Association mapping of starch physicochemical properties with starch synthesis-related gene markers in nonwaxy rice (Oryza sativa L.)

Feng Yang, Yaling Chen, Chuan Tong, Yan Huang, Feifei Xu, Kehu Li, Harold Corke, Mei Sun*, Jinsong Bao

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


Starch physicochemical properties strongly influence eating and cooking quality of rice. The cleaved amplified polymorphic sequences, derived CAPS, and InDel markers for 13 starch synthesis-related genes (SSRGs) were developed, and together with markers developed before, there are 35 markers tagged for 23 SSRGs, with each gene tagged with at least one marker. These and 108 other markers were used for association mapping for 20 starch physicochemical property parameters. A total of 64 main-effect loci or quantitative trait locus (QTLs) was detected. In addition, 56 and 62 loci were identified under the Wx and SSIIa background, respectively. Wx was a major main-effect QTL for apparent amylose content (AAC), pasting viscosity, gel texture, and retrogradation property (P < 0.0001). SSIIa was a major main-effect QTL for pasting temperature, thermal, and retrogradation properties (P < 0.0001), but it was a minor main-effect QTL for some pasting viscosity parameters, such as BD, CS, Stab, and SBratio. Four other SSRGs, SSIIa, BE1, SSIIc, and GBSSII were detected for AAC under Wx background. Wx was detected for Tc and ΔHg under the SSIIa background. PUL was detected for HD as main-effect QTL and under SSIIa background. AGPL2 and ISA1 were detected, respectively, for ΔHg and retrogradation as main-effect QTL, as well as under both Wx and SSIIa backgrounds. This study suggested that retrogradation properties were mainly controlled by Wx, SSIIa, and ISA1 with the relative effects in the order of SSIIa > Wx > ISA1. These results have direct applications to quality breeding programs.

Original languageEnglish
Pages (from-to)1747-1763
Number of pages17
JournalMolecular Breeding
Issue number4
StatePublished - 6 Dec 2014
Externally publishedYes


  • Amylose
  • Association mapping
  • Eating quality
  • Gelatinization temperature
  • QTL
  • RVA pasting viscosity
  • Rice


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