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.