QTL Mapping for the Starch Paste Viscosity of Rice (Oryza Sativa L.) Using a Chromosome Segment Substitution Lines Derived From Two Sequenced Cultivars With Same Wx Allele

Abstract BackgroundEating and cooking qualities (ECQs) of rice (Oryza sativa L.) is one of the most important economic characters which affecting production and market value. The starch viscosity profile tested by Rapid visco analyzer (RVA) is the direct measure of ECQs that represents the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and affected by environment. It is necessary to identify genetic factors controlled the RVA profile characters for development of rice varieties with excellent ECQs. Although it is known that Waxy (Wx) is the major gene control the amylose content (AC) and ECQs, there still have other unknown genetic factors effecting on ECQs.ResultsQuantitative trait loci (QTL) for starch paste viscosity of rice was analyzed using chromosome segment substitution lines (CSSLs) developed from 9311 and Nipponbare with same Wx-b background. With this CSSLs, the effect of major locus Wx could be eliminated and the other locus associated with RVA profile could be identified. QTLs for seven traits of starch RVA profile were tested over 4 years in Nanjing, China. 310 QTLs were identified (from 1 to 55 QTLs for each trait). Among 136 repeated QTLs, 6 QTLs were stable and detected every year. In total of 26 marker intervals detected over 3 years or more, 13 showed pleiotropy with respect to controlling 2 to 6 starch RVA profile properties simultaneously. The stable QTL clusters which we mapped here were overlapped to some of the known starch synthesis–related genes (SSRGs). ConclusionsWithout the effect of major locus Wx, many QTLs associated with RVA profile of rice were identified and some of them were stable. Our study illustrated that the hereditary of rice starch RVA profile is complicated, pleiotropic effects and QTL hot spots are the key factors affecting starch RVA traits.