Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.

Large insertion in radish GRS1 enhances glucoraphanin content in intergeneric hybrids, Raphanobrassica (Raphanus sativus L. x Brassica oleracea var. acephala)

Glucosinolates (GSLs), precursors of isothiocyanates (ITCs), are present in Brassicaceae plants have been found to have health benefits. Sulforaphane (4-(methylsulfinyl)butyl ITC) is an ITC stored in the form of 4-(methylsulfinyl)butyl GSL (glucoraphanin, 4MSOB) in Brassica vegetables, such as broccoli and kale. Sulforaphane activates Nrf2 expression, a transcription factor responsible for inducing physiological activities such as detoxification in the human body, and it represents a functional component unique to cruciferous vegetables. Raphanobrassica is an inter-generic hybrid between radish and kale, and it contains a high amount of 4MSOB. However, Raphanobrassica contains as much 4-methylsulfinyl-3-butenyl GSL (glucoraphenin, 4MSO3B) as it does 4MSOB. GLUCORAPHASATIN SYNTHASE 1 (GRS1) is an enzyme present in radish that synthesizes 4-methylthio-3-butenyl GSL (glucoraphasatin, 4MT3B), a precursor of 4MSO3B, using 4-(methylthio)butyl GSL (glucoerucin, 4MTB) as a substrate. Since the precursor of 4MSOB is also 4MTB, it was considered that both 4MSOB and 4MSO3B accumulate owing to competition in Raphanobrassica. We hypothesized that owing to the impaired function of GRS1 in Raphanobrassica, it may be possible to breed Raphanobrassica cultivars containing a high 4MSOB content. In this study, we generated Raphanobrassica populations with functional and defective GRS1 and compared the GSL composition in the two populations using high-performance liquid chromatography. The mean 4MSOB content in leaves of the defective-type populations was higher than that in the functional-type population, and the defective/functional ratio ranged from 2.02 to 2.51-fold, supporting this hypothesis. Furthermore, leaves, flower buds, stems, and roots contained higher amounts of 4MSOB in the defective population than in the functional population. The leaf 4MSOB content of defective Raphanobrassica grown in this study was comparable to that of previously studied vegetables (such as broccoli sprouts) with high 4MSOB content. Raphanobrassica with defective GRS1 represents a new leafy vegetable with high 4MSOB content which exhibits anti-cancerous and anti-inflammatory potentials.

Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species

Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.

The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.

QTL Mapping for Seed Germination Response to Drought Stress in Brassica napus

Drought stress is one of the most environmental abiotic stresses affecting seed germination and crop growth. In the present study, the genetic characteristics of seed germination under drought stress in a Brassica napus double haploid population were analyzed. Five germination-related indexes, including germination percentage (GP), root length (RL), shoot length (SL), fresh weight (FW), and root-to-shoot length ratio (R/S) under control and drought stress, were calculated, and the drought stress index (DSI), including DSI-GP, DSI-RL, DSI-SL, DSI-FW, and DSI-R/S, was determined using the quantitative trait loci (QTLs) analysis based on high-density genetic linkage map. The phenotypic analysis indicated that the R/S is an effective morphological trait in the determination of drought tolerance in the seedling stage. Thirty-nine identified QTLs were observed for these traits and then integrated into 36 consensus QTLs, in which 18 QTLs were found to affect the DSI of four traits (GP, RL, SL, and R/S). Based on the co-linearity between genetic and physical maps of B. napus, 256 candidate genes were detected, and 128 genes have single-nucleotidepolymorphisms/insertion-deletion (SNP/InDel) variations between two parents, some of which were associated with the drought stress tolerance (for example, BnaC03g32780D, BnaC03g37030D, and BnaC09g27300D). The present results laid insights into drought tolerance and its genetic bases in B. napus.

Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

Background

Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (A_nA_nC_nC_n) relative to its two diploid progenitors, B. rapa (A_rA_r) and B. oleracea (C_oC_o), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach.

Results

The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (A_nA_nC_nC_n vs A_rA_r and A_nA_nC_nC_n vs C_oC_o), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus.

Conclusions

In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover

The merging of distinct genomes, allopolyploidization, is a widespread phenomenon in plants. It generates adaptive potential through increased genetic diversity, but examples demonstrating its exploitation remain scarce. White clover (Trifolium repens) is a ubiquitous temperate allotetraploid forage crop derived from two European diploid progenitors confined to extreme coastal or alpine habitats. We sequenced and assembled the genomes and transcriptomes of this species complex to gain insight into the genesis of white clover and the consequences of allopolyploidization. Based on these data, we estimate that white clover originated ∼15,000 to 28,000 years ago during the last glaciation when alpine and coastal progenitors were likely colocated in glacial refugia. We found evidence of progenitor diversity carryover through multiple hybridization events and show that the progenitor subgenomes have retained integrity and gene expression activity as they traveled within white clover from their original confined habitats to a global presence. At the transcriptional level, we observed remarkably stable subgenome expression ratios across tissues. Among the few genes that show tissue-specific switching between homeologous gene copies, we found flavonoid biosynthesis genes strongly overrepresented, suggesting an adaptive role of some allopolyploidy-associated transcriptional changes. Our results highlight white clover as an example of allopolyploidy-facilitated niche expansion, where two progenitor genomes, adapted and confined to disparate and highly specialized habitats, expanded to a ubiquitous global presence after glaciation-associated allopolyploidization.

Transcriptional Aneuploidy Responses of Brassica rapa-oleracea Monosomic Alien Addition Lines (MAALs) Derived From Natural Allopolyploid B. napus

Establishing the whole set of aneuploids, for one naturally evolved allopolyploid species, provides a unique opportunity to elucidate the transcriptomic response of the constituent subgenomes to serial aneuploidy. Previously, the whole set of monosomic alien addition lines (MAALs, C1-C9) with each of the nine C subgenome chromosomes, added to the extracted A subgenome, was developed in the context of the allotetraploid Brassica napus donor “Oro,” after the restitution of the ancestral B. rapa (RBR Oro) was realized. Herein, transcriptomic analysis using high-throughput technology was conducted to detect gene expression alterations in these MAALs and RBR. Compared to diploid RBR, the genes of all of the MAALs showed various degrees of dysregulated expressions that resulted from cis effects and more prevailing trans effects. In addition, the trans-effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes, instead of gene numbers of extra chromosomes. A total of 10 trans-effect dysregulated genes, among all pairwise comparisons, were mainly involved in the function of transporter activity. Furthermore, highly expressed genes were more prone to downregulation and vice-versa, suggesting a common trend for transcriptional pattern responses to aneuploidy. These results provided a comprehensive insight of the impact of gene expression of individual chromosomes, in one subgenome, on another intact subgenome for one allopolyploid with a long evolutionary history.

Nonadditive expression of lipid metabolism pathway-related genes in intestine of hybrids of Nile tilapia females (Oreochromis niloticus) and blue tilapia males (Oreochromis aureus)

Nonadditive expression contributes to heterosis in hybrids. In this study, the expression profiles of twelve lipid metabolism pathway-related genes were investigated in the intestine of Nile tilapia (Oreochromis niloticus) ♀ × blue tilapia (Oreochromis aureus) ♂ hybrid. The expression of genes from the hybrid were assigned to nonadditive and additive expression pattern groups and compared with expression patterns from Nile tilapia and blue tilapia. In the intestine of the hybrid, apoA4B was expressed at intermediate levels, but apoB and MTP were assigned to ELD-B and ELD-N categories, respectively. The LPL and LRP1 showed transgressive up-regulation in the hybrid, but LDLR was assigned to the ELD-B category. For fatty acid uptake related genes, only FABP11a was categorized as nonadditive expression with transgressive up-regulation, while CD36 and FABP3 were categorized as additive expression in the intestine of the hybrid. Two genes in triacylglycerol metabolism, namely, FAS and DGAT2, showed transgressive up-regulation in the hybrid. Most of the genes analyzed in the present study showed nonadditive expression (8 in 12), and five genes showed transgressive up-regulation. These results indicated that the stimulation of lipid metabolism in the hybrid compared to that of its parents. The hyperactive expression of these genes in the hybrid may be associated with the growth and lipid usage vigor.

Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

Background

Allopolyploids require rapid genetic and epigenetic modifications to reconcile two or more sets of divergent genomes. To better understand the fate of duplicate genes following genomic mergers and doubling during allopolyploid formation, in this study, we explored the global gene expression patterns in resynthesized allotetraploid Brassica napus (AACC) and its diploid parents B. rapa (AA) and B. oleracea (CC) using RNA sequencing of leaf transcriptomes.

Results

We found that allopolyploid B. napus formation was accompanied by extensive changes (approximately one-third of the expressed genes) in the parental gene expression patterns (‘transcriptome shock’). Interestingly, the majority (85%) of differentially expressed genes (DEGs) were downregulated in the allotetraploid. Moreover, the homoeolog expression bias (relative contribution of homoeologs to the transcriptome) and expression level dominance (total expression level of both homoeologs) were thoroughly investigated by monitoring the expression of 23,766 B. oleracea-B. rapa orthologous gene pairs. Approximately 36.5% of the expressed gene pairs displayed expression bias with a slight preference toward the A-genome. In addition, 39.6, 4.9 and 9.0% of the expressed gene pairs exhibited expression level dominance (ELD), additivity expression and transgressive expression, respectively. The genome-wide ELD was also biased toward the A-genome in the resynthesized B. napus. To explain the ELD phenomenon, we compared the individual homoeolog expression levels relative to those of the diploid parents and found that ELD in the direction of the higher-expression parent can be explained by the downregulation of homoeologs from the dominant parent or upregulation of homoeologs from the nondominant parent; however, ELD in the direction of the lower-expression parent can be explained only by the downregulation of the nondominant parent or both homoeologs. Furthermore, Gene Ontology (GO) enrichment analysis suggested that the alteration in the gene expression patterns could be a prominent cause of the phenotypic variation between the newly formed B. napus and its parental species.

Conclusions

Collectively, our data provide insight into the rapid repatterning of gene expression at the beginning of Brassica allopolyploidization and enhance our knowledge of allopolyploidization processes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4966-5) contains supplementary material, which is available to authorized users.

Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus

Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids S^l S^l AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in S^l S^l AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In S^l S^l AA, there was a tendency for expression dominance of S^l over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in S^l S^l AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable S^l S^l AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.

A comparative study of the seed structure between resynthesized allotetraploid and their diploid parents

Brassicaceae is at the forefront of evolution because of its frequent hybridization. Hybridization is responsible for the induction of widespread genetic and phenotype changes, making it important in agricultural production. In this study, we obtained resynthesized allotetraploid Brassica napus by performing interspecific crossing of B. rapa × B. oleracea combined with embryo rescue. We applied light microscopy and electronic microscopy to analyze the microstructure and ultrastructure of seeds of diploid parents and their allotetraploid progeny. Results showed that pigments in the seed coat were mainly distributed in the palisade layer. B. rapa presented the highest amount of pigment followed by B. napus and B. oleracea. B. napus had the thickest palisade layer followed by B. rapa and B. oleracea. The seed coat microsculpturing in B. rapa and B. napus was characterized as reticulate or reticulate-foveate, whereas that in B. oleracea was observed to be rugose and sulcate. The area index of the protein body was higher in central meristematic cells than in parenchyma cells. By contrast, the area index of the oil body was the lowest in central meristematic cells. Protein bodies were found to be heterogeneous with crystal globoids in two diploid parents and resynthesized allotetraploid progenies. Oil bodies consisted of large and small oil bodies, the sizes of which differed between two parents and allotetraploid progenies. Small oil bodies were spheroid, whereas large oil bodies were ovoid in shape. The quantity of oil bodies indicated that oil bodies were spheroid in two parents, ranging in size from 0.12 to 1.18 μm. In comparison, the size of large oil bodies in allotetraploid progenies exceeds 2.0 μm. These findings suggest that the anatomy of resynthesized allotetraploid seeds remarkably differs from that of two diploid parents, and these differences definitely affect the nutritional components of rapeseeds.

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

Extraction of the Constituent Subgenomes of the Natural Allopolyploid Rapeseed (Brassica napus L.)

As the dynamic nature of progenitor genomes accompanies the speciation by interspecific hybridization, the extraction of the constituent subgenome(s) from a natural allopolyploid species of long history and then restitution of the progenitor(s) provides the unique opportunity to study the genome evolution and interplay. Herein, the A subgenome from the allotetraploid oilseed rape (Brassica napus L., AACC) was extracted through inducing the preferential elimination of C-subgenome chromosomes in intertribal crosses and the progenitor B. rapa was restituted (RBR). Then by crossing and backcrossing RBR with B. napus donor, the C subgenome was in situ dissected by adding each of its nine chromosomes to the extracted A subgenome and establishing the whole set of monosonic alien addition lines (MAALs). RBR from spring-type B. napus genotype "Oro" expressed a phenotype resembling some type of B. rapa never observed before, but showed a winter-type flowering habit. This RBR had weaker growth vigor and suffered more seriously from biotic and abiotic stresses compared with Oro. The phenotypes specific for these MAALs showed the location of the related genes on the particular C-subgenome chromosomes. These MAALs exhibited obviously different frequencies in homeologous pairing and transmission of additional C-subgenome chromosomes, which were associated with the distinct degrees of their relatedness, and even with the possible genetic regulation for meiotic pairing evolved in B. napus Finally, large scaffolds undetermined for sequence assembly of B. napus were anchored to specific C-subgenome chromosomes using MAALs.

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in Brassica napus Synthetic Hybrids and Natural Allotetraploid

The young allotetraploid Brassica napus (2n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2n = 19, AC) between the extracted and extant B. rapa (2n = 20, AA) and the same B. oleracea genotype (2n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa. Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus, despite the increased extent over time.