Proteomic analysis reveals that auxin homeostasis influences the eighth internode length heterosis in maize (Zea mays)

Dominant complementation of biological pathways in maize hybrid lines is associated with heterosis

Allele-specific expressed genes (ASEGs) are widespread in maize hybrid lines and play important roles of complementation of biological pathways in heterosis. Heterosis (hybrid vigor) is an important phenomenon with both theoretical and practical value. However, our understanding of the genetic and molecular mechanisms behind heterosis is still limited. Here, we analyzed a comprehensive dataset of maize (Zea mays L.), including RNA-seq data from three hybrid-parent triplets (HPTs) and acetylated protein data from one HPT. The gene expression patterns exhibited extensive variation between the hybrids and their parents, and a substantial number of allele-specific expressed genes (ASEGs) were identified in the hybrids. Notably, ASEGs from different HPTs were significantly enriched in various conserved pathways. The parental alleles of ASEGs with fewer deleterious single-nucleotide polymorphisms were more likely to be expressed in hybrid lines than other parental alleles. ASEGs were mainly enriched in the functional gene ontology terms protein biosynthesis, photosynthesis, and metabolism. In addition, the ASEGs across the three HPTs were involved in key photosynthetic pathways and might enhance the photosynthetic efficiency of the hybrids. These findings suggest that ASEGs involved in complementary biological pathways in maize hybrids contribute to heterosis, shedding new light on the molecular mechanism of heterosis.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus

BACKGROUND

Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear.

RESULTS

In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones.

CONCLUSION

Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.

Novel Role of AaMYBC1 in Regulating Actinidia arguta Vine Architecture by Elongating Internode Based on Multi-Omics Analysis of Transgenic Tobacco

The internode length affects the status of fruiting branches and shapes the vine architecture. MYB TFs (transcription factors) have been widely studied and reported to control many biological processes including secondary metabolism, abiotic stresses, growth and development, etc. However, the roles of MYB TFs in regulating internode length remain poorly understood. Here, we demonstrated that a secondary metabolism-related R2R3-MYB TF AaMYBC1 from Actinidia arguta was involved in the regulation of internode length by combined analysis of transcriptome and metabolome of transgenic tobacco plants. The metabolome analysis of OE (over-expressed tobacco) and WT (wild-typed tobacco) showed that there were a total of 1000 metabolites, 176 of which had significant differences. A key metabolite pme1651 annotated as indole 3-acetic acid belonged to phytohormone that was involved in internode length regulation. The RNA-seq analysis presented 446 differentially expressed genes (DEGs) between OE and WT, 14 of which were common DEGs in KEGG and GO enrichment. Through the combined analysis of metabolome and transcriptome in transgenic and wild-type tobacco, three key genes including two SAUR and a GH3 gene were possibly involved in internode elongation. Finally, a regulatory module was deduced to show the role of AaMYBC1 in internode elongation. Our results proposed a molecular mechanism of AaMYBC1 regulating internode length by mediated auxin signaling, implying the potential role in regulating the vine architecture.

How is auxin linked with cellular energy pathways to promote growth?

Auxin is the 'growth hormone' and modulation of its concentration correlates with changes in photosynthesis and respiration, influencing the cellular energy budget for biosynthesis and proliferation. However, the relative importance of mechanisms by which auxin directly influences photosynthesis and respiration, or vice versa, are unclear. Here we bring together recent evidence linking auxin with photosynthesis, plastid biogenesis, mitochondrial metabolism and retrograde signalling and through it we propose three hypotheses to test to unify current findings. These require delving into the control of auxin conjugation to primary metabolic intermediates, translational control under auxin regulation and post-translational influences of auxin on primary metabolic processes.

Advances in Research on the Mechanism of Heterosis in Plants

Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.

Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

BACKGROUND

Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.

RESULTS

Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value.

CONCLUSIONS

Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

Combating Dual Challenges in Maize Under High Planting Density: Stem Lodging and Kernel Abortion

High plant density is considered a proficient approach to increase maize production in countries with limited agricultural land; however, this creates a high risk of stem lodging and kernel abortion by reducing the ratio of biomass to the development of the stem and ear. Stem lodging and kernel abortion are major constraints in maize yield production for high plant density cropping; therefore, it is very important to overcome stem lodging and kernel abortion in maize. In this review, we discuss various morphophysiological and genetic characteristics of maize that may reduce the risk of stem lodging and kernel abortion, with a focus on carbohydrate metabolism and partitioning in maize. These characteristics illustrate a strong relationship between stem lodging resistance and kernel abortion. Previous studies have focused on targeting lignin and cellulose accumulation to improve lodging resistance. Nonetheless, a critical analysis of the literature showed that considering sugar metabolism and examining its effects on lodging resistance and kernel abortion in maize may provide considerable results to improve maize productivity. A constructive summary of management approaches that could be used to efficiently control the effects of stem lodging and kernel abortion is also included. The preferred management choice is based on the genotype of maize; nevertheless, various genetic and physiological approaches can control stem lodging and kernel abortion. However, plant growth regulators and nutrient application can also help reduce the risk for stem lodging and kernel abortion in maize.

Auxin perception in Agave is dependent on the species' Auxin Response Factors

Auxins are one of the most important and studied phytohormones in nature. Auxin signaling and perception take place in the cytosol, where the auxin is sensed. Then, in the nucleus, the auxin response factors (ARF) promote the expression of early-response genes. It is well known that not all plants respond to the same amount and type of auxins and that the response can be very different even among plants of the same species, as we present here. Here we investigate the behavior of ARF in response to various auxins in Agave angustifolia Haw., A. fourcroydes Lem. and A. tequilana Weber var. Azul. By screening the available database of A. tequilana genes, we have identified 32 ARF genes with high sequence identity in the conserved domains, grouped into three main clades. A phylogenetic tree was inferred from alignments of the 32 Agave ARF protein sequences and the evolutionary relationship with other species was analyzed. AteqARF 4, 15, 21, and 29 were selected as a representative diverse sample coming from each of the different subclades that comprise the two main clades of the inferred phylogenetic reconstruction. These ARFs showed differential species-specific expression patterns in the presence of indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). Interestingly, A. angustifolia showed different phenotypes in the presence and absence of auxins. In the absence of auxin, A. angustifolia produces roots, while shoots are developed in the presence of IAA. However, in the presence of 2,4-D, the plant meristem converts into callus. According to our results, it is likely that AteqARF15 participates in this outcome.

Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.)

Background

Bermudagrass (Cynodon dactylon L.) is an important turfgrass species with two types of stems, shoots and stolons. Despite their importance in determining the morphological variance and plasticity of bermudagrass, the intrinsic differences between stolons and shoots are poorly understood.

Results

In this study, we compared the proteomes of internode sections of shoots and stolons in the bermudagrass cultivar Yangjiang. The results indicated that 376 protein species were differentially accumulated in the two types of stems. Pathway enrichment analysis revealed that five and nine biochemical pathways were significantly enriched in stolons and shoots, respectively. Specifically, enzymes participating in starch synthesis all preferentially accumulated in stolons, whereas proteins involved in glycolysis and diverse transport processes showed relatively higher abundance in shoots. ADP-glucose pyrophosphorylase (AGPase) and pyruvate kinase (PK), which catalyze rate-limiting steps of starch synthesis and glycolysis, showed high expression levels and enzyme activity in stolons and shoots, respectively, in accordance with the different starch and soluble sugar contents of the two types of stems.

Conclusions

Our study revealed the differences between the shoots and stolons of bermudagrass at the proteome level. The results not only expand our understanding of the specialization of stolons and shoots but also provide clues for the breeding of bermudagrass and other turfgrasses with different plant architectures.

Supplementary material

Supplementary information accompanies this paper at 10.1186/s12864-019-6077-3.

Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis

Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.

Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Transcriptome and DNA methylome reveal insights into yield heterosis in the curds of broccoli (Brassica oleracea L var. italic)

BACKGROUND

Curds are the main edible organs, which exhibit remarkable yield heterosis in F₁ hybrid broccoli. However, the molecular basis underlying heterosis in broccoli remains elusive.

RESULTS

In the present study, transcriptome profiles revealed that the hybridization made most genes show additive expression patterns in hybrid broccoli. The differentially expressed genes including the non-additively expressed genes detected in the hybrid broccoli and its parents were mainly involved in light, hormone and hydrogen peroxide-mediated signaling pathways, responses to stresses, and regulation of floral development, which suggested that these biological processes should play crucial roles in the yield heterosis of broccoli. Among them, light and hydrogen peroxide-mediated signaling pathways represent two novel classes of regulatory processes that could function in yield or biomass heterosis of plants. Totally, 53 candidate genes closely involved in curd yield heterosis were identified. Methylome data indicated that the DNA methylation ratio of the hybrids was higher than that of their parents. However, the DNA methylation levels of most sites also displayed additive expression patterns. These sites with differential methylation levels were predominant in the intergenic regions. In most cases, the changes of DNA methylation levels in gene regions did not significantly affect their expression levels.

CONCLUSIONS

The differentially expressed genes, the regulatory processes and the possible roles of DNA methylation modification in the formation of curd yield heterotic trait were discovered. These findings provided comprehensive insights into the curd yield heterosis in broccoli, and were significant for breeding high-yield broccoli varieties.

Proteomic analysis of heterotic seed germination in maize using F1 hybrid DHM 117 and its parental inbreds

A number of differentially expressed proteins (DEPs) were identified in comparative two-dimensional gel electrophoresis analysis of dry and 24-h water-imbibed seeds of maize F1 hybrid DHM 117 (BML 6 × BML 7) and its parental inbreds. Of the DEPs, 53.4% (86/161) in dry seeds and 58% (127/219) in water-imbibed seeds exhibited a nonadditive pattern in the F1 hybrid as compared to parental inbreds. A total of 30 DEPs were categorized into different biological processes, most of which were related to metabolism and energy (34%), followed by storage proteins (27%), stress response (23%), transcription and translation (7%), cell cycle (3%), and hormone biosynthesis (3%). The transcript accumulation pattern of 8 selected genes corresponding to DEPs was examined using qRTPCR. Interestingly, LEA protein Rab28 showed higher accumulation in dry seeds at both protein and transcript levels, whereas indole3-acetaldehyde oxidase showed lower accumulation in water-imbibed seeds of the F1 hybrid than the female parent at the protein level. Thus, the DEPs particularly involved in metabolic and energy processes, as well as hormone biosynthesis in the F 1 hybrid, might be responsible for heterotic seed germination in the F1 hybrid. The DEPs identified in this study provide a scope for improving the seed germination trait of agricultural crops.