Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional rapid visco analyser (RVA) associated loci

Eating and cooking quality (ECQ) have become ever more crucial breeding target in recent decades due to the high level of economic growth. The rapid visco analyser (RVA) profile is an important factor for evaluation of the ECQ. In this study, a series of recombinant lines derived from a cross between indica and japonica were planted into four areas with distinguish ecological condition in 2015 and 2016. The relationships among environment, genetic background and RVA profile were investigated through the phenotypic survey and high-throughput sequence ng. The results showed that the RVA profile was strongly affected by environmental factors, which dynamically changed from heading to mature stage. The high relative humidity had a quality penalty via effecting the RVA profile. The percentage of indica pedigree introgression was not significantly correlated to RVA profile. A totally 102 QTLs of RVA profile were detected in four areas and 2 years, 10 loci of them could be detected at least in two conditions. Moreover, we elucidated that the truncated dep1 allele might affect ECQ through reducing the peak viscosity. The present study evaluated the effects of environmental factors and genetic background to RVA profile, provide insights into the ECQ, which could be improved through sub-species crosses for different ecological conditions.