Navigating the Challenges in Apomixis Population Genetics: Insights from Past, Present, and Future Perspectives

Navigating the challenges in apomixis population genetics requires a comprehensive understanding of its unique genetic consequences. This review explores the population genetics of apomixis, comparing sexual and apomictic populations, research challenges, and outlining future directions. Apomictic plants form clonal seeds, and arise from sexual species through hybridization and/or polyploidy. Sexual species generate genetic variation via meiotic recombination, random mating, and gradual accumulation of beneficial mutations. In contrast, apomicts rely on similar mechanisms to generate genetic variation but at a much slower rate, primarily through ´residual´ sexuality. Clonality in apomicts also promotes the accumulation of deleterious mutations. Additionally, recurrent origins of apomicts from sexual progenitors, especially via hybridization contribute to genetic diversity in apomictic populations. These processes, with varying rates of recombination, gene flow, and genotype fixation, lead to distinct genetic structures between sexual and apomictic populations. Reevaluating the evolutionary mechanisms like gene flow, genetic drift, mutation rates, and selection pressures is, therefore, crucial for understanding the processes driving genetic differentiation and genomic structure in apomictic populations. Research on apomixis has advanced from early documentation in the 18th century to modern cytological and genomic approaches. Early theoretical models of apomixis inheritance, adjusted for polyploid and nonsexual populations, provided foundational insights, while recent genome-wide studies have shed light on the genetic basis and evolutionary dynamics of apomixis across taxa. However, significant gaps remain in understanding population-level evolutionary forces shaping apomixis. Future research in comparative genomics of apomictic and sexual relatives will help identify genes and epigenetic marks of adaptive significance. Functional evaluation of genes associated with selective advantages, coupled with specialized bioinformatic tools, will improve our understanding of genotype-phenotype interactions. Integrative approaches combining multi-omics, morphology, and ecological information are key to resolving the population genetic complexities of apomictic taxa and their adaptation and speciation processes. Moreover, machine learning offers promise for analyzing large genomic datasets and uncovering hidden patterns, while interdisciplinary collaborations could translate findings into conservation, agriculture, and biotechnology applications.

解析无融合生殖（apomixis）种群遗传学面临的各类挑战，需全面掌握其独特的遗传效应。本综述围绕无融合生殖的种群遗传学展开，对比了有性与无融合生殖种群的特征，梳理了当前研究面临的挑战，并展望了未来研究方向。无融合生殖植物可产生克隆种子，其起源多为通过杂交和/或多倍化演化自有性物种。有性物种通过减数分裂重组、随机交配以及有益突变的逐步积累来产生遗传变异。与之相对，无融合生殖类群虽依赖类似机制产生遗传变异，但速率极低，主要通过“残留有性”（residual sexuality）实现。无融合生殖类群中的克隆性还会促进有害突变的积累。此外，从有性祖先反复起源的无融合生殖类群，尤其是通过杂交途径起源的类群，可为无融合生殖种群贡献遗传多样性。这些伴随着不同速率的重组、基因流与基因型固定的过程，使得有性与无融合生殖种群呈现出截然不同的遗传结构。因此，重新评估基因流、遗传漂变、突变率与选择压力等进化机制，对于阐明驱动无融合生殖种群遗传分化与基因组结构形成的过程至关重要。无融合生殖研究已从18世纪的早期记录，发展至现代细胞学与基因组学研究手段。早期针对无融合生殖遗传的理论模型（经多倍体与非有性种群场景调整）为该领域提供了基础认知，而近期的全基因组研究则揭示了不同类群中无融合生殖的遗传基础与进化动态。然而，当前对于塑造无融合生殖的种群水平进化力量仍存在诸多认知空白。未来针对无融合生殖类群与其有性近缘物种的比较基因组学研究，将有助于鉴定具有适应意义的基因与表观遗传标记。结合专用生物信息学工具对携带选择优势的相关基因开展功能验证，将深化我们对基因型-表型互作的理解。整合多组学、形态学与生态学信息的综合研究方法，是解析无融合生殖类群的种群遗传复杂性及其适应与物种形成过程的关键。此外，机器学习为分析大规模基因组数据集、挖掘隐藏模式提供了新思路，而跨学科合作则可将研究成果转化为保护生物学、农业与生物技术领域的应用实践。