Xu Jihua, Tanino Karen K, Horner Kyla N, Robinson Stephen J
Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, Canada.
Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan, Canada.
BMC Plant Biol. 2016 Nov 4;16(1):240. doi: 10.1186/s12870-016-0936-8.
Phenotypic variation is determined by a combination of genotype, environment and their interactions. The realization that allelic diversity can be both genetic and epigenetic allows the environmental component to be further separated. Partitioning phenotypic variation observed among inbred lines with an altered epigenome can allow the epigenetic component controlling quantitative traits to be estimated. To assess the contribution of epialleles on phenotypic variation and determine the fidelity with which epialleles are inherited, we have developed a novel hypomethylated population of strawberry (2n = 2x = 14) using 5-azacytidine from which individuals with altered phenotypes can be identified, selected and characterized.
The hypomethylated population was generated using an inbred strawberry population in the F. vesca ssp. vesca accession Hawaii 4. Analysis of whole genome sequence data from control and hypomethylated lines indicate that 5-azacytidine exposure does not increase SNP above background levels. The populations contained only Hawaii 4 alleles, removing introgression of alternate F. vesca alleles as a potential source of variation. Although genome sequencing and genetic marker data are unable to rule out 5-azacytidine induced chromosomal rearrangements as a potential source of the trait variation observed, none were detected in our survey. Quantitative trait variation focusing on flowering time and rosette diameter was scored in control and treated populations where expanded levels of variation were observed among the hypomethylated lines. Methylation sensitive molecular markers indicated that 5-azacytidine induced alterations in DNA methylation patterns and inheritance of methylation patterns were confirmed by bisulfite sequencing of targeted regions. It is possible that methylation polymorphisms might underlie or have induced genetic changes underlying the observable differences in quantitative phenotypes.
This population developed in a uniform genetic background provides a resource for the discovery of new variation controlling quantitative traits. Genome sequence analysis indicates that 5-azacytidine did not induce point mutations and the induced variation is largely restricted to DNA methylation. Using this resource, we have identified new variation and demonstrated the inheritance of both variant trait and methylation patterns. Although direct associations remain to be determined, these data suggest epigenetic variation might be subject to selection.
表型变异由基因型、环境及其相互作用共同决定。等位基因多样性可同时存在遗传和表观遗传的认识，使得环境因素能够进一步细分。对表观基因组改变的近交系间观察到的表型变异进行划分，有助于估计控制数量性状的表观遗传成分。为了评估表观等位基因对表型变异的贡献，并确定表观等位基因遗传的保真度，我们使用5-氮杂胞苷培育了一个新型的草莓低甲基化群体（2n = 2x = 14），从中可以鉴定、选择和表征表型改变的个体。
使用凤梨草莓（F. vesca）亚种凤梨草莓夏威夷4号（F. vesca ssp. vesca accession Hawaii 4）的近交群体培育出了低甲基化群体。对照和低甲基化品系的全基因组序列数据分析表明，5-氮杂胞苷处理并未使单核苷酸多态性（SNP）增加至背景水平以上。这些群体仅包含夏威夷4号等位基因，排除了其他凤梨草莓等位基因渗入作为潜在变异来源的可能性。尽管基因组测序和遗传标记数据无法排除5-氮杂胞苷诱导染色体重排作为观察到的性状变异潜在来源的可能性，但在我们的调查中未检测到此类情况。在对照和处理群体中对开花时间和莲座直径等数量性状变异进行了评分，在低甲基化品系中观察到变异水平有所扩大。甲基化敏感分子标记表明5-氮杂胞苷诱导了DNA甲基化模式的改变，并且通过对靶向区域的亚硫酸氢盐测序证实了甲基化模式的遗传。甲基化多态性可能是数量表型中可观察到差异的基础，或者诱导了潜在的遗传变化。
在统一遗传背景下培育的这个群体为发现控制数量性状的新变异提供了资源。基因组序列分析表明5-氮杂胞苷未诱导点突变，且诱导变异主要局限于DNA甲基化。利用这一资源，我们鉴定出了新变异，并证明了变异性状和甲基化模式的遗传。尽管直接关联仍有待确定，但这些数据表明表观遗传变异可能受到选择。
