Origin and evolution of the octoploid strawberry genome

First author: Patrick P. Edger; Affiliations: Michigan State University (密歇根州立大学): East Lansing, USA

Corresponding author: Steven J. Knapp

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.

现代栽培种草莓来自于两个野生八倍体草莓的杂交，这两个野生种均来自于一百万年前四个二倍体祖先合并而成的后代。本文中，作者报道了栽培种八倍体草莓染色体层级的基因组组装结果，揭示了八倍体草莓的起源和演化历程。作者在八倍体草莓中广泛鉴定到了每一个二倍体祖先的近缘基因，结果支持了八倍体草莓起源于北美的假说。作者对八倍体草莓的四套亚基因组进行分析，结果显示其中一套亚基因组占据了主要地位，保留了更多的基因，基因表达丰度更高，并且在同源染色体交换时存在偏性。通路分析显示大多数的代谢和疾病抗性相关基因都是由该亚基因组上的基因所控制的。本文的研究结果将作为未来草莓演化和分子育种研究的有力平台。

通讯：Steven J. Knapp (https://knapp.plantsciences.ucdavis.edu/index.php/steve-knapp-pi/)

个人简介：里诺内华达大学，植物科学学士；里诺内华达大学，植物科学硕士；内布拉斯加州大学，农学和植物育种博士。

研究方向：草莓育种。

doi: https://doi.org/10.1038/s41588-019-0356-4

Journal: Nature Genetics

Published date: February 25, 2019