The majority of brown algae (Phaeophyta) exhibit an alternation of generations in which either the gametophyte or sporophyte can be the dominant stage. Ectocarpus is a filamentous brown alga that is used as a model organism to study the life cycle and developmental events (Coelho et al., 2012). Life cycle mutants ouroboros (oro) and immediate upright (imm) were identified in Ectocarpus and provide molecular information about life cycle progression in brown algae. Oro acts as a single, recessive Mendelian locus that is unlinked to the locus of imm mutant and is crucial for sporophyte development. ORO is considered to be a master regulator of the gametophyte-to-sporophyte life cycle transition (Coelho et al., 2011), whereas IMM is required to induce the partial conversion of sporophytic to gametophytic generations (Peters et al., 2008). Transcriptome analysis shows that ORO induces the sporophyte developmental program and represses the gametophyte genetic program (Coelho et al., 2011). More recently, SAMSARA (SAM) has been identified as an interacting partner of ORO (Arun et al., 2019). SAM and ORO form a heterodimer that regulates the expression of genes controlling gametophyte to sporophyte generation, mainly associated with functional categories like “Cell wall and extracellular” and “Cellular regulation and signaling” (Arun et al., 2019). This suggests that TALE-HD transcription factors are of ancient origin and function as gene regulators during sporophytic developmental events.

Chlamydomonas reinhardtii, a unicellular green alga generates two types of gametes, plus-gametes and minus-gametes. The fusion of the gametes, the haploid-to-diploid transition, is regulated by many factors, including GAMETE-SPECIFIC MINUS1 (GSM1)/GAMETE-SPECIFIC PLUS1 (GSP1) which form a heterodimeric transcription factor (Table 1).

The plus-gametes express Gsp1 which encodes a BELL-related TALE-HD protein whereas the minus-gametes express Gsm1 encoding a KNOX–related TALE-HD protein (Lee et al., 2008). Interestingly, these proteins are structural and functional homologs to KNOX/BELL homeobox heterodimers which are engaged in the sporophytic, diploid phase in vascular plants (Lee et al., 2008). During nitrogen starvation in Chlamydomonas, the vegetative cells differentiate into plus- and minus-gametes which display SAG1 (sexual agglutination) and SAD1 (sexual adhesion) agglutinins on their flagella membranes, respectively. The agglutinins on their flagella surface cause adhesion between complementary gametes leading to initial recognition events, triggering an intracellular cAMP burst that activates gametolysin, an enzyme that degrades the cell wall to allow membrane fusion between two gametes. This takes place between plus and minus mating loci structures expressing membrane fusion-enabling factors such as FUS1 and HAP2 on the plasma membrane, respectively (Liu et al., 2010). The fus1 gene encodes a glycoprotein that enables fusion and binding to minus-gametes, while HAP2 plays an essential role in the completion of the membrane fusion process. The species-specific adhesion initiates the fusogenic reorganization of HAP2 from a labile form into a stable homotrimeric form. Hydrophobic residues of the HAP2 homotrimer subsequently interact with lipid bilayers and are involved in converting them into a single lipid bilayer as the fusion product. The adhesion thus exhibits two functions: it allows sex cells to recognize each other, and initiates the biochemical conformational changes required to activate the fusion machinery (Zhang et al., 2021). Following cytoplasmic fusion, FUS1 and HAP2 are degraded (Liu et al., 2010), and the two HD proteins GSP1 and GSM1 physically interact to form a heterodimer and translocate from the cytosol to the nucleus, initiating the zygote developmental program (Liu et al., 2010).

The ectopic expression of GSP1 in minus-gametes results in the transcription of certain genes that would otherwise be exclusively transcribed in zygotes. Lee et al. (2008) extended these findings and reported the molecular regulation of haploid-to-diploid transition through the KNOX-TALE genes in Chlamydomonas reinhardtii. Moreover, the ectopic expression of these proteins in vegetative cells is sufficient to activate the zygote development. A broader comparative analysis led to KNOX-TALE genes in land plants being proposed as candidates for the regulation of alternation of generations (Lee et al., 2008).

Bryophytes spend the majority of their life cycle as persistent haploid gametophytes and exhibit only a short-lived diploid sporophyte generation (Cove, 2005; Szövényi et al., 2021). Bryophytes include three lineages, namely hornworts, liverworts, and mosses.

Lycophyta are one of the oldest lineages of extant vascular plants. Similar to other vascular plants lycophytes reproduce by spores and the sporophyte generation is dominant in these plants. Lycophytes consist of three families namely: Lycopodiaceae (club mosses), Isoeteaceae (quillworts) and Selginellaceae. Lycopodiaceae members produce one single type of spores (homosporous), whereas Isoeteaceae and Selginellaceae species are heterosporous and produce megaspores and microspores. The distinct differentiation of male and female sporophytes with largely different sizes and properties in seed plants is considered to be originated in these species, although heterospory is thought to have evolved independently in several plant groups. Living lycophytes represent a sister group to the seed plant clade and diverged from a common ancestor around 420 million years ago. Thus, they are frequently exploited for comparative studies regarding conservative traits and convergent evolution of traits which have evolved independently, such as leaves and roots.

Selaginella is the model genus for detailed studies of these plants. Selaginella is of particular interest as it retained an autonomous but water-dependent gametophyte generation that is typical of all non-seed plants. In contrast to angiosperms, their gametophytes are not buried within maternal tissues of the sporophyte, so it offers a useful experimental system for investigating how the alternation of generations is regulated. Free-living gametophytes also make it a suitable system to study gametogenesis, gamete recognition, fertilization, and early embryonic developments. Identification of genes involved in the ontogeny control and transition in these plants would help to investigate the evolution of genes and their speciation (Banks, 2009).

Compared to the primary expansion of the number of KNOX genes during the evolution from algae to moss, a second expansion occurred during the transition from lycophytes to angiosperms (Gao et al., 2015). While lycophytes contain four KNOX genes, angiosperms contain a much higher number which is also interpreted in the context of the development of complex leaves with many specialized tissues leading to a neofunctionalization of several KNOX gene duplications during angiosperm evolution.

The main functions of meiosis are the reduction of chromosome numbers and recombination which provides genetic variability. However, it also represents a critical stage for the ontogeny switch, representing the sporophyte-to-gametophyte transition (Hafidh and Honys, 2021). Our efforts to understand meiotic gene functions during the transition from the sporophyte cell lineage (the pollen mother cell) to the gametophyte cell lineage (microspore) are still in their infancy. In contrast, the molecular control of tapetum development has been extensively studied. Tapetal cells never change their ontogeny but instead undergo programmed cell death after performing their specific functions (Ma, 2005; Parish and Li, 2010). Unlike the tapetum cells, the scenario is very different for the pollen mother cells, which after the completion of meiosis have to alter their physiology to accommodate the new ontogeny of gametophyte development (Hafidh and Honys, 2021). Extensive chromatin changes are expected during this transition, with genes involved in this phase transition forming the keys to our understanding of the molecular events that govern the two ontogenies (Hafidh and Honys, 2021).

Rice MICROSPORE AND TAPETUM REGULATOR1 (MTR1) is a fascilin glycoprotein that is essential for the development of male gametes (Figure 2). MTR1 is absent in the tapetum but is expressed from early meiotic (stage 7), tetrad (stage 8) stages until microspore development (stage 9; Tan et al., 2012). Interestingly, even though MTR1 is present at the sporophyte stage of wild-type male reproductive cells, mtr1 plants show no defects at the meiotic and tetrad stages, but fail to undergo mitosis 1 and 2 and are, thus, male sterile. The programmed cell death of tapetum cells, which is their final developmental stage in normal pollen development, is delayed in mtr1 mutants resulting in defective sporopollenin deposition which in turn detaches microspores from their tapetal inner surface. This indicates a crosstalk between MTR1 and tapetal cells, which is suggested to involve a secretion of MTR1 during early microspore development regulating tapetum development via interaction with surface proteins. In conclusion, MTR1 serves as a critical signaling protein that coordinates the development of microspore and tapetal cells (Tan et al., 2012; Feng et al., 2013).

Further cases of male sterility were recently observed in crosses made with pigeon pea (Cajanus cajan) with its wild relative Cajanus sericeus (Pazhamala et al., 2020). One of the lines generated was the thermosensitive male sterile line Evs Sel 107 in which pollen mother cells undergo normal meiosis and form normal tetrads, however, microspores fail to separate and eventually die. The male-sterile condition of this mutant could be reversed to fertility by reducing the day temperature below the critical threshold temperature of 24°C. The morphological studies were compared with transcriptomic, proteomic and metabolomic experiments revealing that the male sterility was caused by a perturbation of auxin homeostasis (Pazhamala et al., 2020). Confirmatory, external application of a natural auxin, indole-3-acetic acid (IAA), rescued the sterile phenotype emphasizing the critical role of auxin in gametophyte development.

Further support for the involvement of auxins in pollen development has also been reported in Arabidopsis. Here, the expression of two auxin biosynthetic genes, YUC2 and YUC6, in the sporophytic pollen mother cell was essential for the early stages of pollen development (Yao et al., 2018). yuc2yuc6 is a male sterile double mutant, and the expression of the bacterial auxin biosynthetic gene iaaM under the control of the YUC6 promoter could restore the fertility of yuc2yuc6, indicating that the fertility defects of yuc2yuc6 were caused by partial auxin deficiency during anther development (Cheng et al., 2006). One open question was whether the sporophytic effect comes from the pollen mother cell directly or through the tapetum. To address this question, ectopic production of auxin in the tapetum failed to rescue the sterile phenotype of yuc2yuc6. Whereas, production of auxin in either pollen mother cells or microspores rescued the defects of pollen development in yuc2yuc6 double mutants. This establishes the direct involvement of genetic factors to control the diploid-to-haploid ontogeny switch (Yao et al., 2018).

The important role of auxins in microspore development is further corroborated by several investigations focusing on the characterization of stress-induced microspore embryogenesis (Rodríguez-Sanz et al., 2015; Testillano, 2019). As this process is extremely taxa-specific, understanding the function of auxins during this process will have commercial benefits in accelerating crop breeding and improvement. Taxa-independent establishment of microspore embryogenesis and increased efficiency will improve the production of isogenic doubled haploid lines suitable for breeding purposes (Pérez-Pérez et al., 2019).

In Arabidopsis, CALLOSE DEFECTIVE MICROSPORE1 (CDM1) is another meiotic gene that is essential for the development of microspores (Lu et al., 2014). CDM1 plays an important role in the regulation of callose metabolism which is highly expressed in meiocytes and tapetum and the cdm1 knockout mutant is male sterile and here also the onset of phenotype starts after the tetrad stage.

All these diverse studies as presented in Figure 2 establish the direct involvement of sporophytic genetic factors in controlling the development and transition of the sporophyte-to-gametophyte stage. In Arabidopsis, BELL1 expression is high during female gametophyte development; in bel1, the female gametophyte fails to develop (Ray et al., 1994; Reiser et al., 1995). It is interesting to note that BELL1 expression remains low during pollen developmental stages. It will be worth testing the ectopic overexpression of BELL1 during the pollen developmental stages (Table 2; data obtained from Arabidopsis eFP Browser, Winter et al., 2007).

Genetic control for the haploid-to-diploid switch is not yet thoroughly established. One of the genes that perform this function is SHORT SUSPENSOR (SSP). SSP is an interleukin-1 receptor-associated kinase (IRAK)/Pelle-like kinase gene that is expressed in pollen but remains untranslated until fertilization and thereafter accumulates in the zygote and the endosperm. SSP acts upstream to YODA (YDA) which requires MAPKKK activity for its activation and proper differentiation of the zygote (Lukowitz et al., 2004). SSP protein produced from paternal transcripts upon fertilization triggers zygotic YDA activity (Bayer et al., 2009). This is a classical study to establish how genes expressed in one ontogeny are required to regulate the essential function of another ontogeny.

It is, thus, evident that ORO, SAM, GSM1, GSP1, KNOX2, and BELL1 are molecular regulators that control gametophyte-to-sporophyte phase transitions in Phaeophyta, Chlorophyta, and Bryophyta. However, in angiosperms such studies are still lacking, possibly because, with the increasing occurrence of gene duplications the molecular controls are much more complex. For instance, the number of BELL and KNOX genes is much higher in dicots and monocots compared with those in the non-vascular plants (Horst et al., 2016; Table 3). Accordingly, the identification of individual functions is hampered by difficulties in generating a loss of function mutants. Moreover, based on different interacting partners at different developmental stages, the same protein performs multiple functions at different developmental stages. This makes it a challenge to decipher specific BELL and KNOX genes involved in the transition of ontogeny.