Genome-wide genotyping-by-sequencing data provide a high-resolution view of wild helianthus diversity, genetic structure, and interspecies gene flow

American Journal of Botany

Volumn 103, Issue 12, 2016, Pages 2170-2177

  Baute, Gregory J ^a   Owens, Gregory L ^a   Bock, Dan G ^a   Rieseberg, Loren H ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b INDIANA UNIVERSITY   (United States)

Author keywords

ABBA BABA; Asteraceae; Crop wild relatives; GBS; Helianthus annuus; Helianthus hybridization; Phylogenetics; Sunflower

Indexed keywords

CULTIVAR; EVOLUTIONARY BIOLOGY; GENE FLOW; GENETIC ANALYSIS; GENETIC STRUCTURE; GENETIC VARIATION; GENOME; GENOTYPE; HERB; HYBRIDIZATION; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; WILD POPULATION;

ASTERACEAE; HELIANTHUS; HELIANTHUS ANNUUS; HELIANTHUS ARGOPHYLLUS; HELIANTHUS BOLANDERI;

ALLELE; BREEDING; DEMOGRAPHY; GENE FLOW; GENE STRUCTURE; GENETIC VARIATION; GENETICS; GENOMICS; GENOTYPE; PHYLOGENY; PLANT GENOME; SUNFLOWER;

ALLELES; BREEDING; DEMOGRAPHY; GENE FLOW; GENETIC STRUCTURES; GENETIC VARIATION; GENOME, PLANT; GENOMICS; GENOTYPE; HELIANTHUS; PHYLOGENY;

EID: 85007072169     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1600295     Document Type: Article

References (48)

1. Barker, M. S., N. C. Kane, M. Matvienko, A. Kozik, R. W. Michelmore, S. J. Knapp, and L. H. Rieseberg. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25: 2445–2455.
2. Baute, G. J., N. C. Kane, C. J. Grassa, Z. Lai, and L. H. Rieseberg. 2015. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytologist 206: 830–838.
3. Bock, D. G., N. C. Kane, D. P. Ebert, and L. H. Rieseberg. 2014. Genome skimming reveals the origin of the Jerusalem artichoke tuber crop species: Neither from Jerusalem nor an artichoke. New Phytologist 201: 1021–1030.
4. Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120.
5. Dorado, O., L. H. Rieseberg, and D. M. Arias. 1992. Chloroplast DNA introgression in southern California sunflowers. Evolution 46: 566–572.
6. Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.
7. Durand, E. Y., N. Patterson, D. Reich, and M. Slatkin. 2011. Testing for ancient admixture between closely related populations. Molecular Biology and Evolution 28: 2239–2252.
8. Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto, E. S. Buckler, and S. E. Mitchell. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6: e19379.
9. Garrison, E., and G. Marth. 2012. Haplotype-based variant detection from short-read sequencing [version 2]. arXiv:1207.3907v2 [q-bio.GN].
10. Goedbloed, D. J., P. van Hooft, H. J. Megens, K. Langenbeck, W. Lutz, R. P. M. A. Crooijmans, S. E. van Wieren, et al. 2013. Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar. BMC Genetics 14: 43.
11. Green, R. E., J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710–722.
12. Hajjar, R., and T. Hodgkin. 2007. The use of wild relatives in crop improvement: A survey of developments over the last 20 years. Euphytica 156: 1–13.
13. Heiser, C. B. 1949. Study in the evolution of the sunflower species Helianthus annuus and H. bolanderi. University of California Publications in Botany 23: 157–196.
14. Heiser, C. B. 1951. Hybridization in the annual sunflowers: Helianthus annuus X H. debilis var. cucumerifolius. Evolution 5: 42–51.
15. Heiser, C. B., D. M. Smith, S. B. Clevenger, and W. C. Martin. 1969. The North American sunflowers (Helianthus). Memoirs of the Torrey Botanical Club 22: 1–218.
16. Huson, D. H. 1998. SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics 14: 68–73.
17. Jansky, S., and A. Hamernik. 2009. The introgression of 2× 1EBN Solanum species into the cultivated potato using Solanum verrucosum as a bridge. Genetic Resources and Crop Evolution 56: 1107–1115.
18. Kane, N. C., J. M. Burke, L. Marek, G. Seiler, F. Vear, G. Baute, S. J. Knapp, et al. 2013. Sunflower genetic, genomic and ecological resources. Molecular Ecology Resources 13: 10–20.
19. Kane, N. C., M. G. King, M. S. Barker, A. Raduski, S. Karrenberg, Y. Yatabe, S. J. Knapp, and L. H. Rieseberg. 2009. Comparative genomic and population genetic analyses indicated highly porous genomes and high levels of gene flow between divergent Helianthus species. Evolution 63: 2061–2075.
20. Korell, M., G. Mösges, and W. Friedt. 1992. Construction of a sunflower pedigree map. Helia 15: 7–16.
21. Kulathinal, R. J., L. S. Stevison, and M. A. F. Noor. 2009. The genomics of speciation in Drosophila: Diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLOS Genetics 5: e1000550.
22. Magnussen, L. S., and T. P. Hauser. 2007. Hybrids between cultivated and wild carrots in natural populations in Denmark. Heredity 99: 185–192.
23. Mandel, J. R., J. M. Dechaine, L. F. Marek, and J. M. Burke. 2011. Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theoretical and Applied Genetics 123: 693–704.
24. Martin, S. H., K. K. Dasmahapatra, N. J. Nadeau, C. Salazar, J. R. Walters, F. Simpson, M. Blaxter, et al. 2013. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research 23: 1817–1828.
25. McCouch, S., G. J. Baute, J. Bradeen, P. Bramel, P. K. Bretting, E. Buckler, J. M. Burke, et al. 2013. Agriculture: Feeding the future. Nature 499: 23–24.
26. Myles, S., A. R. Boyko, C. L. Owens, P. J. Brown, F. Grassi, M. K. Aradhya, B. Prins, et al. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences, USA 108: 3530–3535.
27. Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA 70: 3321–3323.
28. Nguyen, L.-T., H. A. Schmidt, A. von Haeseler, and B. Q. Minh. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268–274.
29. Owens, G. L., G. J. Baute, and L. H. Rieseberg. 2016. Revisiting a classic case of introgression: Hybridization and gene flow in Californian sunflowers. Molecular Ecology 25: 2630–2643.
30. Raduski, A. R., L. H. Rieseberg, and J. L. Strasburg. 2010. Effective population size, gene flow, and species status in a narrow endemic sunflower, Helianthus neglectus, compared to its widespread sister species, H. petiolaris. International Journal of Molecular Sciences 11: 492–506.
31. Rieseberg, L. H. 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211–1216.
32. Rieseberg, L. H., S. J. E. Baird, and A. M. Desrochers. 1998. Patterns of mating in wild sunflower hybrid zones. Evolution 52: 713–726.
33. Rieseberg, L. H., S. Beckstrom-Sternberg, and K. Doan. 1990. Helianthus annuus ssp. texanus has chloroplast DNA and nuclear ribosomal RNA genes of Helianthus debilis ssp. cucumerifolius. Proceedings of the National Academy of Sciences, USA 87: 593–597.
34. Rogers, C. E., T. E. Thompson, and G. J. Seiler. 1982. Sunflower species of the United States. National Sunflower Association, Bismarck, North Dakota, USA.
35. Rosenthal, D. M., A. E. Schwarzbach, L. A. Donovan, O. Raymond, and L. H. Rieseberg. 2002. Phenotypic differentiation between three ancient hybrid taxa and their parental species. International Journal of Plant Sciences 163: 387–398.
36. Scascitelli, M., K. D. Whitney, R. A. Randell, M. King, C. A. Buerkle, and L. H. Rieseberg. 2010. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Molecular Ecology 19: 521–541.
37. Schilling, E. E. 1997. Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data. Theoretical and Applied Genetics 94: 925–933.
38. Schilling, E. E. 2006. Helianthus. In Flora of North America Editorial Committee [eds.], Flora of North America north of Mexico, vol. 21, 141–169. Oxford University Press, New York, New York, USA.
39. Sedlazeck, F. J., P. Rescheneder, and A. von Haeseler. 2013. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29: 2790–2791.
40. Seiler, G. J. 1992. Utilization of wild sunflower species for the improvement of cultivated sunflower. Field Crops Research 30: 195–230.
41. Smith, C. 2015. What the wild things do: The use of crop wild relatives in public international breeding programs and implications for conservation. M.Sc. thesis, University of Waterloo, Waterloo, Ontario, Canada.
42. Stebbins, J., C. J. Winchell, and J. V. H. Constable. 2013. Helianthus winteri (Asteraceae), a new perennial species from the southern Sierra Nevada foothills, California. Aliso 31: 19–23.
43. Stephens, J. D., W. L. Rogers, C. M. Mason, L. A. Donovan, and R. L. Malmberg. 2015. Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment. American Journal of Botany 102: 910–920.
44. Strasburg, J. L., N. C. Kane, A. R. Raduski, A. Bonin, R. Michelmore, and L. H. Rieseberg. 2011. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Molecular Biology and Evolution 28: 1569–1580.
45. Strasburg, J. L., and L. H. Rieseberg. 2008. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris—Large effective population sizes and rates of long-term gene flow. Evolution 62: 1936–1950.
46. Whitney, K. D., R. A. Randell, and L. H. Rieseberg. 2006. Adaptive introgression of herbivore resistance traits in the weedy sunflower Helianthus annuus. American Naturalist 167: 794–807.
47. Whitney, K. D., R. A. Randell, and L. H. Rieseberg. 2010. Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus. New Phytologist 187: 230–239.
48. Zheng, X., D. Levine, J. Shen, S. M. Gogarten, C. Laurie, and B. S. Weir. 2012. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28: 3326–3328.