Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Abstract

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Figure 1:. Circos plots for the blueberry and cranberry pangenomes.

Circos plots for the blueberry (panel A) and cranberry (panel B) pangenomes are shown. Tracks from exterior to interior are as follows: (1) karyotype of the 12 main pseudomolecules, (2) density of LTR transposons in black, (3) density of core genes in pink, and (4) density of auxiliary genes in gray. For panel A, northern highbush blueberry is shown on the third and fourth tracks, while the two innermost tracks reflect southern highbush blueberry core and auxiliary genes.

Figure 2:. Core and auxiliary genome modeling for cranberry and blueberry

Panel A depicts the model for the core (circle) and auxiliary (triangle) pangenome for cranberry. For each point along the x-axis, we take every possible combination of that size from our genome samples and plot the average number of core and auxiliary genes as a point. Panel B depicts the model for the core (triangles) and auxiliary genes (circles) for northern (dark blue) and southern (light blue) highbush blueberry. Note the y-axes do not start at zero.

Figure 3:. Differences between core and auxiliary genes.

Density plots showing the differences between core (pink) and auxiliary (gray) genes for cranberry (CB), northern highbush blueberry (NHB) and southern highbush blueberry (SHB). We compared (A) gene length (transcription start site to transcription end site), (B) coding sequence length (CDS) length, (C) CDS count, (D) intron length, and (E) fruit transcripts per million (TPM).

Figure 4:. Pangenomic resources available on Genome Database for Vaccinium

All genomic resources developed here are publicly available for the community to use on the Genome Database for Vaccinium (GDV; https://www.vaccinium.org/) (Panel A). A wide variety of tools are available to analyze individual genomes and/or compare genomes (Panel B). A multiple sequence alignment is available to identify structural variants, including deletions (Panel C), single nucleotide polymorphisms (Panel D), and place genetic variants into a phylogenetic context (Panel E). Panel F depicts a pangenome graph view of the multiple sequence alignment.

Figure 5:. Conservation of highbush blueberry-cranberry (BC) core gene content

Panel A depicts the phylogenetic relationships among five Vaccinium species, previously estimated by.Panel B depicts the comparison of the highbush blueberry and cranberry syntenically conserved core genes.