Meta-analysis of quantitative trait loci associated with grain quality traits in rice (Oryza sativa L.)

Abstract

Rice grain quality is a crucial factor in determining its economic value. Numerous studies have identified quantitative trait loci (QTLs) associated with grain quality. However, to date, no meta-analysis of QTLs for rice cooking and eating quality traits has been reported. Therefore, we conducted a meta-analysis of QTLs to identify consensus QTLs located at the same locus across multiple studies, aiming to detect significant meta-QTLs (MQTLs) that can be targeted for marker-assisted selection (MAS) applications. In this study, 26 MQTLs were identified from 193 initial independent QTLs related to grain quality traits, including amylose content (AC), gel consistency (GC), and gelatinization temperature (GT). The substantial reduction in the confidence interval of the initial QTLs compared to the MQTLs (from 20.91 to 7.21 cM) led to the identification of both annotated and putative candidate genes associated with the traits. The highest number of MQTLs (eight) was found on chromosome 6. The phenotypic variance explained (R²) by the MQTLs ranged from 2 to 51%, with an average of 19%. Out of the 561 candidate genes identified within the MQTLs, 461 had available expression data. Analysis of their expression patterns in various rice tissues showed that 181 genes had an expression value (FPKM) greater than 10 in at least one tissue, making them promising candidate genes. Gene ontology (GO) analysis of these promising genes highlights their significant roles in various biological processes in rice. This is the first study to identify meta-QTLs associated with cooking and eating grain quality in rice.