Genome balance and dosage effect drive allopolyploid formation in Brassica

Proportion of parental genomes in hybrids Allium cepa × A. roylei determines which one becomes dominant

Interspecific hybridization leads to complex interactions between the parental genomes, often in the form of genome dominance, where one genome prevails over the other. This phenomenon has been attributed to differential chromosome behavior during meiotic division and may involve either female or male meiosis, or both. In hybrids of Allium cepa × A. roylei, only female meiosis is involved, favoring the transmission of A. roylei chromosomes; male meiosis leads to the development of gametes with equal proportion of parental genomes. Female meiotic drive shifts the genome composition from 8R (A. roylei) + 8C (A. cepa) chromosomes in F1 to 9.3R + 6.7C in F2. In this study of two successive backcross generations with A. cepa (BC1 [first backcross generation] and BC1F1 [progeny after intercross of the first backcross generation]), we observed a change in genome dominance: the A. roylei genome, initially dominant during the meiosis in the F1 hybrids, became submissive in BC1, resulting in a genome composition skewed toward A. cepa. Among 23 BC1 and 236 BC1F1 plants, we observed a significant deviating trend of gradual reduction in A. roylei chromosome representation. The reduction was higher in the lineages with more unequal starting proportion of the parental genomes. This study highlights the dynamic nature of genomic interactions in hybrids and raises questions about the underlying molecular mechanisms driving these changes in dominance, as well as the potential for manipulating these interactions for agricultural benefit. Further exploration of the chromosomal behavior during meiosis across various hybrids will deepen our understanding of non-Mendelian inheritance patterns and their implications in plant breeding.

Karyotype variation patterns and phenotypic responses of hybrid progenies of triploid loquat (Eriobotrya japonica) provide new insight into aneuploid germplasm innovation

The sexual reproduction of triploids induces chromosomal karyotype variations, which are significant for germplasm resource innovation. Most triploid plants are with low fertility. Therefore, triploid offspring karyotypes' variation pattern and phenotypic response remain poorly understood. Here, we employed three diploids with diverse genetic distances as male parents to cross-pollinate the female fertile triploid loquat Q24 to construct three experimental populations. The chromosome numbers of 93.82% of hybrid plants were 34~46 in three hybrid populations. All 168 aneuploids with 160 karyotypes and a small percentage of euploids were detected among 178 hybrids by the improved molecular karyotype analysis method. Further analysis revealed that when being transmitted to offspring, chromosome 5 of Q24 as disomy had the highest frequency (>50%), while chromosome 12 had the lowest frequency (≤30%). The frequency of Q24's chromosomes being transmitted to offspring as disomy was influenced by the gene function on the chromosomes and the number of interchromosome collinear gene links. Whole-genome resequencing showed that the Q24 alleles exhibited segregation distortions in the offspring aneuploid population. Transgenic experiments demonstrated that the EjRUN1 gene, which was on one segregation distortion region of Q24, promoted the seed viability of triploid Arabidopsis. Furthermore, chromosome number, dosage, and male parent genotype affected the aneuploid phenotype. These findings advance the understanding of genome genetic characteristics of triploid loquat, and provide a reference for germplasm innovation of loquat rapidly through triploid sexual reproduction.

Genomic Divergence Shaped the Genetic Regulation of Meiotic Homologous Recombination in Brassica Allopolyploids

The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation of rapeseed (Brassica napus L.) ∼7,500 years ago. Indeed, the presence of the haploid C genome induces supernumerary crossovers between homologous A chromosomes with dramatically reshaped distribution. However, the genetic mechanisms driving this phenomenon and their divergence between nascent and established lineages remain unclear. To address these concerns, we generated hybrids carrying additional C chromosomes derived either from an established lineage of the allotetraploid B. napus or from its diploid progenitor B. oleracea. We then assessed recombination variation across twelve populations by mapping male meiotic crossovers using single nucleotide polymorphism markers evenly distributed across the sequenced A genome. Our findings reveal that the C09 chromosome of B. oleracea is responsible for the formation of additional crossovers near pericentromeric regions. Interestingly, its counterpart from an established lineage of B. napus shows no significant effect on its own, despite having a similar content of meiotic genes. However, we showed that the B. napus C09 chromosome influences crossover formation through inter-chromosomal epistatic interactions with other specific C chromosomes. These results provide new insights into the genetic regulation of homologous recombination in Brassica and emphasize the role of genomic divergence since the formation of the allopolyploid B. napus.

Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated rice Oryza sativa L

Anagenesis accumulates favorable mutations that enable crops to adapt to continually improving artificial production environments, while cladogenesis results in the deposition of beneficial variations across diverse ecotypes. Integrating advantageous genetic variations from diverse evolutionary sources establishes the foundation for the continued genetic improvement of crops. For a long time, rice breeding practices have been guided by the established belief that the Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and subsp. japonica. Integrating elite genetic variants from both subspecies has been a major strategy for genetic improvement. This approach has proven successful through the achievements of temperate japonica breeding programs in China, Japan, and Korea over the past decades. The genetic differentiation within the Asian cultivated rice has been successfully harnessed for heterosis breeding, thereby enhancing rice yield productivity. Genomic investigations have revealed more genetic divergences in the Asian cultivated rice, prompting the proposal of six subgroups within it. This indicates that there is greater potential for uncovering additional genetic divergences and diversity in future breeding practices. Genetic introgression and gene flow among subgroups have led to improvements in agronomic traits within the indica, temperate japonica, and tropical japonica subgroups during the modern rice breeding process. The introgression process has widened the genetic diversity within subgroups and reduced the genetic distance between them, resulting in the creation of new genetic blocks and subpopulations. Artificial introgression has accelerated the evolution process in rice breeding history. Advancements in the study of genetic divergence and diversity in rice offer valuable insights to guide breeding practices. The mini subgroups aus, basmatic, and rayada possess untapped genetic potential but have been poorly studied worldwide; more samples should be further investigated. This information will be invaluable for harnessing these advantageous variations through introgression breeding. Further studying the nature of reproductive barriers among subgroups will enhance our understanding of genetic differentiation, allow us to overcome these barriers and facilitate effective genetic exchange, and even enable us to harness heterosis among subgroups.

Transgressive expression and dosage effect of A09 chromosome genes and their homoeologous genes influence the flowering time of resynthesized allopolyploid Brassica napus

BACKGROUND

The genomes of allopolyploids newly formed through hybridization and polyploidization exhibit substantial changes including those at genetic and epigenetic levels. These alterations may affect their gene expression patterns, leading to nonadditive gene expression. Currently, only a few reports are available on the impact of nonadditive gene expressions on traits.

RESULTS

Using six isogenic resynthesized Brassica napus lines across the first 10 generations, we studied the impact of gene expression patterns on flowering time. The expression levels of a group of genes, located on chromosome A09, were significantly positively correlated with flowering time. According to the expression analysis, the expression levels of the homologous pairs of 139 genes on chromosome A09 were lower in allopolyploids than in their diploid parents, which indicated a phenomenon of transgressive expression. Additionally, independent subgenomic analysis of homoeologous gene pairs on chromosome A09 of the allopolyploids demonstrated that the gene expression levels of B. napus subgenome A (BnA) and subgenome C (BnC) were similar. However, in two aneuploids carrying monosomic or trisomic A09 chromosome, the gene expression levels of BnA were lower or higher than those of BnC, and the corresponding flowering times of these two aneuploids were earlier and later, respectively.

CONCLUSIONS

These findings indicate that changes in gene dosage introduce biases in the expression of homoeologous genes. Moreover, upregulation or downregulation of homoeologous gene expression on a single chromosome partially alters the flowering time of the newly formed allopolyploid B. napus, which is of great significance for horticultural applications and future research on genetic mechanisms.

Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus

Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects of climate change on crop yields, we need to develop varieties that are more tolerant to water-limited conditions. We aimed to determine how diverse crop types (winter/spring oilseed, tuberous, and leafy) of the allopolyploid Brassica napus, a species that contains the economically important rapeseed oilseed crop, respond to prolonged water limitation. We exposed plants to an 80% reduction in water and assessed growth and color on a high-throughput phenotyping system over 4 weeks and ended the experiment with tissue collection for a time course transcriptomic study. We found an overall reduction in growth across cultivars but to varying degrees. Diel transcriptome analyses revealed significant accession-specific changes in time-of-day regulation of photosynthesis, carbohydrate metabolism, and sulfur metabolism. Interestingly, there was extensive variation in which homoeologs from the two parental subgenomes responded to water limitation across crop types that could be due to differences in regulatory regions in these allopolyploid lines. Follow-up experiments on select cultivars confirmed that plants maintained photosynthetic health during the prolonged water limitation while slowing growth. In two cultivars examined, we found significant time of day changes in levels of glucosinolates, sulfur- and nitrogen -rich specialized metabolites, consistent with the diel transcriptomic responses. These results suggest that these lines are adjusting their sulfur and nitrogen stores under water-limited conditions through distinct time of day regulation.

Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation

Interspecific hybridization is a common method in plant breeding to combine traits from different species, resulting in allopolyploidization and significant genetic and epigenetic changes. However, our understanding of genome-wide chromatin and gene expression dynamics during allopolyploidization remains limited. This study generated two Brassica allotriploid hybrids via interspecific hybridization. We observed that accessible chromatin regions (ACRs) and DNA methylation interact to regulates gene expression after interspecific hybridization, ultimately influencing the agronomic traits of the hybrids. In total, 234,649 ACRs were identified in the parental lines and hybrids; the hybridization process induces changes in the distribution and abundance of their accessible chromatin regions, particularly in gene regions and their proximity. Genes associated with proximal ACRs were more highly expressed than those associated with distal and genic ACRs. More than half of novel ACRs drove transgressive gene expression in the hybrids, and the transgressive upregulated genes showed significant enrichment in metal ion binding, especially magnesium ion, calcium ion, and potassium ion binding. We also identified Bna.bZIP11 in the single-parent activation ACR, which binds to BnaA06.UF3GT to promote anthocyanin accumulation in F1 hybrids. DNA methylation plays a role in repressing gene expression, and unmethylated ACRs are more transcriptionally active. Additionally, the A-subgenome ACRs were associated with genome dosage rather than DNA methylation. The interplay among DNA methylation, transposable elements, and sRNA contributes to the dynamic landscape of ACRs during interspecific hybridization, resulting in distinct gene expression patterns on the genome.

Establishment and Characterization of Bisexually Fertile Triploid Dwarf Surf Clam Mulinia lateralis

Triploids are widely used to rapidly achieve genetic improvements of organisms due to their fast growth and enhanced environmental adaptability. Artificially induced triploids are generally considered to be infertile owing to the obvious inhibition of gonadal development. Recently, some fertile individuals with reduced advantages have been found in triploid bivalves, which is a notable deviation from the original intention of artificially inducing triploids. This study utilized dwarf surf clams (Mulinia lateralis), a promising model organism of bivalves, to develop a model for exploring the potential mechanism of triploid reproduction. The results showed that the optimal induction condition for triploid M. lateralis, determined by orthogonal experiments, was 0.5 mg/L cytochalasin B (CB) to inhibit PB2 for 20 min, resulting in a triploidy rate of 95.57% and a hatching rate of 60.25%. By tracking the development of M. lateralis, we found that the induced triploids could develop normally to maturity and exhibited significant growth and survival advantages post-metamorphosis. Although the triploidy rate exhibited a slight decline overtime, it remained high, with a ratio of 90.63% at 120 dpf. Histological observation confirmed that the gonadal development pattern of triploid M. laterali was similar to that of diploids, but it also showed characteristics such as developmental retardation, few mature gametes, and gamete gigantism. The dynamic expression of genes related to gonadal development provided further molecular evidence for this phenomenon. Additionally, 82.6% of triploid M. laterali exhibited normal spawning behavior, produced fewer but larger viable gametes, and could generate offspring with full developmental potential. Flow cytometry analysis revealed that sperm of triploid M. laterali was aneuploid, with a DNA content of about 1.5 times that of diploid sperm, and the ploidy levels of mating offspring were 2N (DD, diploid female × diploid male), 2.5N (DT, diploid female × triploid male), 2.5N (TD, triploid female × diploid male), and 3N (TT, triploid female × triploid male), respectively. Overall, the artificially induced triploid M. laterali has been confirmed to be bisexually fertile, which will provide a unique model for exploring the underlying mechanisms of advantageous trait formation and fertility regulation in triploids, and offer a valuable platform for the study of ploidy control and polyploidization in bivalves. Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary. Yes, i have checked and it is OK.

Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos

Woody bamboos (Bambusoideae) are renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, based on the in vitro system combined with a high-quality reference genome, our study provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboos.

Unambiguous chromosome identification reveals the factors impacting irregular chromosome behaviors in allotriploid AAC Brassica

KEY MESSAGE

The major irregular chromosome pairing and mis-segregation were detected during meiosis through unambiguous chromosome identification and found that allotriploid Brassica can undergo meiosis successfully and produce mostly viable aneuploid gametes. Triploids have played a crucial role in the evolution of species by forming polyploids and facilitating interploidy gene transfer. It is widely accepted that triploids cannot undergo meiosis normally and predominantly produce nonfunctional aneuploid gametes, which restricts their role in species evolution. In this study, we demonstrated that natural and synthetic allotriploid Brassica (AAC), produced by crossing natural and synthetic Brassica napus (AACC) with Brassica rapa (AA), exhibits basically normal chromosome pairing and segregation during meiosis. Homologous A chromosomes paired faithfully and generally segregated equally. Monosomic C chromosomes were largely retained as univalents and randomly entered daughter cells. The primary irregular meiotic behaviors included associations of homoeologs and 45S rDNA loci at diakinesis, as well as homoeologous chromosome replacement and premature sister chromatid separation at anaphase I. Preexisting homoeologous arrangements altered meiotic behaviors in both chromosome irregular pairing and mis-segregation by increasing the formation of A-genomic univalents and A-C bivalents, as well as premature sister chromatid separation and homologous chromosome nondisjunction. Meiotic behaviors depended significantly on the genetic background and heterozygous homoeologous rearrangement. AAC triploids mainly generated aneuploid gametes, most of which were viable. These results demonstrate that allotriploid Brassica containing an intact karyotype can proceed through meiosis successfully, broadening our current understanding of the inheritance and role in species evolution of allotriploid.

Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.

Global analysis of gene expression in response to double trisomy loquat (Eriobotrya japonica)

Aneuploidy generally has severe phenotypic consequences. However, the molecular basis for this has been focused on single chromosomal dosage changes. It is not clear how the karyotype of complex aneuploidies affects gene expression. Here, we identified six different double-trisomy loquat strains from Q24 progenies of triploid loquat. The differences and similarities of the transcriptional responses of different double trisomy loquat strains were studied systematically via RNA-seq. The global modulation of gene expression indicated that both cis and trans-effects coordinately regulated gene expression in aneuploid loquat to some extent, and this coordinated regulation was determined by different gene functional groups. Aneuploidy can induce specific transcriptional responses on loquat chromosomes. The differentially expressed genes exhibited regional gene expression dysregulation domains along chromosomes. Furthermore, Aneuploidy could also promote the expression of genes with moderate and high in loquats. Our results provide new insights into the genome-wide transcriptional effects of karyotypes with complex aneuploidies.

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.

Interspecific transfer of genetic information through polyploid bridges

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

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.

Morphological and genetic evidence suggest gene flow among native and naturalized mint species

PREMISE

Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens.

METHODS

We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments.

RESULTS

The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate.

CONCLUSIONS

Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.

Genome dosage alteration caused by chromosome pyramiding and shuffling effects on karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids

KEY MESSAGE

We developed an array of Zea-Tripsacum tri-hybrid allopolyploids with multiple ploidies. We unveiled that changes in genome dosage due to the chromosomes pyramiding and shuffling of three species effects karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. Polyploidy, or whole genome duplication, has played a major role in evolution and speciation. The genomic consequences of polyploidy have been extensively studied in many plants; however, the extent of chromosomal variation, genome dosage, phenotypic diversity, and heterosis in allopolyploids derived from multiple species remains largely unknown. To address this question, we synthesized an allohexaploid involving Zea mays, Tripsacum dactyloides, and Z. perennis by chromosomal pyramiding. Subsequently, an allooctoploid and an allopentaploid were obtained by hybridization of the allohexaploid with Z. perennis. Moreover, we constructed three populations with different ploidy by chromosomal shuffling (allopentaploid × Z. perennis, allohexaploid × Z. perennis, and allooctoploid × Z. perennis). We have observed 3 types of sexual reproductive modes and 2 types of asexual reproduction modes in the tri-species hybrids, including 2n gamete fusion (2n + n), haploid gamete fusion (n + n), polyspermy fertilization (n + n + n) or 2n gamete fusion (n + 2n), haploid gametophyte apomixis, and asexual reproduction. The tri-hybrids library presents extremely rich karyotype heterogeneity. Chromosomal compensation appears to exist between maize and Z. perennis. A rise in the ploidy of the trihybrids was linked to a higher frequency of chromosomal translocation. Variation in the degree of phenotypic diversity observed in different segregating populations suggested that genome dosage effects phenotypic manifestation. These findings not only broaden our understanding of the mechanisms of polyploid formation and reproductive diversity but also provide a novel insight into genome pyramiding and shuffling driven genome dosage effects and phenotypic diversity.

Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus

KEY MESSAGE

Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.

Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena

BACKGROUND

The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes).

RESULTS

Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa.

CONCLUSIONS

The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.

Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing

BACKGROUND

Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples.

RESULTS

In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data.

CONCLUSIONS

This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.