SNP Diversity, Genome Mapping, and Association Genetics in Sunflower
J.M. Burke1, J.R. Mandel1, J.E. Bowers1, E. Bachlava2, L. Marek3, S. Nambeesan1, C.A. Taylor4, S.
Tang4, L.H. Rieseberg5, and S.J. Knapp2
1
Dept. of Plant Biology, Univ. of Georgia, Athens, GA, USA; 2Monsanto Co., Woodland, CA, USA;
3
Dept. of Agronomy, Iowa State Univ., Ames, IA 50011, USA; 4Monsanto Co., Chesterfield, MO, USA;
5
Dept. of Botany, Univ. of British Columbia, Vancouver, BC, Canada.
• Until recently, a major limitation in the genetic dissection of complex traits and the identification of
beneficial alleles for crop improvement has been the lack of availability of large numbers of genetic
markers that can be assayed in an efficient manner. When combined with rapid advances in nextgeneration sequencing technologies, however, the high levels of single nucleotide polymorphism (SNP)
diversity that are present in most plant species has made possible the development of high-throughput
genotyping platforms. These platforms, which allow for the simultaneous interrogation of thousands of
SNPs from throughout the genome, make possible the rapid development high-density genetic maps and
also enable genome-wide association studies as well as molecular breeding approaches in many taxa.
• We have developed a large-scale SNP genotyping resource for Helianthus annuus (sunflower) and used
it to construct high-density genetic maps of sunflower and two congeners, assay SNP diversity across the
sunflower gene pool, investigate the structure of linkage disequilibrium (LD) across the genome, and to
perform association analyses for a variety of traits. This work involved the development of a reference
transcriptome assembly, the discovery of thousands of SNPs based on extensive re-sequencing data, the
selection of 10,640 SNPs for inclusion on the array, the genotypic of multiple genetic mapping
populations, and the phenotypic/genotypic characterization of our association mapping population.
• Greater than 95% of the successful SNP assays were polymorphic, and over 90% of these assays could
be successfully transferred to related wild species. Our mapping efforts, which were based on the
genotyping of four sunflower genetic mapping populations, resulted in the development of a consensus
genetic map containing ca. 8500 SNPs along with ca. 1500 previously mapped SSRs, for a total of ca. 10k
markers. We have also used the array to construct genetic maps of the silverleaf sunflower (H.
argophyllus) and the Algodones sunflower (H. niveus spp. tephrodes), and to genotype our recently
developed association mapping population, which is includes 288 lines that capture nearly 90% of the
allelic diversity present within the sunflower gene pool.
• A comparison of the silverleaf and Algodones sunflower genetic maps against our consensus sunflower
map resulted in the identification of numerous chromosomal rearrangements, some of which were shared
between silverleaf and Algodones sunflower, while others were species-specific. Analysis of the
genotypic data from our association mapping population revealed some localized islands of elevated LD
within the sunflower genome, though LD was found to decay rapidly across the majority of the genome.
Interestingly, two of these islands co-localized with clusters of previously mapped quantitative trait loci
(QTL) underlying key traits on linkage groups 10 and 16. In terms of our association mapping results, we
identified significant association for a number of traits, including flowering time, seed oil content and
composition, germination/dormancy, and plant architecture. While some of these associations co-localize
with previously identified QTL, others are completely novel.
• Taken together, our genetic mapping results have provided detailed insight into the extent of genomic
rearrangement between sunflower and its wild relatives, as well as a much better understanding of the
genomic regions that will be recalcitrant to the introgression from the wild. At the same time, our LD and
association analyses have revealed the potential for genome-wide association studies in sunflower, with
large numbers of significant associations, many of which were previously unknown, having been
identified within the context of single experiment.
Key words: association mapping, comparative genome mapping, genetic diversity, SNP genotyping