-2 dominant 275710 − 276232 absent 523 / − F: TGAGATAGCCGTCAAGATGCT

R: AAGGACCACCATTCCATAGC

K46 − 2 OsPupK46-2 dominant 276371 − 276597 absent 227 / − F: AGGAAGATGGTTGTCGTTGG

R: TTCACACCAAACAGTGTTGTC

K48 OsPupK48-1 dominant 282795 − 283640 absent 847 / − F: CAGCATTCAGCAAGACAACAG

R: ATCCGTGTGGAGCAACTCATC

− −

K52 OsPupK52-1 dominant 300870 301374 absent 505 / F: ACCGTTCCCAACAGATTCCAT

R: CCCGTAATAGCAACAACCCAA

K59 OsPupK59-1 dominant 324843 − 325392 absent 550 / − F: GGACACGGATTCAAGGAGGA

R: TGCTTTCCATTTGCGGCTC

F: forward primer; R: reverse primer.