Fine Mapping of Lobed‐Leaf Genes in Two Brassica napus Lines Using SLAF Sequencing

Abstract

Plant ideotypes may be useful for increasing yield in Brassica napus L., and leaves play an important role in the development of ideotypes. Previously, we bred two lobed‐leaf B. napus lines, ll1 and ll2. In the present study, we report the fine mapping of lobed‐leaf genes in ll1 and ll2 and annotate their putative functions. We conduct specific‐locus amplified fragment sequencing (SLAF‐seq) to determine the candidate intervals. Crosses between two lobed‐leaf lines ll1 and ll2 and their corresponding wild types el1 and el2 were used to generate two sets of F1 and F2 populations. Genome‐wide comparison of single‐nucleotide polymorphism profiles between lobed‐ and entire‐leaf bulks identified ll1 and ll2 candidate intervals on ChrA10. Lobed‐leaf gene ll1 was located in two regions within genomic positions 16,055,155 to 16,158,378 (100 kb in size) and 16,651,387 to 17,120,610 (470 kb in size), whereas the ll2 gene was located within the genomic region of 16,767,957 to 17,024,885 (260 kb in size), which overlapped with the second region of ll1. These results suggest that the lobed‐leaf candidate genes for ll1 and ll2 are alleles. Basic Local Alignment Search Tool (BLAST) analysis identified 139 genes and 49 genes in the associated regions of ll1 and ll2, respectively. Approximately 135 genes in ll1 and 49 genes in ll2 could be functionally annotated, with the majority playing important roles in the regulation of leaf margin and leaf growth. These studies provide useful information for constructing ideotypes and breeding high‐yielding B. napus hybrids.