Copy Number Variation (CNV) Across the Cultivated Sunflower (Helianthus annuus) Gene Pool

Gene copy number variation (CNV) is hypothesized to drive important phenotypic variation within and between species. Using next generation sequencing technology and variation in depth-of-coverage, we assessed patterns of CNV across the cultivated sunflower (Helianthus annuus) gene pool, including representatives of both heterotic groups as well as both market types (i.e., oil and confectionery). Compared to other crop plants, a high proportion of genes in the sunflower genome exhibit CNV and these genes are distributed evenly across the genome suggesting a genome-wide susceptibility to gene CNV, including presence/absence variation. Analysis of gene ontology information revealed that a wide variety of gene families are affected by CNV, consistent with the view that much of the genome is susceptible to gene gain/loss events. Similar to other studies, we found a number of cases in which genes related to plant defense, disease resistance, and stress-response exhibited CNV. Many of these instances of CNV colocalize with QTL and/or candidate genes for resistance to several important diseases and are in regions of high linkage disequilibrium and elevated F_ST. Taken together, these observations suggest that CNV may have played an important role in the divergence of the sunflower gene pool following domestication and may be related to agriculturally relevant traits.