A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources

Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression

Whole genome duplication (WGD) is a powerful evolutionary mechanism in plants. Autopolyploids have been comparatively less studied than allopolyploids, with sexual autopolyploidization receiving even less attention. In this work, we studied the transcriptomes of neotetraploids (2n = 4x = 32) obtained by crossing two diploid (2n = 2x = 16) plants of Medicago sativa that produce a significant percentage of either 2n eggs or pollen. Diploid progeny from the same cross allowed us to separate the transcriptional outcomes of hybridization from those of WGD. This material can help to elucidate events at the base of the domestication of cultivated 4x alfalfa, the world's most important leguminous forage. Three 2x and three 4x progeny plants and 2x parental plants were used for this study. The RNA-seq data revealed that WGD did not dramatically affect the transcription of leaf protein-coding genes. The two parental genotypes did not contribute equally to the progeny transcriptomes, and genome-wide expression level dominance of the male parent was observed. A large majority of the genes whose expression level changed due to WGD presented increased expression, indicating that the 4x state requires the upregulation of approximately 2.66% of the protein-coding genes. Overall, we estimated that 3.63% of the protein-coding genes were transcriptionally affected by WGD and may contribute to the phenotypic novelty of the neotetraploid plants. Pathway analysis suggested that WGD could affect secondary metabolite biosynthesis, which in turn may influence forage quality. We found four times as many transcription factor genes among the polyploidization-affected genes than among those affected only by hybridization. Several of these belong to classes involved in stress response. Small RNA-seq revealed that very few miRNAs were significantly associated with WGD, but they target several hundred genes, and their role in the WGD response may be relevant. Integrated network analysis led to the identification of putative miRNA: mRNA interactions potentially involved in transcriptome reprogramming. Allele-specific expression analysis indicated that parent-of-origin bias was not a significant outcome of WGD, but we found that parentally biased RNA editing may be a significant source of variation in neopolyploids.

RNA-seq analyses on gametogenic tissues of alfalfa (Medicago sativa) revealed plant reproduction- and ploidy-related genes

BACKGROUND

In alfalfa (Medicago sativa), the coexistence of interfertile subspecies (i.e. sativa, falcata and coerulea) characterized by different ploidy levels (diploidy and tetraploidy) and the occurrence of meiotic mutants capable of producing unreduced (2n) gametes, have been efficiently combined for the establishment of new polyploids. The wealth of agronomic data concerning forage quality and yield provides a thorough insight into the practical benefits of polyploidization. However, many of the underlying molecular mechanisms regarding gene expression and regulation remained completely unexplored. In this study, we aimed to address this gap by examining the transcriptome profiles of leaves and reproductive tissues, corresponding to anthers and pistils, sampled at different time points from diploid and tetraploid Medicago sativa individuals belonging to progenies produced by bilateral sexual polyploidization (dBSP and tBSP, respectively) and tetraploid individuals stemmed from unilateral sexual polyploidization (tUSP).

RESULTS

Considering the crucial role played by anthers and pistils in the reduced and unreduced gametes formation, we firstly analyzed the transcriptional profiles of the reproductive tissues at different stages, regardless of the ploidy level and the origin of the samples. By using and combining three different analytical methodologies, namely weighted-gene co-expression network analysis (WGCNA), tau (τ) analysis, and differentially expressed genes (DEGs) analysis, we identified a robust set of genes and transcription factors potentially involved in both male sporogenesis and gametogenesis processes, particularly in crossing-over, callose synthesis, and exine formation. Subsequently, we assessed at the same floral stage, the differences attributable to the ploidy level (tBSP vs. dBSP) or the origin (tBSP vs. tUSP) of the samples, leading to the identification of ploidy and parent-specific genes. In this way, we identified, for example, genes that are specifically upregulated and downregulated in flower buds in the comparison between tBSP and dBSP, which could explain the reduced fertility of the former compared to the latter materials.

CONCLUSIONS

While this study primarily functions as an extensive investigation at the transcriptomic level, the data provided could represent not only a valuable original asset for the scientific community but also a fully exploitable genomic resource for functional analyses in alfalfa.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

Mitotic defects lead to unreduced sperm formation in cdk1-/- mutants

Unreduced gametes, that are important for species evolution and agricultural development, are generally believed to be formed by meiotic defects. However, we found that male diploid loach (Misgurnus anguillicaudatus) could produce not only haploid sperms, but also unreduced sperms, after cyclin-dependent kinase 1 gene (cdk1, one of the most important kinases in regulating cell mitosis) deletion. Observations on synaptonemal complexes of spermatocyte in prophase of meiosis and spermatogonia suggested that the number of chromosomes in some spermatogonia of cdk1^-/- loach doubled, leading to unreduced diploid sperm production. Then, transcriptome analysis revealed aberrant expressions of some cell cycle-related genes (such as ppp1c and gadd45) in spermatogonia of cdk1^-/- loach relative to wild-type loach. An in vitro and in vivo experiment further validated that Cdk1 deletion in diploid loach resulted in mitotic defects, leading to unreduced diploid sperm formation. In addition, we found that cdk1^-/- zebrafish could also produce unreduced diploid sperms. This study provides important information on revealing the molecular mechanisms behind unreduced gamete formation through mitotic defects, and lays the foundation for a novel strategy for fish polyploidy creation by using cdk1 mutants to produce unreduced sperms, which can then be used to obtain polyploidy, proposed to benefit aquaculture.

Asexual reproduction through seeds: the complex case of diplosporous apomixis

Apomixis is considered a potentially revolutionary tool to generate high-quality food at a lower cost and shorter developmental time due to clonal seed production through apomeiosis and parthenogenesis. In the diplosporous type of apomixis, meiotic recombination and reduction are circumvented either by avoiding or failing meiosis or by a mitotic-like division. Here, we review the literature on diplospory, from early cytological studies dating back to the late 19th century to recent genetic findings. We discuss diplosporous developmental mechanisms, including their inheritance. Furthermore, we compare the strategies adopted to isolate the genes controlling diplospory with those to produce mutants forming unreduced gametes. Nowadays, the dramatically improved technologies of long-read sequencing and targeted CRISPR/Cas mutagenesis justify the expectation that natural diplospory genes will soon be identified. Their identification will answer questions such as how the apomictic phenotype can be superimposed upon the sexual pathway and how diplospory genes have evolved. This knowledge will contribute to the application of apomixis in agriculture.

Exploiting Unreduced Gametes for Improving Ornamental Plants

The formation of gametes with somatic chromosome number or unreduced gametes (2n gametes) is an important process involved in the origin of polyploid plants in nature. Unreduced gametes are the result of meiotic mutations occurring during micro- and mega-sporogenesis. 2n gametes have been identified or artificially induced in a large number of plant species. Breeding of plants through 2n gametes can be advantageous because it combines genetic effects of polyploidy with meiotic recombination and sexual hybridization to produce tremendous genetic variation and heterosis. 2n gametes also occur in ornamental plants, but the potential of using 2n gametes in ornamental plant breeding has not been extensively exploited. Ornamental plants are primarily produced for their esthetic appearance and novelty, not for food and yield, and they can be readily propagated through vegetative means. Triploids, tetraploids, and plants with even higher ploidy levels produced through 2n gametes can be propagated through tissue culture to fix their phenotypes, thus leading to the development of new cultivars. In this review article, we intend to discuss the mechanisms underlying the formation of 2n gametes, techniques for 2n gamete identification, methods for enhancing 2n gamete formation, and the current status in the use of 2n gametes for development of novel ornamental plants. We believe that polyploidy breeding through 2n gametes represents a viable way of developing new cultivars, new species, and even new genera of ornamental plants.