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Background Soluble starch synthase IIa (ALK, SSII-3) is the major gene regulating gelatinization temperature (GT) and SSII-3M1 is an effective marker for identifying SSIIa alleles. However, the haplotypes of SSIIa alleles amplified by SSII-3M1, their allelic effects under different Waxy (Wx) in non-glutinous rice remain unclear. Results Through integrating the genetic background analysis and the identification of genotype of Wx and SSIIa, We found SSIIa alleles amplified by SSII-3 M1 were haplotype 1 (G/G/GC, indica-type) and 4 (A/G/TT,
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