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BSA-seq has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/BSR-seq method, which we named Phenotypic Recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F6 population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82 Mb region (101,743,223–108,564,267 bp) on chromosome B05, whereas the FBP-related locus was mapped to a 2.16 Mb region (117,682,534–119,846,824 bp) on chromosome B02. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF–F6 population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data. |
