Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals Candidate Genes for Chlorophyll Content in Oilseed Rape Leaves

Increasing leaf chlorophyll content in crops through genetic improvement is a feasible way to increase crop yield. However, the genetic mechanism that regulates the chlorophyll content of rapeseed leaves is not clear, which is not conducive to improving it through genetic pathways. In this study, a population of 189 recombinant inbred lines of Brassica napus was used to identify quantitative trait loci (QTLs) that regulate leaf chlorophyll content. A total of 12 QTLs were identified, of which two QTLs, qCHC.A6-2 and qCHC.C5-1 , explained 10.19% and 13.70% of the phenotypic variations in chlorophyll content, respectively, and were considered to be major QTLs. Furthermore, five of the 12 QTLs were inherited from APL01, while seven were inherited from Holly. Comparative transcriptomic analysis revealed that the differential expression of genes associated with the response to light stimulation, chloroplast organization, and glutathione peroxidase activity is the molecular basis for the difference in leaf chlorophyll content between APL01 and Holly. Further combining the variation analysis of the genomic DNA sequence and the functional annotation of homologous genes, four promising candidate genes ( BnaA06g37690D , BnaA06g37710D , BnaC05g00280D, and BnaC05g00300D ) were obtained, all of which are potentially involved in the response to light stimulation and/or chloroplast organization. These results help to clarify the genetic mechanism of chlorophyll content in B. napus leaves.