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Table 1 Molecular markers used in this study

From: Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonetype, good grain quality and disease resistance to bacterial blight

Marker

Gene-of-interest

DNA sequence

Type of marker

Reference

sd1STS

sd1

F: 5′ACAAATACCCCACCCTCCTGCC3′

STS, co-dominant

(Luo and Yin [2013])

  

R: 5′TAGTAGCCTCGCTCCACGCCC3′

  

21

Xa21

F: 5′ATAGCAACTGATTGCTTGG3′

STS, co-dominant

(Chen et al. [2000])

  

R:5′ GATCGGTATAACAGCAAAAC3′

  

RM224a

Xa4

F:5′ ATCGATCGATCTTCACGAGG3′

SSR, co-dominant

(Sun et al. [2003])

  

R:5′ TGCTATAAAAGGCATTCGGG3′

  

PCR-Acc Ib

Wx

F: 5′GCTTCACTTCTCTGCTTGTG3′

CAPS, co-dominant

(Cai et al. [2002])

  

R: 5′ATGATTTAACGAGAGTTGAA3′

  
  1. F, forward primer; R, reverse primer; STS, sequence-tagged site; SSR, simple sequence repeat; CAPS, Cleaved amplified polymorphic sequence.
  2. aThe genetic distance between RM224 and the Xa4 locus is 1.1 cM.
  3. bCAPS marker at the Wx locus by digesting PCR product with Acc I to show polymorphism.