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Hübner S, Bercovich N, Todesco M, Mandel JR, Odenheimer J, Ziegler E, Lee JS, Baute GJ, Owens GL, Grassa CJ, Ebert DP, Ostevik KL, Moyers BT, Yakimowski S, Masalia RR, Gao L, Ćalić I, Bowers JE, Kane NC, Swanevelder DZH, Kubach T, Muños S, Langlade NB, Burke JM, Rieseberg LH. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nat Plants 2019; 5:54-62. [PMID: 30598532 DOI: 10.1038/s41477-018-0329-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.
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Affiliation(s)
- Sariel Hübner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biotechnology, Tel-Hai Academic College, Upper Galilee, Israel.
- MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | | | | | - Joon S Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregory J Baute
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Christopher J Grassa
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Harvard University Herbaria , Cambridge, MA, USA
| | - Daniel P Ebert
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- The Beef Industry Centre, University of New England, Armidale, New South Wales, Australia
| | - Katherine L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology , Duke University, Durham, NC, USA
| | - Brook T Moyers
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Sarah Yakimowski
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rishi R Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Lexuan Gao
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Irina Ćalić
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - John E Bowers
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Nolan C Kane
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dirk Z H Swanevelder
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, South Africa
| | - Timo Kubach
- SAP SE, Dietmar-Hopp-Allee 16, Walldorf, Germany
| | - Stephane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Bock DG, Kane NC, Ebert DP, Rieseberg LH. Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol 2014; 201:1021-1030. [PMID: 24245977 DOI: 10.1111/nph.12560] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/14/2013] [Indexed: 05/19/2023]
Abstract
The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today. Despite the cultural and economic importance of this tuber crop species, its origin is debated. Competing hypotheses implicate the occurrence of polyploidization with or without hybridization, and list the annual sunflower H. annuus and five distantly related perennial sunflower species as potential parents. Here, we test these scenarios by skimming the genomes of diverse populations of Jerusalem Artichoke and its putative progenitors. We identify relationships among Helianthus taxa using complete plastomes (151 551 bp), partial mitochondrial genomes (196 853 bp) and 35S (8196 bp) and 5S (514 bp) ribosomal DNA. Our results refute the possibility that Jerusalem Artichoke is of H. annuus ancestry. We provide the first genetic evidence that this species originated recursively from perennial sunflowers of central-eastern North America via hybridization between tetraploid Hairy Sunflower and diploid Sawtooth Sunflower.
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Affiliation(s)
- Dan G Bock
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Daniel P Ebert
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biology Department, Indiana University, Bloomington, IN, 47405, USA
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