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Background  Rice amylose content and amylopectin structure corporately determine rice eating and cooking qualities (ECQs).  Soluble starch synthase  ( SS )  IV-2  is a member of the soluble starch synthesis gene family but with unknown effects on ECQs.    Results  In this study, three populations derived from a cross of two parents who possess the same major genes of starch bio-synthesis were employed to investigate the influence of  SSIV-2  and its combined effects with  ADPglucose pyrophorylase large unit  ( AGPlar ) and  Pullulanase  ( PUL ) on ECQs. The results illustrated that the polymorphism of  SSIV-2  alleles significantly affected gel consistency (GC), gelatinization temperature (GT), percent of retrogradation (PR) and three crucial rapid viscosity analysis (RVA) profile parameters: peak viscosity (PKV), breakdown viscosity (BDV) and setback viscosity (SBV). And  SSIV-2  allele derived from CG173R had better quality traits with lower GT, SBV and PR. Moreover, its interaction with  AGPlar  was responsible for the variations of GC, apparent amylose content (AAC), GT, PR and all RVA parameters except for pasting temperature (PaT) and peak time (PeT), in terms of GC, PKV and CSV,  AGPlar  derived from CG173R had an epistatic effect on  SSIV-2 ; additionally, interaction of  SSIV-2  and  PUL  mainly affected GC, AAC, PKV, CPV, CSV and SBV. I-C and C-1 (I, allele of  AGPlar  from Guangzhan 63S; C, allele of  SSIV-2  from CG173R; 1, allele of  PUL  from Guangzhan 63S) combinations had better ECQs.    Conclusions   SSIV-2  alleles significantly affect rice quality, especially the parameters relevant to gelatinized and thermal characteristics of starch (GC, PR, GT, PKV, BDV and SBV) under the same major genes ( Waxy  and  SSII-3 ) background. It indicates that  SSIV-2  functions elongation of starch chain. These findings suggest that the effects of  SSIV-2  and its interaction with  AGPlar  and  PUL  are vital for rice quality breeding with the same major genes.

Genetic Effects of Soluble Starch Synthase IV-2 and It with ADPglucose Pyrophorylase Large Unit and Pullulanase on Rice Qualities