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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (8): 1275-1282.doi: 10.3724/SP.J.1006.2020.91068

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Comparative proteomic analysis of two wheat genotypes with contrasting grain softness index

LIU Pei-Xun1,MA Xiao-Fei2,WAN Hong-Shen1,ZHENG Jian-Min1,LUO Jiang-Tao1,PU Zong-Jun1,*()   

  1. 1Crop Research Institute, Sichuan Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, Sichuan, China
    2Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen 041000, Shanxi, China
  • Received:2019-11-23 Accepted:2020-03-30 Online:2020-08-12 Published:2020-05-17
  • Contact: Zong-Jun PU E-mail:pzjun68@163.com
  • Supported by:
    National Natural Science Foundation of China(31671683);National Natural Science Foundation of China(31401383);Financial Innovation Capacity Improvement Project of Sichuan Province(2016ZYPZ-016);Financial Innovation Capacity Improvement Project of Sichuan Province(2019QNJJ-007);Financial Innovation Capacity Improvement Project of Sichuan Province(2019QYXK034);Science and Technology Planning Project of Sichuan Province(2017JY0077)


Wheat is the crop most widely grown in the world and provides the daily protein and 20% food calories for 4.5 billion people. It is crucial to understand the genetic basis of grain hardness for improving wheat quality. In order to explore the molecular basis of the formation of wheat grain hardness, two wheat cultivars Chuanmai 66 and Shumai 969 with significant hardness difference in southwest wheat region were selected to analyze the proteins differential expression by TMT quantitative proteomics (tandem mass tags) and bioinformatic methods of function and pathway enrichment analysis. A total of 6020 effective proteins were identified and quantified, including 113 differentially expressed proteins (DEPs), of which 69 were up-regulated and 44 were down-regulated in soft wheat Chuanmai 66. These DEPs were enriched into 65 GO terms, including a biological process term, a cellular component term and six molecular function terms at extremely significant level. Based on the enrichment analysis, we suggested that nutrient reservoir activity proteins, enzyme inhibitor proteins and glutathione metabolism proteins might participate in the formation of wheat grain hardness, and grain hardness related proteins might mainly distribute in the extracellular region of cells and had defensive function. According to the phylogenetic analysis, it was inferred that puroindolines and its homologous proteins might be as not only wheat grain storage proteins, but also enzyme inhibitors regulating grain development. This study provides a basis for further exploring the genetic mechanism of wheat grain hardness.

Key words: Triticum aestivum L., grain hardness, TMT, protemics

Fig. 1

Comparison of the grain quality between Chuanmai 66 and Shumai 969"

Fig. 2

Result of protein functional annotations"

Fig. 3

Differential protein volcano map"

Fig. 4

Differential protein GO enrichment results A belongs to BP (biological process), B belongs to CC (cellular component), C, D, E, F, G, H, I, J belong to MF (molecular function). A: defense response; B: extracellular region; C: nutrient reservoir activity; D: enzyme inhibitor activity; E: enzyme regulator activity; F: serine-type endopeptidase inhibitor activity; G: endopeptidase inhibitor activity; H: aspartic-type endopeptidase activity; I: electron carrier activity; J: chitin binding."

Table 1

DEPs with nutrient reservoir activity (Chuanmai 66 vs. Shumai 969)"

Protein ID
Fold change
B2Y2Q6 B2Y2Q6_WHEAT LMW-B2 1.5425 Up
B2BZC7 B2BZC7_WHEAT LMW-m glutenin subunit 0154A5-M 1.8737 Up
A0A173DQZ1 A0A173DQZ1_WHEAT type-b avenin-like protein 3.8163 Up
Q8H0J5 Q8H0J5_WHEAT low molecular weight glutenin subunit (fragment) 5.0056 Up
TraesCS7A01G035300.1 Gliadin-like avenin 2.9853 Up
Q6WZC3 Q6WZC3_WHEAT low molecular weight glutenin subunit 2.1622 Up
TraesCS4A01G453400.1 Gamma-gliadin 7.2606 Up
A0A286QTK1 A0A286QTK1_WHEAT avenin-like protein A2 0.5984 Down
F8SGL3 F8SGL3_WHEAT low-molecular-weight glutenin subunit 0.5493 Down
Q0QBR3 Q0QBR3_WHEAT LMW-glutenin P3-5 0.3190 Down
B2Y2R3 B2Y2R3_WHEAT low molecular weight glutenin subunit 0.5725 Down
B6UKN9 B6UKN9_WHEAT gamma-gliadin 0.6340 Down
TraesCS2A01G211800.1 Germin-like protein 1-1 0.5875 Down
A0A2P1H6A2 A0A2P1H6A2_WHEAT alpha-gliadin 0.5908 Down
A0A0K2QJY6 A0A0K2QJY6_WHEAT alpha/beta-gliadin 0.6081 Down
I0IT65 I0IT65_WHEAT alpha-gliadin 0.6241 Down

Table 2

DEPs with enzyme inhibitor activity (Chuanmai 66 vs. Shumai 969)"

Protein ID
Fold change
Q5UHH6 Q5UHH6_WHEAT 0.19 dimeric alpha-amylase inhibitor (fragment) 1.6788 Up
TraesCS5D01G004300.1 Puroindoline-b, protease inhibitor/seed storage/LTP family 2.8227 Up
P81713 IBB3_WHEAT Bowman-Birk type trypsin inhibitor 1.5092 Up
TraesCS4A01G460900.1 Invertase inhibitor, plant invertase/pectin methylesterase inhibitor 1.5169 Up
TraesCS1D01G028500.1 Chymotrypsin inhibitor 2.3465 Up
TraesCS5D01G561800.1 Invertase inhibitor, plant invertase/pectin methylesterase inhibitor 2.0582 Up
A0A080YTU1 A0A080YTU1_WHEAT uncharacterized protein 1.5779 Up
A0A2X0S1F0 A0A2X0S1F0_WHEAT peptidase A1 domain-containing protein 1.9149 Up
TraesCS4D01G205800.1 ADP-ribosylation factor GTPase-activating protein 1.6650 Up
TraesCS7A01G502500.1 Eukaryotic aspartyl protease family protein 2.3542 Up
TraesCS3D01G467500.1 Eukaryotic aspartyl protease family protein 0.3700 Down
TraesCS4D01G250000.1 Dimeric alpha-amylase inhibitor 0.3659 Down
TraesCS1D01G265900.1 Wound-induced protease inhibitor 0.5474 Down
TraesCS3D01G025700.1 Trypsin inhibitor 0.1974 Down
TraesCS6B01G407700.1 Aspartic proteinase nepenthesin-1 0.6473 Down

Table 3

DEPs related to Glutathione metabolism (Chuanmai 66 vs. Shumai 969)"

Protein ID
Fold change
TraesCS3D01G491400.1 6-phosphogluconate dehydrogenase 2.5968 Up
TraesCS2B01G096200.1 Ascorbate peroxidase 1.5695 Up
TraesCS3A01G488200.1 Glutathione S-transferase 1.5215 Up
TraesCS3B01G536100.1 Glutathione S-transferase 1.9499 Up
TraesCS3D01G445400.1 Glutathione S-transferase 0.6058 Down
W5D4D9 W5D4D9_WHEAT uncharacterized protein 0.5675 Down

Fig. 5

Phylogenetic tree constructed by differentially expressed proteins and the puroindolines The proteins with solid circles are puroindolines, the proteins with squares belong to nutrient reservoir activity category, the proteins with triangles belong to enzyme inhibitor activity category, and the proteins with circles belong to glutathione metabolism category."

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