Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

First author: Sariel Hübner; Affiliations: University of British Columbia (不列颠哥伦比亚大学): Vancouver, Canada

Corresponding author: Sariel Hübner

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.

驯化的动物和植物通常对于选择的响应有所差异，但我们对其中所隐藏的遗传多样性还了解甚少。除了驯化和改良瓶颈，栽培种向日葵具有非常高的遗传变异，可能是由于栽培种和近缘野生种的杂交所导致的。为了摸索向日葵中的遗传多样性以及向日葵野生近缘种对于现在栽培种遗传资源的贡献，作者对287个栽培种品系、17个美国地方种以及代表了11个向日葵野生近缘种的189个个体进行了重测序分析。作者将栽培种每个基因型重测序数据未能比对到向日葵参考基因组上的序列进行了从头组装，以获得全部栽培种向日葵的基因库，也就是泛基因组信息。通过对组装的栽培种的基因与野生近缘种的基因进行比较，以确定基因的起源。结果显示，向日葵栽培种泛基因组总共61205个基因，其中27%在不同基因型之间存在变异。大约10%的栽培种泛基因组来自于野生近缘种的渗入，而1.5%的基因来自于基因渗入。GO富集分析进一步的揭示了在基因滲入区域显著富集了与生物抗性相关的一些基因，这与育种实践中所观察到的现象一致。霜霉病抗性相关的等位基因变异分析作为一个鲜明的例子，说明了基因滲入在提升向日葵对某些日益严重的疾病抗性反面发挥重要作用。

通讯：Sariel Hübner (http://www.migal.org.il)

个人简介：2009年，耶路撒冷希伯来大学，硕士；2013年，海法大学，博士。

研究方向：作物栽培种及其野生近缘种适应和驯化的遗传基础。

doi: https://doi.org/10.1038/s41477-018-0329-0

Journal: Nature Plants

Published date: 31 December, 2018