Recent advances and future challenges for a multi-omics analysis pipeline as a breeding tool in Allium research community

Multi-omics approaches have emerged as successful technologies for understanding responses to biotic and abiotic stress in Allium crops. For whole genome sequencing project, de novo assembly and ab initio annotation of DHCU0666 genome, resulted in the assembly of first high-quality genome sequence. A high-quality transcriptome data of Allium monosomic addition lines (MALs) were generated using RNA-seq, which enabled us to understand the regulations of saponin and flavonoid biosynthesis, the key bioactive metabolites for disease resistance. The transcriptome sequence reads of MALs were mapped onto unigene sequences of the shallot doubled haploid to identify chromosome-anchoring SNP markers in A. cepa. The F2 mapping population produced from a single F1 between shallot and onion DHs was subjected to transcriptome-based genotyping for generating SNP markers and subsequently constructing A. cepa high-density genetic linkage map. We applied advanced metabolome-based discrimination analysis for various Allium genetic resources. Metabolome profiling of the F2 population combined with transcriptome-based genotyping and Fusarium inoculation test, enabled the identification of several metabolite QTLs associated with saponin and Fusarium disease resistance in A. cepa genome.