Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY Evolutionary Applications Pub Date : 2024-10-25 DOI:10.1111/eva.70018
Christina Waesch, Max Pfeifer, Steven Dreissig
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Abstract

Annuality and perenniality represent two different life-history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population-level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low-recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by FST-outlier scans, were located in low-recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when FST outlier scans were performed separately in low- and intermediate-recombining regions, but not in high-recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low-input farming. Although the resolution of our analysis is limited to a broad-scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

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表征一年生黑麦和多年生黑麦之间的基因组分化。
一年生和多年生代表了植物两种不同的生活史策略,分析不同生活史的近缘物种之间的基因组差异有可能确定选择的潜在目标。此外,了解重组模式与自然选择特征之间的相互作用也是进化生物学的一个核心目标,因为重组模式会影响选择的效果,从而影响基因组的进化。在这里,我们的目的是描述杂草一年生黑麦(Secale cereale L.)和野生多年生黑麦(Secale strictum C. Presl)之间基因组分化的特征,并探索选择特征受重组率变化影响的程度。我们利用一年生黑麦和多年生黑麦的种群级序列数据分析了种群结构及其人口历史。根据我们的分析,一年生黑麦和多年生黑麦是在大约 26500 年前(ya)从大约 85000 个个体的祖先种群规模分化而来的。我们分析了遗传多样性和遗传分化的模式,发现高分化区域位于低重组区域,表明存在关联选择。虽然通过 F ST-outlier 扫描发现的所有高分化区域都位于低重组区域,但并非所有染色体都表现出这种趋势。因此,我们进行了基因本体富集分析,结果表明高分化区域包括参与光合作用的基因。在低重组区和中重组区分别进行 F ST 离群扫描时,这种富集得到了证实,而在高重组区则没有,这表明黑麦的局部重组率变化会影响离群扫描。栽培黑麦是一年生作物,但在土壤质量差或低投入耕作的地区,引入多年生作物可能是有利的。虽然我们的分析仅限于大范围的分辨率,但有关一年生黑麦和多年生黑麦之间进化分化的知识可能会支持为种植多年生黑麦而进行的育种工作。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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