About sunflowers

A global oilseed

Sunflower (Helianthus annuus L.) is one of the world’s important oilseed crops, with production valued at ca. $20B/year (source: FAO). Because sunflower is grown widely in developing countries and used primarily for food, it is the only oilseed included in the Global Crop Diversity Trust’s list of 25 priority food security crops (source: Crop Trust). Sunflower is also an important ornamental crop and source of confectionery seeds (the current focus of Canadian production).

Canada is the world’s 13th largest exporter of sunflower, but there is a supply deficit in North America of this healthy vegetable oil. Canadian production is currently limited by salt and flooding (yield loss is 100% when flooding or extreme salt stress occurs). However, where it is grown elsewhere, low nutrients and drought limit its production. With climate change, these environmental factors will become increasingly important.

System-level understanding of stress resistance may facilitate the development of improved varieties that can be grown on marginal farmlands currently unsuitable for crops. Sunflower is ideal for the proposed research because of its diverse extremophile and cross-compatible wild relatives, both of which have marked utility for research and breeding.

Ancient food source

Sunflower was domesticated from the common sunflower (alsoH. annuus) ca. 4,000 years ago in what is now the east-central USA. It is the most economically important member of the genus Helianthus, which includes 49 wild species, all native to North America. Many of the wild species are cross-compatible with the cultivated sunflower, occur in extreme environments including desert sand dunes, salt marshes, serpentine soils, coastal beaches, etc., and therefore represent important reservoirs of valuable resistance alleles. Moreover, the genus as a whole has emerged as a model for evolutionary and ecological analyses, including studies of hybridization, speciation, and adaptation.

  • Seed production valued at $20 billion US
  • Hybrid seed valued at $1 billion US, second only to maize
  • Priority food security crop
  • Production in Canada & worldwide to expand with climate change

Genetic Considerations

Sunflower is amenable to both classical and molecular genetic analyses. Individual plants can readily produce over a thousand seeds with a generation time of 3-5 months, and excellent genomic resources (available from the Sunflower Genome Database) are available to support the proposed project. These resources, developed by the PIs as part of previously funded Genome Canada and NSF Plant Genome projects, include numerous genetic mapping populations, SNP and expression arrays, a sequence-based physical map, ultra-dense genetic maps, an extensive collection of EST/transcriptome and gene space sequencing data, and a high quality reference sequence84-89. The reference genome for sunflower was generated by merging independent assemblies of 454 and Illumina sequence and then further scaffolding of the merged assembly with mate pair libraries and BAC-end sequences at progressively more local scales (using our genetic and physical maps) to reduce the likelihood of mis-assembly. The resulting integrated assembly is similar to the expected genome length (3.64 Gb versus 3.6 Gb expected), with an N50 of 210Kb. The genome includes >98% of CEGMA (Core Eukaryotic Genes Mapping Approach) genes, of which 90% are full length, indicating that the gene space is well covered.

The annotated assembly, which includes 39k strongly supported protein-coding gene models (excluding transposable elements), is displayed in JBrowse and is accompanied by numerous tools for searching, mapping, and functional analyses. In addition to the reference sequence, the Genome Canada project supported the development of high-density genetic maps and draft genome assemblies of two wild species (H. argophyllus andH. petiolaris), as well as the wholegenome shotgun (WGS) sequencing of 486 cultivated and wild sunflower genotypes, including individuals from 13 wildHelianthus species and our full association mapping population (see below). Lastly, it is also worth noting that cultivated sunflower can be transformed withAgrobacterium tumefaciens, making possible the detailed functional characterization of candidate genes. Sunflower germplasm collections comprise 40,000 cultivated and wild accessions globally and have served as the basis for our development of a cultivated sunflower association mapping (SAM) population.

This population is composed of 288 inbred lines that capture ca. 90% of the allelic diversity in the sunflower gene pool. Genotypic characterization of this population using a 10k SNP array85 revealed that linkage disequilibrium (LD; the non-random association of alleles across loci) decays rapidly across much of the genome. Thus, while there are some restricted islands of elevated LD, this population provides us with a powerful tool for investigating the genetic basis of a wide variety of traits in a highly diverse population, and with much higher resolution than typically afforded by traditional genetic map-based approaches. As mentioned above, we recently completed WGS sequencing of this population, which resulted in the discovery of 72 million high quality SNPs. Of these, 4.1 million were retained after removing SNPs with a minor allele frequency of <10% and <30 % missing data. Notably, preliminary analyses of the SAM population using the 4.1 million SNPs have revealed numerous significant genetic associations for a variety of traits relevant to the present proposal, including salt tolerance (measured as Geometric Mean Productivity growth of reproductive biomass across high and low salt concentrations – see Activity 1 in Experimental Approaches), as well as leaf δ13C, leaf N, and leaf mass per area (LMA) measured under optimal conditions (Fig. 2). As we had hoped, in many cases associations can be narrowed down to a single gene (Fig. 2) and can have sizable effects, ranging from 6% PVE for salt tolerance to 30% PVE for LMA.