QTL And Meta-QTL Analysis Of Rice Quality Related To Rice

Detection of quantitative trait loci(QTLs)related to rice quality can provide a basis for breeding and utilization of genes related to excellent cooking and eating quality of rice.The DH population,derived from a cross between CJ06(Oryza sativa ssp.japonica)and TN1(Oryza sativa ssp.indica),was used to detect QTLs of grain shape,amylose content(AC),and starch viscosity(rapid viscosity analysis,RVA).Thirteen QTLs related to grain type,amylose content and RVA parameters were obtained by QTL analysis.The QTLs were mapped to chromosome 1,2,3,6,7,8,and 10,included qHPV-6,qCPV-6,qBDV-6,qCSV-6,qSBV-1,qSBV-6,qSBV-7,qRL-2,qRLW-2,qRLW-3,qRLW-8-1,qRLW-10,and qAC-6.Seven QTLs on chromosome 1,6,and 7 that accounted for 7.03% to 49.05% of the total phenotypic variance and their LOD values ranged from 2.55 to 13.18.In these QTLs,contribution rate of different single QTL was more than 25% except qSBV-1 and qSBV-7.Furthermore,qHPV-6,qCPV-6,qBDV-6,qCSV-6,and qSBV-6 were mapped to the same region of chromosome 6,a main effect QTL qAC-6,whose contribution rate was 45.21%,was also detected in the region.Bioinformatics analysis indicated that the region contained a reported Waxy(Wx)gene which regulates amylose synthesis.Five QTLs with additive effects were detected in grain shape.The LOD values ranged from 3.16 to 8.47 and single QTL contribution rate was 8.95% to 27.23%.Three regions of qRLW-2,qRLW-3,and qRLW-8 contained 3 major reported QTLs GW2,GS3 and GW8.Besides,In order to obtain real and effective QTL information of rice cooking and eating quality,and to narrow the QTL confidence interval and candidate genes in the prediction interval.In this study,the integration results of 13 genetic maps of rice were used as public maps,and 592 QTLs related to cooking and eating quality were collected.Using BioMercator V4.2 software,based on the integration of the maps,the QTLs related to rice RVA spectra were obtained based on the meta-analysis calculation method.A total of 82 MQTLs related to rice RVA spectra were obtained,which were obtained on 12 chromosomes of rice.There is a distribution indicating that rice cooking and eating quality is a complex quantitative trait and is controlled by multiple genes.Among the 82 MQTL obtained,the genetic distance of 76 MQTL is smaller than the minimum confidence interval in the initial QTL,indicating that the meta-analysis narrows the interval distance of the original QTL.In addition,among the 82 MQTL,the QTLs enriched on chromosome 6 were the most,and by bioinformatics analysis,we found that it is related to the Waxy(Wx)gene involved in the synthesis of amylose cloned in this region.In this study,QTL analysis and Meta-QTL analysis were used to map the RVA profile-related genes and map the related genes,in order to understand the impact of the ecological environment on rice quality.This study enriched the genetic regulatory network of RVA-related traits by QTL analysis of RVA-related traits,and used Meta-QTL analysis to integrate existing QTL loci,providing a preliminary theoretical reference for further mining related genes and rice molecular breeding.Therefore,to improve the breeding efficiency of high-quality rice,analysis,discovery of new genetic loci,and other purposes,provide atheoretical basis for the analysis and breeding of rice quality.