Guava cv. Allahabad Safeda Chromosome scale assembly and comparative genomics decodes breeders’ choice marker trait association for pink pulp colour

Deciphering chromosomal length genome assemblies has the potential to unravel an organism’s evolutionary relationships and genetic mapping of traits of commercial importance. We assembled guava genome using a hybrid sequencing approach with ∼450x depth Illumina short reads, ∼35x PacBio long reads and Bionano maps to ∼594 MB Scaffold length on 11 pseudo chromosomes (∼479 MB contig length). Maker pipeline predicted 17,395 genes, 23% greater from earlier draft produced in same cultivar Allahabad Safeda. The genome assembly clarified guava evolutionary history, for example revealing predominance of gene expansion by dispersed duplications, in particular contributing to abundance of monoterpene synthases; and supporting evidence of a whole genome duplication event in guava as in other Myrtaceae. Guava breeders have been aiming to reduce screening time for selecting pink pulp colour progenies using marker-trait associations, but a previous comparative transcriptomics and comparative genomics approach with draft genome assembly to identify the effector gene associated with pink pulp was unsuccessful. Here, genome re-sequencing with Illumina short reads at ∼25x depth of 20 pink fleshed and/or non-coloured guava cultivars and comprehensive analysis for genes in the carotenoid biosynthesis pathway identified structural variations in Phytoene Synthase 2. Further, ddRAD based association mapping in core-collection of 82 coloured and non-coloured genotypes from Indian sub-continent found strong association with the same causal gene. Subsequently, we developed PCR based Indel/SSR breeder friendly marker that can readily be scored in routine agarose gels and empowers accurate selection for seedlings that will produce fruits with pink pulp.