Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance
Sariel Hubner
(1, 2, 3)
,
Natalia Bercovich
(2)
,
Marco Todesco
(2)
,
Jennifer R. Mandel
(4)
,
Jens Odenheimer
(5)
,
Emanuel Ziegler
(5)
,
Joon S. Lee
(2)
,
Gregory J. Baute
(2)
,
Gregory L. Owens
(6, 2)
,
Christopher J. Grassa
(7, 2)
,
Daniel P. Ebert
(8, 2)
,
Katherine L. Ostevik
(9, 2)
,
Brook T. Moyers
(2, 10)
,
Sarah Yakimowski
(2)
,
Rishi R. Masalia
(11, 2)
,
Lexuan Gao
(2)
,
Irina Calic
(11)
,
John E. Bowers
(11)
,
Nolan C. Kane
(2, 12)
,
Dirk Z. H. Swanevelder
(13)
,
Timo Kubach
(5)
,
Stephane Munos
(14)
,
Nicolas Langlade
(14)
,
John M. Burke
(11)
,
Loren H. Rieseberg
(2)
1
MIGAL -
Galilee Research Institute [Israël]
2 Department of Botany and Biodiversity Research Centre
3 Department of Biotechnology
4 Department of Biological Sciences
5 SAP
6 Department of Integrative Biology
7 Herbaria
8 UNE - University of New England
9 Department of Biology
10 CSU - Colorado State University [Fort Collins]
11 Department of Plant Biology, Miller Plant Sciences
12 Faculty of Biology - Department of Ecology and Evolutionary Biology
13 ARC - Agricultural Research Council
14 LIPM - Laboratoire des interactions plantes micro-organismes
2 Department of Botany and Biodiversity Research Centre
3 Department of Biotechnology
4 Department of Biological Sciences
5 SAP
6 Department of Integrative Biology
7 Herbaria
8 UNE - University of New England
9 Department of Biology
10 CSU - Colorado State University [Fort Collins]
11 Department of Plant Biology, Miller Plant Sciences
12 Faculty of Biology - Department of Ecology and Evolutionary Biology
13 ARC - Agricultural Research Council
14 LIPM - Laboratoire des interactions plantes micro-organismes
Stephane Munos
- Fonction : Auteur
- PersonId : 1203158
- IdHAL : stephane-munos
- ORCID : 0000-0003-0261-2759
Nicolas Langlade
- Fonction : Auteur
- PersonId : 737679
- IdHAL : nicolas-langlade
- ORCID : 0000-0002-5651-1446
- IdRef : 188172653
Résumé
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.