Hardigan Michael A, Feldmann Mitchell J, Lorant Anne, Bird Kevin A, Famula Randi, Acharya Charlotte, Cole Glenn, Edger Patrick P, Knapp Steven J
Department of Plant Sciences, University of California, Davis, Davis, CA, United States.
Department of Horticulture, Michigan State University, East Lansing, MI, United States.
Front Plant Sci. 2020 Feb 7;10:1789. doi: 10.3389/fpls.2019.01789. eCollection 2019.
Allo-octoploid cultivated strawberry ( × ) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in . subsp. , and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in . × . These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.
异源八倍体栽培草莓（×）起源于多倍体和同倍体杂交、种间杂交谱系的驯化以及过去300年间野生种的持续混合。虽然基因似乎在八倍体祖先之间自由流动，但八倍体物种的基因组结构和多样性仍知之甚少。八倍体基因组的复杂性以及缺乏相关研究，使得早期研究染色体进化、解析亚基因组结构以及建立统一的连锁群命名法的努力受挫。在这里，我们表明八倍体物种含有数百万个亚基因组特异性DNA变异。它们的多样性足以区分重复的（同源和旁系同源）DNA序列，并开发出50K和850K SNP基因分型阵列，其中包含分布在整个八倍体基因组中的共显性、二体SNP标记。对一个种间分离群体进行全基因组鸟枪法基因分型，在凤梨草莓亚种的5521个单倍体区域中产生了190万个遗传定位的亚基因组变异，覆盖3394厘摩；在弗州草莓×凤梨草莓的3179个单倍体区域中产生了160万个遗传定位的亚基因组变异，覆盖2017厘摩。这些研究提供了一个密集的亚基因组特异性DNA标记的基因组框架，用于无缝交叉引用遗传和物理图谱信息，并统一现有的染色体命名法。通过比较基因组学，我们表明地理上不同的野生八倍体有效地二倍体化，几乎完全共线，并与二倍体祖先物种保持强烈的宏观共线性。异源八倍体类群中基因组结构的保存是花园草莓独特历史中的一个关键因素，在那里不受阻碍的基因流动通过种间杂交的重复循环支持了它的起源和驯化。
