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Background  The eating and cooking qualities (ECQs) of rice ( Oryza sativa  L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a direct measure of ECQs and represent the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and are also affected by the environment. Although  Waxy  ( Wx ) is the major gene controlling amylose content (AC) and ECQs, there are still other unknown genetic factors that affect ECQs.    Results  Quantitative trait loci (QTLs) for starch paste viscosity in rice were analyzed using chromosome segment substitution lines (CSSLs) developed from the two cultivars 9311 and Nipponbare, which have same  Wx-b  allele. Thus, the effect of the major locus  Wx  was eliminated and the other locus associated with the RVA profile could be identified. QTLs for seven parameters of the starch RVA profile were tested over four years in Nanjing, China. A total of 310 QTLs were identified (from 1 to 55 QTLs per trait) and 136 QTLs were identified in more than one year. Among them, 6 QTLs were stalely detected in four years and 26 QTLs were detected in at least three years including 13 pleiotropic loci, controlling 2 to 6 RVA properties simultaneously. These stable QTL hotspots were co-located with several known starch synthesis-related genes (SSRGs). Sequence alignments showed that nucleotide and amino acid sequences of most SSRGs were different between the two parents. Finally, we detected stable QTLs associated with multiple starch viscosity traits near  Wx  itself, supporting the notion that additional QTLs near  Wx  control multiple characteristic values of starch viscosity.    Conclusions  By eliminating the contribution from the major locus  Wx , multiple QTLs associated with the RVA profile of rice were identified, several of which were stably detected over four years. The complexity of the genetic basis of rice starch viscosity traits might be due to their pleiotropic effects and the multiple QTL hot spots. Minor QTLs controlling starch viscosity traits were identified by using the chromosome segment substitution strategy. Allele polymorphism might be the reason that QTLs controlling RVA profile characteristics were detected in some known SSRG regions.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07913-7.

bmc genomics

QTL mapping for starch paste viscosity of rice (Oryza sativa L.) using chromosome segment substitution lines derived from two sequenced cultivars with the same Wx allele