Introduction

Heterosis is a biological phenomenon in which hybrids have better phenotypic characteristics than their parents do for traits such as biomass production, grain yield, growth rate, and stress resistance1,2,3. Many heterotic crops, such as those of hybrid rice, maize, and many vegetable species, have been developed extensively worldwide. To date, dominance, overdominance, epistasis, and several other theories have been proposed to explain heterosis from multiple genetic perspectives4,5,6. However, these genetic models have not adequately described the molecular basis of heterosis7,8, and why hybrids display superior growth and fertility is still a mystery that awaits further exploration9.

Plant microRNAs (miRNAs) regulate gene expression through epigenetic regulation and posttranscriptional mechanisms10. Most miRNAs cause target gene degradation through the RNA-induced silencing complex effector11. Indeed, expression differences of miRNAs have been identified in many hybrid crops compared with their parental lines1. A recent study showed that the expression level of most miRNA clusters in F1 hybrids of Brassica napus was higher than that of their parents12. In both Arabidopsis and hexaploid wheat hybrids, changes in miRNA expression result in nonadditive expression of target genes, thereby affecting growth, vitality and adaptability13,14. Several miRNAs and their target genes have thus far been found to contribute to leaf development in various plant species, including miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) in Arabidopsis15, miR160-AUXIN RESPONSE FACTOR (ARF) in tomato16, miR319-TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP)17, and miR396-GROWTH REGULATING FACTOR (GRF)18. Nevertheless, the miRNA-pathway networks of leaf development, which contribute to the increased leaf biomass of hybrids, should be further analyzed.

Biomass heterosis is a distinct phenotype in which the production of larger leaves of hybrids is due to the increase in cell number and/or cell size19. For example, leaf heterosis in Arabidopsis hybrids is tightly associated with increased cell number19, and this has also been observed in maize with changes in the auxin response20. In addition, increases in cell size have been found to have a proportional effect on leaf size, meaning that different parental inbred lines can make distinct contributions to heterosis21. Nevertheless, relatively large leaves contribute to hybrids having a higher photosynthesis capacity compared with that of their parents, with more total chlorophyll and higher photosynthesis carbon fixation capacity19,21.

Chinese cabbage (Brassica rapa L. subsp. pekinensis) is a major leafy crop species grown worldwide, F1 hybrids of which have been widely used in production for more than 30 years22. The developmental process is very similar between Chinese cabbage and Arabidopsis except for the leaf heading morphotype, which was domesticated approximately 500 years ago23. Several studies have been performed on Brassica species, including genetic distance, combining ability, and transcriptional and epigenetic analyses12,24,25,26,27,28. In Chinese cabbage and pak choi, the increase in photosynthesis is crucial to the formation of heterosis;25,26,27,28 furthermore, several genes have been identified, including the light-harvesting complex of photosystem II (LHC) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) genes28. However, little is known about its underlying molecular basis. Therefore, to understand the gene regulatory networks underlying leaf development and biomass heterosis in Chinese cabbage, it is important to thoroughly investigate the gene expression changes and posttranscriptional mechanisms that occur during specific developmental stages.

The current study aims to identify heterosis-regulating miRNAs and genes in Chinese cabbage and to verify the target transcripts by transcriptome-based degradome analysis. In this study, we used the F1 hybrid cultivar (F1 hereafter) Xin No. 3, which is one of the most popular varieties planted in China. Due to its high yield and good nutritional properties, Xin No. 3 accounts for 90 and 50% of the autumn planting area in Beijing and North China, respectively29. We found that the expression levels of the majority of miRNA clusters in the F1 hybrid was lower than the MPVs. Furthermore, 1819 target genes were identified via degradome sequencing. Transcriptome analysis revealed that photosynthesis and chlorophyll synthesis hybrid-MPVs of the DEGs were significantly different between the F1 hybrid and its parents, with increased photosynthesis capacity and chlorophyll content. Consequently, BrGRF4.2- and bra-miR396-overexpressing Arabidopsis plants showed significant changes in leaf size. Overall, we report miRNAs and genes that are thought to play a role in heterosis for Chinese cabbage biomass and provide new insight into this complex trait, thereby aiding crop improvement programs.

Results

Hybrids show significant heterosis compared to that of the parents during development

The Chinese cabbage F1 hybrid Xin No. 3, derived from a cross of the inbred lines SD (P1) and JEY (P2), exhibits strong heterosis for biomass during vegetative growth and development (Fig. 1a). The significantly increased biomass of the F1 hybrid was first observed at the seedling stage (S), and it further increased at the early-heading stage (H) (Fig. 1b). We therefore used tissue from plants at two important vegetative stages (S and H) to determine the potential molecular basis underlying heterosis of Chinese cabbage.

Fig. 1: Comparisons of the growth and heterosis of a Chinese cabbage F1 hybrid and its inbred parent lines.
figure 1

a Phenotypes of the F1 hybrid and inbred parent lines at four vegetative growth stages. b Biomass (gross weight) of the F1 hybrid and its parental lines at four stages in the open field. The letters above the bars indicate significant differences at P < 0.05 (Student’s t-test) (Use the same statistical method hereafter). c The MPH and BPH of each trait for Xin No. 3 plants grown both in the open field (left) and in the greenhouse (right) at the S stage (15 days after sowing (DAS)). d The MPH and BPH of each trait for Xin No. 3 plants grown both in the open field (left) and in the greenhouse (right) at the H stage (60 DAS). GW, PH, SLW, LN, LL, and LW represent gross weight, plant height, single-leaf weight, leaf number, leaf length, and leaf width, respectively

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Mid-parent heterosis (MPH) and better-parent heterosis (BPH) were used to evaluate biomass in terms of single-leaf weight, leaf number, leaf length, leaf width, plant height, and gross weight at the S and H stages in both the open field and greenhouse, respectively. The MPH and BPH in the open field were consistent with the values obtained in the greenhouse (Fig. 1c, d). Notably, we found strong positive MPH and BPH for gross weight (90–108% S-MPH, 55–60% S-BPH, 92–96% H-MPH, and 83–85% H-BPH) and single-leaf weight at both growth stages (Fig. 1c, d). In addition, positive MPH and BPH values for leaf length, leaf width, plant height, and leaf number were also observed for Chinese cabbage (Fig. 1c, d). Positive correlations were observed among gross weight, single-leaf weight, leaf width, and leaf length (correlation coefficients r = 0.46–0.94; Supplementary Fig. S1), while negative correlations were observed between leaf number and the other traits (Supplementary Fig. S1). These results indicate that the increased biomass yield observed for the Chinese cabbage F1 hybrid is mainly due to significantly increased leaf weight (a function of increased leaf length and leaf width) rather than leaf number.

Increased numbers of nonadditively repressed miRNAs in the Chinese cabbage F1 hybrid

To characterize the potential roles of different miRNAs during heterosis in Chinese cabbage, we compared the dynamic changes in miRNA expression profiles between the two parents and the resulting hybrid at the S and H stages. A total of 154 known miRNAs among 30 miRNA families were identified in the hybrid and two parental lines. At a significance level of P ≤ 0.05 and a fold-change of ≥1.5, 130 DEMs were identified comparing the three genotypes at the S and H stages. When F1 values were compared with the P1 values, P2 values, and MPVs, 69, 69, and 63 DEMs were identified at the S stage, revealing 101 nonoverlapping DEMs (Fig. 2a). Additionally, 53, 64, and 51 DEMs were identified in the three comparisons at the H stage, revealing 89 DEMs without overlap (Fig. 2a). All DEMs in each comparison between the F1 values, MPVs, and two parental inbred line values are provided in Supplementary Table S1.

Fig. 2: Overview of differentially expressed miRNAs (DEMs) in the F1 hybrid and the mid-parent value (MPV).
figure 2

a Venn diagram analyses of the total numbers of DEMs between F1, P1, and P2 at the S stage (left) and the H stage (right). b Statistics of up- or downregulated MVP-DEMs at the seedling stage (top) and early-heading stage (bottom). c Heatmaps showing relative fold-changes in MVP-DEM expression in the F1 hybrid compared with P1 values, P2 values, and MPVs at the S stage (left) and the H stage (right). The MVP-DEMs detected at both the S and H stages are marked in red

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The miRNAs in the F1 hybrid showing significantly different expression levels compared to the MPVs (P ≤ 0.05 and fold-change ≥1.5) were designated hybrid MPV differentially expressed miRNAs (MVP-DEMs). Since these miRNAs were potentially responsible for generating the heterosis phenotype, MPV-DEMs were subsequently compared between the hybrid and two parental lines. Overall, 63 and 51 MPV-DEMs were identified at the S and H stages, respectively (Fig. 2b). Interestingly, of the 63 S-stage MPV-DEMs, 52 were nonadditively repressed in Xin No. 3, while 11 were nonadditively activated (Fig. 2b, c). Furthermore, we identified 46 nonadditively repressed MPV-DEMs and only five nonadditively activated MPV-DEMs at the H stage (Fig. 2b, c). This suggests that, compared with its parents, the F1 hybrid has more nonadditive miRNAs, most of which were nonadditively repressed. Moreover, 17 MPV-DEMs were identified at both the S and H stages (Fig. 2c).

Low parental ELD of miRNAs in Chinese cabbage

To determine miRNA expression patterns, we classified genes into eight P1-hybrid-P2 (P1-H-P2) expression patterns for the S and H stages (Fig. 3a and Supplementary Table S2), as described by Shen et al. (2017). miRNAs whose expression levels in the F1 were statistically similar to those in the parents were subsequently designated parental ELD miRNAs. Large numbers of ELD miRNAs were revealed at the S (64) and H (86) developmental stages (Supplementary Table S2). Of these ELD miRNAs, most were expressed at levels similar to those of the parent associated with the low values, in which 40 (S) and 72 (H) low-ELD miRNAs were detected. Known miRNAs, such as bra-miR156, bra-miR319, bra-miR391, and bra-miR396, were all low-ELD miRNAs. In addition, three transgressive upregulated miRNAs (bra-miR168b, bra-miR168c, and bra-miR9555a) and one downregulated miRNA (bra-miR168a) were identified at both the S and H stages (Supplementary Table S2).

Fig. 3: Expression patterns of differentially expressed miRNAs (DEMs) in a Chinese cabbage F1 hybrid.
figure 3

miRNAs with similar expression levels in the F1 hybrid and the P1 and P2 parents were designated ELD-P1 and ELD-P2, respectively. a Expression patterns of DEMs at the S stage (top row) and H stage (bottom row). The numbers of DEMs in each of the eight expression types are shown in the figure. b qRT-PCR validation of the expression levels of leaf development-related miRNAs (bra-miR396, bra-miR156a, bra-miR5722, and bra-miR319) in four Chinese cabbage F1 hybrids and their respective parental inbred lines, as well as the MPVs

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To verify the RNA sequencing results and confirm their general heterosis-related expression patterns in Chinese cabbage, we performed qRT-PCR analysis of four different hybrids and their five corresponding parents (two from the SD inbred line and three from the JEY inbred line) with four randomly selected miRNAs (bra-miR156a, bra-miR5722, bra-miR319, and bra-miR396). The results of the qRT-PCR assays showed that the differential expression of the miRNAs was in accordance with the sequencing results (Fig. 3b), indicating that the expression of low-ELD miRNAs might exhibit general dynamic changes in different Chinese cabbage hybrids compared with their parental lines.

Degradome analysis of DEMs and their target mRNAs

To reveal the target genes of the identified heterosis-related miRNAs in Chinese cabbage, we carried out degradome sequencing in this study. In total, 1819 target genes degraded by DEMs were identified (Supplementary Table S3). Based on functional enrichment analysis, the targets of the DEMs described above were significantly enriched in photosynthesis, nitrogen compound metabolic processes, chloroplast organization, and leaf development (Supplementary Fig. S2a). Moreover, 1488 target genes with 1665 target sites of the MPV-DEMs were identified (Supplementary Table S4) and significantly enriched in leaf morphogenesis, signal transduction, leaf shaping, and leaf development (Supplementary Fig. S2b). In addition, we identified 1219 target genes with 1343 target sites of the MPV-DEMs at the S stage and 841 target genes with 898 target sites of the MPV-DEMs at the H stage (Supplementary Table S5). In addition, the targets of low-ELD miRNAs were significantly enriched in genes involved in leaf morphogenesis and leaf shaping (Fig. 4a). These results suggest that DEMs, MPV-DEMs, and low-ELD miRNAs act in concert with each other to regulate the expression of genes involved in photosynthesis and leaf development during heterosis in Chinese cabbage.

Fig. 4: Target (T) plots of miRNAs verified by degradome sequencing and GO enrichment.
figure 4

a GO enrichment of the ELD-DEM target genes showing that ELD-DEMs function in leaf morphogenesis, organ development, and leaf shaping. b The bra-miR396 network and that of its targets. c T-plot showing that bra-miR396-5p cleaves the BrGRF4.2 gene transcript. d T-plot showing that bra-miR396-5p cleaves the BrHEMA1 gene transcript. e T-plot showing that bra-miR5722 cleaves the BrLHCB1.2 gene transcript. f T-plot showing that bra-miR9557 cleaves the BrLHY2 gene transcript. The red dots represent the expected cleavage positions on the target mRNAs

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In the Chinese cabbage degradome results, bra-miR396-5p, a miRNA known to be involved in leaf development, was notably verified to degrade 11 growth-regulating factors (GRFs) and many other functional genes (Fig. 4b and Supplementary Table S3). The degradome T-plot of BrGRF3.1 and BrGRF4.2, which were identified as members of category 030, showed a single clear peak at the degradation site (Fig. 4c and Supplementary Fig. S3). Importantly, the target gene of bra-miR5722 encodes chlorophyll a-b binding protein 1 (BrLHCB1.2) (Fig. 4d), and its homologous genes have previously been shown to play a role in regulating photosynthesis28. Additionally, bra-miR9557-3p was verified to degrade LATE ELONGATED HYPOCOTYL (BrLHY2), which interacts with EE- and CBS domain-containing downstream proteins involved in photosynthesis and starch metabolism (Fig. 4f). The T-plots for the remaining 12 targets of bra-miR396-5p are shown in Supplementary Fig. S3. We subsequently performed qRT-PCR analysis of BrGRF4.2 and BrLHCB1.2 in four different hybrids and their five corresponding parents. The results showed that the expression patterns of the target genes in different hybrid combinations were essentially consistent (Supplementary Fig. S4).

Differentially expressed genes in the F1 hybrid and parental lines

Dynamic changes in the transcriptomes of the F1 hybrid and its inbred parents were investigated by analyzing leaf transcripts at the S and H stages. A total of 3653 and 2146 DEGs were identified by comparing the three accessions at the S and H stages, respectively (Fig. 5a and Supplementary Table S6). At the S and H stages in the hybrid, there were 2197 (1080 up- and 1117 downregulated) and 356 (120 up- and 236 downregulated) genes (Fig. 5b and Supplementary Table S7) whose expression levels differed from the MPVs (MPV-DEGs), representing 1.1–6.7% of the expressed genes; therefore, these genes were considered to be related to heterosis. GO analysis revealed that all MPV-DEGs were enriched in various functional categories, including photosynthesis, cell division, cell proliferation, and response to auxin (Supplementary Fig. S5), suggesting a combined role of each biological pathway in heterosis for Chinese cabbage biomass. However, only 417 DEM target mRNAs were differentially expressed between the two stages, representing 8.53% of the total DEGs (Supplementary Fig. S6). We also found that only 158 and nine MPV-DEGs were targets of MPV-DEMs at the S and H stages, respectively, with 90 and four of them being negatively expressed (Supplementary Table S8).

Fig. 5: Overview of differentially expressed genes in an F1 hybrid and its parents at two developmental stages.
figure 5

a Venn diagram analyses showing the total numbers of DEGs in comparisons between the F1, P1, and P2 at the S stage (top) and H stage (bottom). b Genes whose expression was up- and downregulated at the S stage (top) and the H stage (bottom). c Expression patterns of eight groups of differentially expressed genes in the F1 hybrid and its parents at the S stage (top row) and H stage (bottom row). Genes showing a similar expression level in the F1 hybrid and the P1 and P2 parents were designated ELD-P1 and ELD-P2, respectively. d KEGG enrichment of parental expression level dominance genes

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We then classified the expression of the DEGs into eight patterns (Fig. 5c and Supplementary Table S9), as described above. A total of 2384 ELD genes and 1103 ELD genes were identified at the S and H developmental stages (Supplementary Table S9), respectively. Of the genes found to exhibit ELD, some were expressed at the same level as that in the parent with the highest level of expression (high-parental ELDs; Fig. 5c), while others were expressed at the level of the parent showing the lowest level of expression (low-parental ELDs; Fig. 5c). At the S and H developmental stages, more than 70% (1663/2384) and 83% (915/1,103) of the ELD genes were high-parental ELDs, respectively. Among these genes, only 66 and 21 high-parental ELD genes were negatively correlated with 26 and 15 low-ELD miRNAs, respectively (Supplementary Table S10). KEGG functional analysis of the high-parental ELD genes revealed significant enrichment in various functional categories, including porphyrin and chlorophyll metabolism, photosynthesis—antenna proteins, carbon metabolism, and carbon fixation in photosynthesis organisms (Fig. 5d).

Photosynthesis capacity and chlorophyll content increased in the leaves of the Chinese cabbage F1 hybrid

Transcriptome analysis revealed the photosynthesis genes that are enriched in the Chinese cabbage F1 hybrid. We further analyzed these genes and separated them based on their GO categories. In total, 52 S-MPV genes and eight H-MPV genes involved in photosynthesis-related biosynthesis were identified at the two developmental stages (Fig. 6). At the S stage, there were 37 genes whose expression was upregulated and 15 genes whose expression was downregulated, while three genes whose expression was upregulated and five genes whose expression was downregulated were identified at the H stage. The miRNAs that target these photosynthesis genes were subsequently identified (Supplementary Table S11). Importantly, the expression of BrLHCB1.2, the target of bra-miR5722, was upregulated at both the S and H stages in the hybrid, meaning that the improvement in photosynthesis capacity may contribute to heterosis in Chinese cabbage (Fig. 6a). Furthermore, the expression between the bra-miR5722 and BrLHCB1.2 pairs was negatively correlated (correlation coefficient r = −0.62; Supplementary Fig. S7). To verify our findings, we compared the rate of photosynthesis per unit area between the F1 hybrid and its parents. As expected, the rate of photosynthesis per unit area was higher in the hybrid than in the parents from the seedling stage to the heading stage (Fig. 6b).

Fig. 6: Differentially expressed genes involved in photosynthesis and chlorophyll biosynthesis.
figure 6

a Heatmaps showing relative changes in the expression of the DEGs involved in photosynthesis in F1, P1, and P2. b Photosynthesis rates of the F1 hybrid and its representative parental lines (P1 and P2) at five stages of Chinese cabbage development. Significant differences between the hybrids and P2 were calculated using Student’s t-test; **P < 0.01. c Heatmaps showing the fold-changes in the expression of genes involved in the tetrapyrrole and chlorophyllide biosynthesis pathways in the F1 hybrid, P1 and P2 at the S stage and H stage. Genes in the F1 hybrid whose expression was upregulated compared with that in the parental lines are shown in red. The expression levels were verified via qRT-PCR. d Chlorophyll contents of the Chinese cabbage F1 hybrid and the parental lines at the S stage (left) and H stage (right)

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Increased chlorophyll content can result in increased photosynthesis21. In this study, we identified 27 Arabidopsis orthologous genes involved in tetrapyrrole and chlorophyll biosynthesis based on previous research21 and analyzed their transcript levels at both the S and H stages. We identified seven MPV genes and one MPV gene whose expression was upregulated and downregulated, respectively, at the S stage of the F1 hybrid (Fig. 6c), while no MPV genes were found at the H stage. However, the FPKM values showed that the expression of several genes was upregulated, even if the levels did not reach the MPV criterion (Fig. 6c). The miRNAs for these chlorophyll genes were subsequently identified (Fig. 6c). We also measured the chlorophyll content per gram of fresh weight in the F1 hybrid and the parents at the S and H stages (Fig. 6d) and found that the total chlorophyll content was greater in the hybrid than in the parents (Fig. 6d). These findings indicate that the higher chlorophyll content in the hybrid compared with its parents leads to increased biomass of the hybrid.

Expression of genes controlling leaf size differs in the Chinese cabbage F1 hybrid

At the seedling stage (30 DAS), the leaf area was significantly larger for the Chinese cabbage F1 hybrid than for the parents due to increases in both leaf length and width (Fig. 7a, b), with strong positive MPH and BPH values (158% and 99.1%, respectively). The contribution of cell number and cell size in the larger leaves of the hybrid was therefore examined via electron microscopy (Fig. 7e). We counted the number and measured the size of epidermal cells at 600× magnification in the F1 hybrid and its parents and found that the cell number and size in the hybrid were intermediate between those of the two parents (Fig. 7c, b). These data indicate that the larger leaves of the hybrid are mainly caused by an increase in total cell number of the leaves.

Fig. 7: Comparisons of leaf size and expression levels of 19 genes involved in regulating leaf size.
figure 7

a Leaves of the Chinese cabbage F1 hybrid and its parental lines at 30 DAS. b Leaf area, c number of cells per leaflet (600x), and d cell size in the F1 hybrid and parental lines (P1 and P2). e Microscopy images of leaf cells from P1, P2 and F1 at 600x magnification. f Heatmaps showing the relative expression of 19 genes from five broad functional categories in P1, P2, and F1, as well as the MPVs

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Thus, we identified 112 homologs of 71 Arabidopsis genes31,32 involved in transcription, hormone regulation, and cell modification and then checked their expression levels in the F1 hybrid. Of these 112 genes, 19 were differentially expressed at the S or H stages (Fig. 7f). For most of these 19 genes, which are involved in several different regulatory networks, the changes in expression required to produce a larger leaf matched those observed in the F1 hybrid. The expression of BrLHY1 and the circadian gene BrCCA1, the levels of which were below the MPV in all the hybrids, resulted in upregulated expression of downstream genes containing EE and CBS domains and involved in photosynthesis and carbohydrate metabolism, thereby increasing chlorophyll synthesis and starch metabolism33. The expression level of BrARF2, a repressor of cell division and leaf growth, was downregulated compared with the MPV at the seedling stages, while it showed an expression level similar to the MPV at the H stage (Fig. 7f). Furthermore, the expression level of BrGRF4.2, a positive regulator of both cell proliferation and cell enlargement, was upregulated in the hybrid compared with the MPV (Fig. 7f). However, the relative expression of several genes was opposite the phenotype or showed different patterns at different stages, indicating that increases in leaf size are regulated by multiple genetic pathways.

Overexpression of bra-miR396 and BrGRF4.2 affects leaf development

To further understand the function of the miR396 and GRF regulatory mechanisms in Chinese cabbage, we constructed bra-miR396 and BrGRF4.2 overexpression vectors driven by an enhanced CaMV 35S promoter, after which the vectors were transformed into Arabidopsis. Compared with those of the wild-type (WT) control lines, the leaves of transgenic plants overexpressing BrGRF4.2 were significantly enlarged, while bra-miR396-overexpressing plants had notably smaller leaves at 25 DAS (Fig. 8a). In general, the width and length of the 35::BrGRF4.2 plant leaves increased by approximately 28 and 27% (Fig. 8b, c), respectively, and the leaf weight and plant fresh weight were nearly 39 and 32% greater, respectively, than those of WT plants (Fig. 8d, e). In addition, the width and length of the leaves were reduced by approximately 20 and 10% (Fig. 8b, c), respectively, in 35S::bra-miR396 plants, and the leaf weight and the plant fresh weight were reduced by nearly 23 and 33%, respectively, compared with those of the WT plants (Fig. 8d, e). However, leaf numbers were not significantly different in the two transgenic lines compared to the control (Fig. 8f).

Fig. 8: Phenotypes of transgenic Arabidopsis plants and effects of heterosis-related miRNAs in regulating leaf development.
figure 8

a Phenotypes of 25-day-old WT, 35::BrGRF4.2, and 35S::bra-miR396 transgenic plants grown under 16 h light/8 h dark conditions. b–f Statistics of leaf length (b), leaf width (c), fresh weight (d), leaf weight (e), and leaf number (f). g Proposed model for the role of heterosis-related miRNAs in the regulation of leaf development in F1 hybrid Chinese cabbage

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Discussion

Chinese cabbage as a model vegetable species for studies on biomass heterosis

Heterosis is a persistent mystery in biology and has been recognized for centuries34. Modern technologies, such as genomics and transcriptomics, are now used to identify heterosis-related genes that lead to increased crop yields, but the findings have been inconsistent. Since heterosis is a quantitative trait affected by multiple aspects, genomic analysis alone is not enough9. Researchers have focused on traits such as grain and fruit yield to interpret the possible molecular mechanisms for heterosis in crop species such as rice35,36, maize37,38, wheat14,39, rapeseed12, and tomato40. Indeed, biomass heterosis has been extensively studied in Arabidopsis13,41, whereas few studies of biomass heterosis have been conducted in vegetable crop species.

Chinese cabbage varieties have superior biomass yields compared with that of their progenitors. At present, the genetic basis of heterosis for Chinese cabbage biomass is still unclear, although F1 hybrids have been widely used in commercial production for more than 30 years22. To date, only a few studies have focused on the potential mechanisms underlying heterosis for Chinese cabbage biomass, and the role of different traits in biomass heterosis is still unclear. In this study, we confirmed the significant contributions of leaf weight, leaf width, and leaf length to biomass heterosis. The increased biomass of the F1 was not the result of increased leaf number, because the leaf number of the F1 plants was found to be similar to that of the two parents. However, leaf weight is a complex quantitative trait influenced by leaf blade weight, petiole weight, leaf size, and leaf thickness42, and more-detailed studies are needed.

miRNAs are important regulators of heterosis for Chinese cabbage biomass

miRNAs involved in plant growth and vigor are known to be differentially regulated in hybrids relative to their parents, affecting the expression patterns of respective targets during metabolism1. In Arabidopsis, wheat, and B. napus hybrids, a large number of well-known miRNAs are nonadditively expressed, leading to nonadditive expression of their targets, which can affect growth12,13,14. The observation that some miRNAs also exhibit nonadditive expression during the seedling and early-heading stages indicated that the heterosis expression patterns of miRNAs are similar in different species. Furthermore, the expression of a large proportion of nonadditively expressed miRNAs was found to be repressed in Chinese cabbage F1 hybrids, while only 79 and four upregulated targets were identified (Supplementary Table S8). This is consistent with what has been reported in strawberry and B. napus studies12,43, demonstrating that the expression of target mRNAs may also be modulated by other regulators or methylation-type modifications.

Leaf development involves the complex regulation of different miRNA pathways that cooperate with each other to form a multilayer network. Our degradome data also show that the targets of the DEMs in this study are enriched in leaf morphogenesis and leaf shaping. During leaf development in Arabidopsis, miR396 expression increases, while that of the target gene GRF decreases, acting as an important indicator of leaf size44. Previous studies have shown that miR156, miR164, and miR319 also act as key regulators of leaf development15,17 by targeting multiple SPL, CUC, and TCP genes, respectively. However, we did not detect the expected SPL, CUC, and TCP genes in our degradome data. It is therefore possible that the miR396-GRF pathway is significantly associated with leaf size heterosis in B. rapa hybrids.

Leaf morphogenesis is modulated by GRF genes, which play a role in cell division and expansion. Overexpression of GRF1/2/3 resulted in larger leaves, while loss-of-function mutants had smaller leaves44. It has been shown that GRF interacting factor 1 (GIF1) interacts with GRF proteins to maintain cell proliferation in vegetative and primordial reproductive organs45. The B. rapa homologs of AtGRF4 and AtGIF2 were found to be nonadditively expressed in the F1, suggesting that the miR396-GRF pathway is conserved and potentially involved in heterosis for biomass during leaf development. Consequently, our bra-miR396 and BrGRF4.2 overexpression results also revealed functions similar to those of the Arabidopsis genes during leaf development.

Multiple metabolic pathways are associated with heterosis of Chinese cabbage

The larger leaves of the F1 hybrids lead to increased photosynthesis and energy production, both of which have important effects on hybrid growth and yield21,26,27,28. This is obvious in hybrids of Arabidopsis, Chinese cabbage, and pak choi, where the greater capacity for photosynthesis increases under high light21,26,27,28. Furthermore, previous reports have shown that the DEGs were enriched in the photosynthesis, thylakoid, chloroplast, and hormone categories26,28. This coincides with our observations in B. rapa that the photosynthesis rate and chlorophyll content of the F1 hybrid increased due to transcriptional and posttranscriptional factors. Increased expression of the chlorophyll gene LHCB is associated with larger cells and an increased number of granum thylakoids28, while damage to chloroplasts treated with norflurazon leads to a decrease in cell size46. One B. rapa homolog of AtLHCB was found to be nonadditively upregulated in the F1, and this gene is the target of the nonadditively repressed bra-miR5722 (Fig. 8g and Supplementary Fig. S7), which may provide new insight into the regulation of BrLHCB.

Changes in the circadian rhythm have been shown to provide the energy production needed to support increased hybrid growth19,33. The circadian rhythm regulates many key processes, including photosynthesis and nighttime starch use, and its oscillation patterns are different between parents, with changes in these patterns affecting the formation of heterosis33. At both the S and H stages of the hybrid, we found that key circadian clock regulatory genes show patterns and levels of expression that differ from those of the parents in the daytime. Although we did not have nighttime transcription data, daytime changes in the expression of circadian clock genes in Arabidopsis F1 hybrids and allopolyploids were similar to those in the Chinese cabbage hybrid. The circadian clock is under miRNA control12,33, suggesting that these circadian regulators may be caused by posttranscriptional changes in hybrids.

Conclusion

In conclusion, our study revealed the importance of combining miRNA data and transcriptome analysis data to determine the comprehensive factors related to heterosis for biomass. We identified several miRNAs in the F1 hybrids that play important roles in regulating target genes associated with photosynthesis, leaf development, and plant growth. Taken together, the results provide new insight into the key regulatory networks and genes related to leaf development during heterosis of Chinese cabbage.

Materials and Methods

Plant materials and phenotyping

For the heterosis study, we used two inbred parental lines, SD (P1), JEY (P2), and their F1 hybrid (Xin No. 3). The first leaf (counted from the edge) at the seedling stage (15 DAS) and the fifth leaf (from the edge) at the early-heading stage (60 DAS) were used in all experiments. Total DNA and RNA samples were extracted from three replicates.

The phenotypes were evaluated during the day at two locations (field and greenhouse) (three replicates each) in 2018. Whole-plant gross weight (GW), single-leaf weight (SLW), leaf number (LN), leaf length (LL), leaf width (LW), and plant height (PH) were measured at 15 and 60 DAS, respectively. The fifth outside leaf was chosen for measurements in our study. Five plants were measured for each genotype. The BPH was calculated as BPH = (F1 – BP)/BP, where F1 is the hybrid and BP is the better-performing parental line. MPH was calculated using the equation MPH = (F1 – MP)/MP, where F1 is the hybrid and MP is the mean of the two parental lines.

Small RNA (sRNA) library construction and sequencing

sRNA libraries were constructed from the Chinese cabbage F1 hybrid Xin No. 3 and its parental lines SD and JEY. A total of 18 leaf samples (3 materials x 2 growth stages x 3 biological replicates) were prepared for sRNA analysis using a TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA), as directed by the manufacturer. The RNA concentration was measured using a NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Single-end sequencing (50 bp) was then conducted on a BGISEQ-500 platform (BGI, Wuhan, China).

Identification of Chinese cabbage miRNAs via deep RNA sequencing

The raw deep-sequencing data were preprocessed to eliminate low-quality tags, yielding sRNA tags. The clean sRNA reads were then aligned to the GenBank and Rfam 12.2 (http://rfam.xfam.org/) databases using BLAST searches and bowtie47 to screen and remove sequences associated with other types of small RNAs (rRNA, scRNA, snoRNA, snRNA, and tRNA). The remaining sRNAs mapped to the B. rapa reference genome (V3.0) were used as search queries against the miRBase 21.0 database (http://www.mirbase.org/) to identify known miRNAs. Novel miRNAs were predicted using MIREAP software (http://sourceforge.net/projects/mireap/). Levels of miRNA expression were calculated using the transcripts per kilobase million (TPM) method. The R package DESeq248 was used to identify DEMs by the use of negative binomial generalized linear models. For each conserved miRNA, MPVs were calculated based on comparable expression levels. miRNAs whose expression level in the F1 hybrid differed from the MPVs were then selected as candidate heterosis-related miRNAs.

Degradome library construction, sequencing, and data processing

In accordance with the research of German et al.49, a degradome library was constructed using leaf samples (15 DAS) from the F1 hybrid Xin No. 3. Briefly, poly(A)-enriched RNA was captured by magnetic beads. Reverse transcription was then performed to generate first-strand cDNA using biotin-labeled random primers. The target sequences were then captured using magnetic beads instead of PAGE-gel purification. Finally, the purified cDNA library was sequenced on an Illumina HiSeq 2000 instrument (LC Sciences, Hangzhou, China). The categories of cleaved miRNA targets were identified and classified using the CleaveLand 3.0 pipeline30 and the ACGT301-DGE v1.0 program (LC Sciences, Hangzhou, China), after which T-plot figures were constructed.

RNA sequencing

Total RNA was extracted from each sample using TRIzol reagent (Invitrogen, Life Technologies, USA) according to the manufacturer’s instructions. RNA-seq libraries were prepared using an Illumina standard mRNA-seq Library Preparation Kit and sequenced on an Illumina HiSeq 2000 instrument in paired-end mode. The NGS QC Toolkit v2.3.350 was first used to discard paired-end reads containing adapters, reads with poly-Ns, or reads with more than 20% low-quality bases (PHRED-like score <20). All the clean reads were then mapped to the B. rapa genome sequence using HISAT v2.0.451 with the default settings. After genome mapping, StringTie52 was used to reconstruct novel transcripts, which were then identified using the genome annotation information together with Cuffcompare53. DESeq2 version: 1.22.248 was used to identify DEGs that had a fold-change of ≥1.5 and an adjusted P value of ≤0.05. GO functional enrichment was carried out using GOseq software54.

Validation of miRNA and target gene expression via qRT-PCR analysis

Total RNA was extracted from the first outside leaf of four F1 hybrids and their five corresponding parents at the seedling stage (15 DAS) using a mirVana RNA Isolation Kit (Ambion, USA) as directed by the manufacturer.

Quantification was carried out according to a two-step reaction process: reverse transcription (RT) and PCR. The RT reaction and real-time PCR assay were conducted in accordance with published methods55. Three technical replicates for each biological reaction and three biological replicates were evaluated for each sample. The expression levels of the miRNAs were normalized to those of 5S rRNA and were calculated using the 2−ΔΔCt method56. The sequences of all the miRNAs and gene-specific primers are listed in Supplementary Table S12 and Supplementary Table S13, respectively.

Vector construction and plant transformation

To clone BrGRF4.2 from Chinese cabbage, specific primers for BrGRF4.2 were designed based on sequence information of the B. rapa reference genome57. The full-length cDNA of BrGRF4.2 was amplified from Chinese cabbage total RNA using gene-specific PCR primers. The resulting PCR products were then cloned into a pMD18-T vector (Takara, Japan) for DNA sequencing. To construct 35S::BrGRF4.2 overexpression vectors, we amplified the entire 1149 bp coding sequence of BrGRF4.2 and subcloned it into pCR8/GW/TOPO entry vectors (Invitrogen) according to the manufacturer’s instructions. The CDS fragment was then inserted into a pCAMBIA2300-EGFP vector through LR recombination reactions.

The 840 bp genomic fragment containing the precursor sequence of bra-miR396 (162 bp) was amplified from Chinese cabbage and then cloned into a pCAMBIA2300-EGFP vector under the control of the CaMV 35S promoter for bra-miR396 overexpression. The 35S::BrGRF4.2 and 35S::bra-miR396 plasmids were then introduced into Agrobacterium tumefaciens strain GV3101, which were subsequently transformed into Arabidopsis Col-0 plants according to the floral dip method58.

Chlorophyll extraction and quantification

The first outside leaf at the seedling stage (15 DAS) and the fifth outside leaf at the early-heading stage (60 DAS) were ground in 80% (v/v) acetone, after which the absorbance of the supernatants was determined at 646.6 and 663.6 nm. The concentrations of chlorophyll a and b were then calculated as follows: chlorophyll a (μg/mL) = 12.25 × A663.6 − 2.55 × A646.6; chlorophyll b (μg/mL) = 20.31 × A646.6 − 4.91 × A663.6. The total chlorophyll content was then determined using the sum of chlorophyll a and chlorophyll b.

Leaf size, cell size, cell number, and photosynthesis rate measurements

The first leaf of Chinese cabbage at 30 DAS was cut into thin (5 mm wide) slices and then processed in accordance with a previously reported method59. The tissues were then observed under a scanning electron microscope (Hitachi S-3400N). A similar region of each leaf was used for observations of epidermal cells of all the samples. Images were captured at 600x magnification, and the cell number per unit area was counted using ImageJ software to determine the average cell size. The number of epidermal cells for each leaf was also calculated.

The photosynthesis rate (Pn) of the first outside Chinese cabbage leaf was measured with a portable photosynthesis system (LI-6400; LI-COR, Inc., Lincoln, NE) at 15 DAS, 20 DAS, 45 DAS, 60 DAS, and 80 DAS. The light intensity was maintained at 100, 400, and 1200 μmol/m2/s, the CO2 was maintained at 380 to 400 μmol/mol, and the temperature was 25 °C.