Identification of quantitative trait loci (QTL) and meta-QTL analysis for kernel size-related traits in wheat (Triticum aestivum L.)

Background: Kernel size-related traits, as critical determinants of wheat kernel weight and yield potential, are complex quantitative traits controlled by polygenes. Genome-wide identification of important and stable quantitative trait loci (QTL) and functional genes for these traits can advance molecular genetic improvement of wheat kernel yield. Results In this study, Thirty-two QTLs for kernel size-related traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR) and kernel thickness (KT), were discovered using a series of recombinant inbred lines (RILs) which explained 3.06–14.2% of the phenotypic variation. Of these, eleven QTLs were confirmed as stable QTLs in multiple environments. The 1103 original QTLs from 34 previous studies and the present study were employed for the MQTL analysis, in which 346 of the 1103 original QTLs were refined to 58 MQTLs. Compared to the original QTLs, the average confidence intervals of the target MQTLs decreased 3.26-fold, but the average genetic contribution rates to explain phenotypic variation increased 1.72-fold. Through comprehensive analysis of wheat publicly available transcriptome data, a total of 70 putative candidate genes for kernel size development were ultimately identified within the MQTL regions. Conclusions kernel size-related traits predominantly regulated by genetic factors and can be detected in different water conditions. Potential candidate genes expressed in spike and grain were identified through meta-QTL and in-silico expression analysis. The identification of stable QTLs and candidate genes for kernel size-related traits provides a novel insight to understand the genetic basis of kernel size-related traits in wheat.