BSA-seq identified candidate genes and diagnostic KASP markers for anemone type flower in chrysanthemum

Chrysanthemum is one of the most leading commercial flower crops well-known for its flower shape diversity. Anemone type chrysanthemums receive increasing market attention that are distinguished by their pigmented and elongated disk florets. However, there are few reports on quantitative trait loci (QTL) mapping and the identification genes for anemone in chrysanthemum. In this study, bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) approach was employed to detect candidate genomic regions controlling anemone type flower. Two mixed DNA pools composed of 28 anemone type and 20 non-anemone type F1 lines derived from a cross between ‘Nannong Xuefeng’ and ‘Monalisa’ together with two parents were used for high-throughput sequencing. A total of 42 consistent QTLs covering 30.00 Mb were simultaneously identified by |△(SNP/InDel-index)| and Euclidean distance (ED) algorithms based on 15,783,313 SNPs (single-nucleotide polymorphisms) and 1,546,200 small InDels (insertions and deletions). Twenty-two key candidate genes were screened out by a combination of gene functional annotation and transcriptome analysis, in which evm.model.scaffold_915.436 (CBF5), evm.model.scaffold_24.208 (U2AF65A), and a uncharacterized gene evm.model.scaffold_260.201 were highlighted by qRT-PCR. Furtherly, four associations were successfully converted to KASP (kompetitive allele specific PCR) markers, among them, the KASP markers developed for SNP locus Chr6__33961007 and Chr6__179207697 were proven to efficiently discriminate anemone and non-anemone type chrysanthemums being a couple of diagnostic markers in two populations. The results presented herein provide insights for further research on elucidating the formation mechanism of anemone type flower, and the anemone-specific KASP marker will be highly useful for applying MAS to accelerate breeding improvement of chrysanthemum.