When genomes collide: aberrant seed development following maize interploidy crosses

Parental dialectic: Epigenetic conversations in endosperm

Endosperm is a major evolutionary innovation of flowering plants, and its proper development critically impacts seed growth and viability. Epigenetic regulators have a key function in parental control of endosperm development. Notably, epigenetic regulation of parental genome dosage is a major determinant of seed development success, and disruption of this balance can produce inviable seed, as observed in some interploidy and interspecific crosses. These postzygotic reproduction barriers are also a potent driver of speciation. The molecular machinery and regulatory architecture governing endosperm development is proposed to have evolved under parental conflict. In this review, we emphasize parental conflict as a dialectic conflict and discuss recent findings about the epigenetic molecular machinery that mediates parental conflict in the endosperm.

Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.

Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development

BACKGROUND AND AIMS

The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review.

METHODS

Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions.

KEY RESULTS

TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage.

CONCLUSIONS

The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.

Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.

Seed size, endosperm and germination variation in sexual and apomictic Boechera

Asexual reproduction results in offspring that are genetically identical to the mother. Among apomictic plants (reproducing asexually through seeds) many require paternal genetic contribution for proper endosperm development (pseudogamous endosperm). We examined phenotypic diversity in seed traits using a diverse panel of sexual and apomictic accessions from the genus Boechera. While genetic uniformity resulting from asexual reproduction is expected to reduce phenotypic diversity in seeds produced by apomictic individuals, pseudogamous endosperm, variable endosperm ploidy, and the deviations from 2:1 maternal:paternal genome ratio in endosperm can all contribute to increased phenotypic diversity among apomictic offspring. We characterized seed size variation in 64 diploid sexual and apomictic (diploid and triploid) Boechera lineages. In order to find out whether individual seed size was related to endosperm ploidy we performed individual seed measurements (projected area and mass) using the phenoSeeder robot system and flow cytometric seed screen. In order to test whether individual seed size had an effect on resulting fitness we performed a controlled growth experiment and recorded seedling life history traits (germination success, germination timing, and root growth rate). Seeds with triploid embryos were 33% larger than those with diploid embryos, but no average size difference was found between sexual and apomictic groups. We identified a maternal effect whereby chloroplast lineage 2 had 30% larger seeds than lineage 3, despite having broad and mostly overlapping geographic ranges. Apomictic seeds were not more uniform in size than sexual seeds, despite genetic uniformity of the maternal gametophyte in the former. Among specific embryo/endosperm ploidy combinations, seeds with tetraploid (automomous) endosperm were on average smaller, and the proportion of such seeds was highest in apomicts. Larger seeds germinated more quickly than small seeds, and lead to higher rates of root growth in young seedlings. Seed mass is under balancing selection in Boechera, and it is an important predictor of several traits, including germination probability and timing, root growth rates, and developmental abnormalities in apomictic accessions.

Developmental evidence for parental conflict in driving Mimulus species barriers

The endosperm, a tissue that nourishes the embryo in the seeds of flowering plants, is often disrupted in inviable hybrid seeds of closely related species. A key question is whether parental conflict is a major driver of this common form of reproductive isolation. Here, we performed reciprocal crosses between pairs of three monkeyflower species (Mimulus caespitosa, Mimulus tilingii, and Mimulus guttatus). The severity of hybrid seed inviability varies among these crosses, which we inferred to be due to species divergence in effective ploidy. By performing a time series experiment of seed development, we discovered parent-of-origin phenotypes that provide strong evidence for parental conflict in shaping endosperm evolution. We found that the chalazal haustorium, a tissue within the endosperm that is found at the maternal-filial boundary, shows pronounced differences between reciprocal hybrid seeds formed from Mimulus species that differ in effective ploidy. These parent-of-origin effects suggest that the chalazal haustorium might act as a mediator of parental conflict, potentially by controlling sucrose movement from the maternal parent into the endosperm. Our study suggests that parental conflict in the endosperm may function as a driver of speciation by targeting regions and developmental stages critical for resource allocation and thus proper seed development.

Maternal-filial transfer structures in endosperm: A nexus of nutritional dynamics and seed development

Although the ultimate purpose of a seed is the successful establishment of the next generation, seed development involves more than embryo growth. In angiosperms, seed development requires the intimate coordination of three distinct entities - maternal tissue and two offspring, embryo and embryo-nourishing endosperm. Although seeds are cornerstones of many terrestrial ecosystems and human diets, we are only beginning to understand the interactions among seed tissues and the molecular processes and genes that determine them. Recent studies of gene expression and function in distantly related angiosperms, combined with over 100 years of embryological research, have repeatedly highlighted the endosperm associated with maternal-filial boundaries as a central point in seed developmental dynamics. In this review, we highlight evidence that links this zone with nutritional dynamics, developmental signaling, and imprinted gene expression. We suggest that the underappreciated diversity of this specialized endosperm across angiosperms deserves further study from developmental, molecular, and genetic perspectives.

Endosperm-based incompatibilities in hybrid monkeyflowers

Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.

Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance

The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Family plot: the impact of the endosperm and other extra-embryonic seed tissues on angiosperm zygotic embryogenesis

The zygotic embryos of angiosperms develop buried deep within seeds and surrounded by two main extra-embryonic tissues: the maternally derived seed coat tissues and the zygotic endosperm. Generally, these tissues are considered to play an important role in nurturing the developing embryo by acting as conduits for maternally derived nutrients. They are also critical for key seed traits (dormancy establishment and control, longevity, and physical resistance) and thus for seed and seedling survival. However, recent studies have highlighted the fact that extra-embryonic tissues in the seed also physically and metabolically limit embryonic development and that unique mechanisms may have evolved to overcome specific developmental and genetic constraints associated with the seed habit in angiosperms. The aim of this review is to illustrate how these studies have begun to reveal the highly complex physical and physiological relationship between extra-embryonic tissues and the developing embryo. Where possible I focus on Arabidopsis because of space constraints, but other systems will be cited where relevant.

Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation

Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.

Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids

Parental imbalances in the endosperm leading to impaired development and eventual hybrid seed failure are common causes of postzygotic isolation in flowering plants. Endosperm sensitivity to parental dosage is reflected by canonical phenotypes of "parental excess" in reciprocal interploid crosses. Moreover, parental-excess traits are also evident in many homoploid interspecific crosses, potentially reflecting among-lineage variation in "effective ploidy" driven by endosperm properties. However, the genetic basis of effective ploidy is unknown and genome-wide expression perturbations in parental-excess endosperms from homoploid crosses have yet to be reported. The tomato clade (Solanum section Lycopersicon), encompassing closely related diploids with partial-to-complete hybrid seed failure, provides outstanding opportunities to study these issues. Here, we compared replicated endosperm transcriptomes from six crosses within and among three wild tomato lineages. Strikingly, strongly inviable hybrid crosses displayed conspicuous, asymmetric expression perturbations that mirror previously characterized parental-excess phenotypes. Solanum peruvianum, the species inferred to have evolved higher effective ploidy than the other two, drove expression landscape polarization between maternal and paternal roles. This global expression divergence was mirrored in functionally important gene families such as MADS-box transcription factors and E3 ubiquitin ligases, and revealed differences in cell cycle tuning that match phenotypic differences in developing endosperm and mature seed size between reciprocal crosses. Our work starts to uncover the complex interactions between expression divergence, parental conflict, and hybrid seed failure that likely contributed to plant diversity.

A Small RNA Pathway Mediates Allelic Dosage in Endosperm

Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here, we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24-nt small RNAs are reduced in transposable elements and enriched in genes compared with the embryo. We find an inverse relationship between the parent of origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates the transcriptional balance between maternally and paternally inherited genomes in endosperm.

Evidence for parent-of-origin effects and interparental conflict in seeds of an ancient flowering plant lineage

Theoretical and empirical studies have long connected the evolutionary innovation of endosperm, a genetically biparental product of a double fertilization process unique to flowering plants (angiosperms), to conflicting parental interests over offspring provisioning. Yet, none of these studies examined interparental conflict in representatives of any of the most ancient angiosperm lineages. We performed reciprocal interploidy crosses in the water lily Nymphaea thermarum, a member of one of the most ancient angiosperm lineages, Nymphaeales. We find that an excess of paternal genomes is associated with an increase in endosperm growth. By contrast, maternal ploidy negatively influences development or growth of all seed components, regardless of paternal genome dosage. Most relevant to the conflict over distribution of maternal resources, however, is that growth of the perisperm (seed storage tissue derived from the maternal sporophyte, found in all Nymphaeales) is unaffected by paternal genome dosage-ensuring maternal control of maternal resources. We conclude that the evolutionary transfer of embryo-nourishing function from a genetically biparental endosperm to a genetically maternal perisperm can be viewed as an effective maternal strategy to recapture control of resource distribution among progeny, and thus that interparental conflict has influenced the evolution of seed development in this ancient angiosperm lineage.

Parental-genome dosage effects on the transcriptome of F1 hybrid triploid embryos of Arabidopsis thaliana

Genomic imprinting in the seed endosperm could be due to unequal parental-genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental-genome contribution effects, we generated a whole-genome transcriptome dataset of F1 hybrid triploid embryos (as mimics of F1 hybrid triploid endosperm). For the vast majority of genes, the parental contributions to their expression levels in the F1 triploid hybrid embryos follow a biallelic and linear expression pattern. While allele-specific expression (ASE) bias was detected, such effects were predominantly parent-of-origin independent. We demonstrate that genomic imprinting is largely absent from F1 triploid embryos, strongly suggesting that neither triploidy nor unequal parental-genome contribution are key triggers of genomic imprinting in plants. However, extensive parental-genome dosage effects on gene expression were observed between the reciprocal F1 hybrid embryos, particularly for genes involved in defence response and nutrient reservoir activity, potentially leading to the seed size differences between reciprocal triploids. We further determined that unequal parental-genome contribution in F1 triploids can lead to overexpression effects that are parent-of-origin dependent, and which are not observed in diploid or tetraploid embryos in which the parental-genome dosage is balanced. Overall, our study demonstrates that neither triploidy nor unequal parental-genome contribution is sufficient to trigger imprinting in plant tissues, suggesting that genomic imprinting is an intrinsic and unique feature of the triploid seed endosperm.

Polyspermy barriers: a plant perspective

A common denominator of sexual reproduction in many eukaryotic species is the exposure of an egg to excess sperm to maximize the chances of reproductive success. To avoid potential harmful or deleterious consequences of supernumerary sperm fusion to a single female gamete (polyspermy), many eukaryotes, including plants, have evolved barriers preventing polyspermy. Typically, these checkpoints are implemented at different stages in the reproduction process. The virtual absence of unambiguous reports of naturally occurring egg cell polyspermy in flowering plants is likely reflecting the success of this multiphasic strategy and highlights the difficulty to trace this presumably rare event. We here focus on potential polyspermy avoidance mechanisms in plants and discuss them in light of analogous processes in animals.

Epigenetic processes in flowering plant reproduction

Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability. Global changes of DNA methylation, histone modifications, and small RNAs are closely associated with epigenome programming during plant reproduction. Here, we review current knowledge on chromatin changes occurring during sporogenesis and gametogenesis, as well as early seed development in major flowering plant models.

Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe

Based on the biological species concept, two species are considered distinct if reproductive barriers prevent gene flow between them. In Central Europe, the diploid species Arabidopsis lyrata and Arabidopsis arenosa are genetically isolated, thus fitting this concept as "good species." Nonetheless, interspecific gene flow involving their tetraploid forms has been described. The reasons for this ploidy-dependent reproductive isolation remain unknown. Here, we show that hybridization between diploid A. lyrata and A. arenosa causes mainly inviable seed formation, revealing a strong postzygotic reproductive barrier separating these two species. Although viability of hybrid seeds was impaired in both directions of hybridization, the cause for seed arrest differed. Hybridization of A. lyrata seed parents with A. arenosa pollen donors resulted in failure of endosperm cellularization, whereas the endosperm of reciprocal hybrids cellularized precociously. Endosperm cellularization failure in both hybridization directions is likely causal for the embryo arrest. Importantly, natural tetraploid A. lyrata was able to form viable hybrid seeds with diploid and tetraploid A. arenosa, associated with the reestablishment of normal endosperm cellularization. Conversely, the defects of hybrid seeds between tetraploid A. arenosa and diploid A. lyrata were aggravated. According to these results, we hypothesize that a tetraploidization event in A. lyrata allowed the production of viable hybrid seeds with A. arenosa, enabling gene flow between the two species.

Endosperm and Imprinting, Inextricably Linked

Recent developments advance our understanding of imprinted gene expression in plants.

Dynamic transcriptome landscape of maize embryo and endosperm development

Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants.

Dissection of two major components of the post-zygotic hybridization barrier in rice endosperm

A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. In Arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. Therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. However, these two types of hybridization barrier may be initiated by different intrinsic cues: the interspecific cross barrier arises after hybridization of genomes with differences in DNA sequences, while the interploidy cross barrier arises after hybridization of genomes with the same DNA sequences but differences in ploidy levels. In this study, we performed interploidy crosses to identify components of the post-hybridization barrier in the endosperm of rice. We performed an intra-cultivar cross of autotetraploid (4n) × diploid (2n) rice, and found precocious cellularization and a decreased rate of nuclear division in the syncytial endosperm. By contrast, seeds from the reciprocal cross showed delayed cellularization and an increased rate of nuclear division. This differential effect on nuclear division rates contrasts with the outcome of rice interspecific crosses, which were previously shown to have altered timing of cellularization without any change in nuclear division rates. Thus, we propose that the post-zygotic hybridization barrier in rice endosperm has two separable components, namely control of the timing of cellularization and control of the nuclear division rates in the syncytial stage of endosperm development.

Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids

Pollen mRNAs were different in reciprocal F 1 hybrids, which were probably caused by a cytoplasm-nuclear chromosomal genes interaction. We have found reciprocal differences in crossability between F1 hybrids of Solanum tuberosum (T) and a Mexican wild potato species S. demissum (D). When the reciprocal hybrids were crossed as pollen parents with S. demissum, a significantly higher berry-setting rate was obtained in TD compared with DT. In this study, we performed a whole-genome transcript analysis of the pollen mRNA using a high-throughput sequencer. We obtained 12.6 billion bases that were aligned into 13,020 transcripts with 9,366 loci. All possible genetic modes were observed between the parents and their progeny, where over-dominance and under-recessive types were relatively frequent (15.7 and 15.3 %, respectively). We found that 59.1 % of transcripts were more abundant in TD and over fourfold higher transcription levels were found in 66 TD transcripts and three DT transcripts. A higher proportion of over-dominance and a lower proportion of under-recessive transcription types were also observed in TD. The percentage contributions of multiple transcripts at the same locus varied greatly and were transcribed differently between species. In the new allelic combinations created by hybridization, approximately three-fourth of the transcripts had intermediate percentage contributions between the parents but no differential transcription patterns were apparent between the reciprocal hybrids. A broad spectrum of functionally different nuclear genes was over-represented in TD pollen, some of which were directly related to pollen behavior. Since TD and DT pollen had the same composition of nuclear genes, a cytoplasm-nuclear chromosomal genes interaction is suggested for the cause of transcriptional and phenotypic differences between reciprocal hybrids.

Kin conflict in seed development: an interdependent but fractious collective

Seeds are complex structures that unite diploid maternal tissues with filial tissues that may be haploid (gametophyte), diploid (embryo), or triploid (endosperm). Maternal tissues are predicted to favor smaller seeds than are favored by filial tissues, and filial genes of maternal origin are predicted to favor smaller seeds than are favored by filial genes of paternal origin. Consistent with these predictions, seed size is determined by an interplay between growth of maternal integuments, which limits seed size, and of filial endosperm, which promotes larger seeds. Within endosperm, genes of paternal origin favor delayed cellularization of endosperm and larger seeds, whereas genes of maternal origin favor early cellularization and smaller seeds. The ratio of maternal and paternal gene products in endosperm contributes to the failure of crosses between different ploidy levels of the same species and crosses between species. Maternally expressed small-interfering RNAs (siRNAs) are predicted to associate with growth-enhancing genes.

Kin recognition within a seed and the effect of genetic relatedness of an endosperm to its compatriot embryo on maize seed development

As one of two sexual products resulting from double fertilization in angiosperms, the endosperm nourishes its compatriot embryo during seed development and/or germination and ultimately dies. Theoretical studies suggest that the genetic relatedness of an endosperm to its embryo in the same seed might determine the amount of resources ultimately available for the embryo during seed development. We took advantage of the phenomenon of heterofertilization in cultivated maize to empirically test whether genetic relatedness between a triploid embryo-nourishing endosperm and its compatriot diploid embryo impacts the process of resource allocation between these two sexually produced entities. We used genetically distinct maize inbred lines to perform two crossing experiments. Dry weights of dissected embryos and endosperms of mature heterofertilized and adjacent homofertilized kernels were compared. Embryo weight of heterofertilized kernels was significantly less than that of embryos of homofertilized kernels, whereas there was no significant difference in endosperm weight between the two types of kernels. Our results suggest that the degree of genetic relatedness of an endosperm to its compatriot embryo affects seed development and specifically the amount of maternal resources allocated to an endosperm that are eventually turned over to an embryo. The lower the coefficient of relatedness of an endosperm to its compatriot embryo, the smaller the embryo. Thus, the endosperm of a heterofertilized seed appears to behave less cooperatively with respect to resource transfer toward its less closely related embryo compared with the endosperm of a homofertilized seed.

Female gametophyte development and double fertilization in Balsas teosinte, Zea mays subsp. parviglumis (Poaceae)

Over the course of maize evolution, domestication played a major role in the structural transition of the vegetative and reproductive characteristics that distinguish it from its closest wild relative, Zea mays subsp. parviglumis (Balsas teosinte). Little is known, however, about impacts of the domestication process on the cellular features of the female gametophyte and the subsequent reproductive events after fertilization, even though they are essential components of plant sexual reproduction. In this study, we investigated the developmental and cellular features of the Balsas teosinte female gametophyte and early developing seed in order to unravel the key structural and evolutionary transitions of the reproductive process associated with the domestication of the ancestor of maize. Our results show that the female gametophyte of Balsas teosinte is a variation of the Polygonum type with proliferative antipodal cells and is similar to that of maize. The fertilization process of Balsas teosinte also is basically similar to domesticated maize. In contrast to maize, many events associated with the development of the embryo and endosperm appear to be initiated earlier in Balsas teosinte. Our study suggests that the pattern of female gametophyte development with antipodal proliferation is common among species and subspecies of Zea and evolved before maize domestication. In addition, we propose that the relatively longer duration of the free nuclear endosperm phase in maize is correlated with the development of a larger fruit (kernel or caryopsis) and with a bigger endosperm compared with Balsas teosinte.

Reproductive cross-talk: seed development in flowering plants

Flowering plants have evolved to be a predominant life form on earth. A common principle of flowering plants and probably one of the main reasons for their evolutionary success is the rapid development of an embryo next to a supporting tissue called the endosperm. The embryo and the endosperm are protected by surrounding maternal tissues, the integuments, and the trinity of integuments, embryo and endosperm comprise the plant seed. For proper seed development, these three structures have to develop in a highly controlled and co-ordinated manner, representing a paradigm for cell-cell communication during development. Communication pathways between the endosperm and the seed coat are now beginning to be unravelled. Moreover, recently isolated mutants affecting plant reproduction have allowed a genetic dissection of seed development, and revealed that the embryo plays a previously unrecognized yet important role in co-ordinating seed development.

Epigenomic plasticity within populations: its evolutionary significance and potential

Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.

Balance between maternal and paternal alleles sets the timing of resource accumulation in the maize endosperm

Key aspects of seed development in flowering plants are held to be under epigenetic control and to have evolved as a result of conflict between the interests of the male and female gametes (kinship theory). Attempts to identify the genes involved have focused on imprinted sequences, although imprinting is only one mechanism by which male or female parental alleles may be exclusively expressed immediately post-fertilization. We have studied the expression of a subset of endosperm gene classes immediately following interploidy crosses in maize and show that departure from the normal 2 : 1 ratio between female and male genomes exerts a dramatic effect on the timing of expression of some, but not all, genes investigated. Paternal genomic excess prolongs the expression of early genes and delays accumulation of reserves, while maternal genomic excess foreshortens the expression period of early genes and dramatically brings forward endosperm maturation. Our data point to a striking interdependence between the phases of endosperm development, and are consonant with previous work from maize showing progression from cell proliferation to endoreduplication is regulated by the balance between maternal and paternal genomes, and from Arabidopsis suggesting that this 'phasing' is regulated by maternally expressed imprinted genes. Our findings are discussed in context of the kinship theory.