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

Abstract

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.

Keywords: Heterosis; Maize; Non-additive protein; Proteomic analysis.

Fig. 1

Flow chart of the proteomics analysis of maize hybrids and their parental lines

Fig. 2

Statistical analysis of three biological repeats of two hybrids and their parental lines. (A) Pearson’s correlation analysis of maize hybrid Zhongdan 808 and its female parent CL11 and male parent NG5. (B) Pearson’s correlation analysis of maize hybrid Zhongdan 909 and its female parent Z58 and male parent HD568. (C) Venn diagram of up-regulated and down-regulated DAPs in hybrids compared independently with the female and male parents. (D) Venn diagram of up-regulated and down-regulated DAPs in Zhongdan 808 when compared with its female parent CL11 and male parent NG5. (E) Venn diagram of up-regulated and down-regulated DAPs in Zhongdan 909 when compared with its female parent Z58 and male parent HD568. (F) NAPs in Zhongdan 808 and Zhongdan 909. (G) Heatmaps for cluster analysis of all the non-additive proteins in Zhongdan 808 and its parents. (H) Heatmaps for cluster analysis of all the non-additive proteins in Zhongdan 909 and its parents. ‘ZD808’ indicates Zhongdan 808, ‘ZD909’ indicates Zhongdan 909, ‘↑’ indicates a protein up-regulated in hybrids by at least a 2-fold change compared with any parent, ‘↓’ indicates a protein down-regulated in hybrids by at least a 2-fold change compared with one parent, ‘+’ indicates high parent abundance NAPs, ‘++’ indicates above-high parent abundance NAPs, ‘−’ indicates low parent abundance NAPs, ‘− −’ indicates below-low parent abundance NAPs. The selection criterion for DAPs was fold change > 2, and the criteria for NAPs was fold change > 1.5 and p < 0.05

Fig. 3

Pathway classification of DAPs and NAPs identified from Zhongdan 808 and Zhongdan 909. MapMan software was used to conduct the functional categorization. The numbers of DAPs and NAPs enriched in pathways were subjected to log2 transformation. Each size and color of circles indicated the number of DAPs or NAPs in hybrids when compared with its parents

Fig. 4

Heat map of NAPs involved in stress factors. The NAPs grouped into stress were visualized using MapMan software. Each square and color indicated the fold change of a NAP in hybrids when compared with the parents. Blue and red indicate a decrease and increase, respectively, in fold change compared with the parents, and gray indicates unidentified. MAPK, mitogen-activated protein kinase; PR, pathogenesis-related

Fig. 5

Heat map of NAPs involved in photosynthesis. The NAPs grouped into photosynthesis were visualized using MapMan software. Each square and color indicated the fold change of a NAP in hybrids when compared with the parents. Blue and red indicate a decrease and increase, respectively, in fold change compared with the parents, and gray indicates unidentified. Chlorophyll a-b binding protein (tr|B6SSN3|B6SSN3_MAIZE, CAB1; tr|B4FL55|B4FL55_MAIZE, CAB2; tr|B6SUC4|B6SUC4_MAIZE, CAB3; tr|K7TXI5|K7TXI5_MAIZE, CAB4; tr|B6SZT9|B6SZT9_MAIZE, CAB5)

Fig. 6

PRM verification of some proteins related to photosynthesis and stress. Stress response-related proteins: chaperone protein ClpB3 (ClpB3), D-3-phosphoglycerate dehydrogenase (PGDH), glutathione S-transferase 6 (GST6), and membrane steroid-binding protein 1 (MSBP1). Photosynthesis-related proteins: fructose-bisphosphate aldolase 7 (FBA7), ferredoxin-NADP reductase (FNR), Photosystem II subunit PsbS1 (PsbS1), post-illumination chlorophyll fluorescence increase (PIFI), chlorophyll a-b binding proteins (CAB), Photosystem I P700 chlorophyll a apoprotein A2 (psaB), and photosynthetic NDH subunit of lumenal location 1 (PNSL1). ‘Midparent value’ of LFQ data indicated the average LFQ intensity of female and male parents, ‘Midparent value’ of PRM data indicated the average area of female and male parents. ‘**’ indicated p-value< 0.01; ‘*‘indicated p-value< 0.05