Figures (5)  Tables (3)
    • Figure 1. 

      Differentially expressed genes (DEGs) in Z. japonica in response to cold acclimation. (a) Number of DEGs identified in the 'Meyer' (resistant) and 'Victoria' (susceptible) genotypes. (b) Venn diagram of differentially expressed genes, showing the unique and overlapping genes expressed among comparison groups. NM vs CM: non-cold acclimated 'Meyer' vs cold acclimated 'Meyer' (R genotype); NV vs CV: non-cold acclimated 'Victoria' vs cold acclimated 'Victoria' (S genotype). G1−G8 indicated eight groups.

    • Figure 2. 

      Gene Ontology (GO) classification of the up-regulated DEGs identified in (a) CM vs NM and (b) CV vs NV comparisons. DEGs were annotated in three categories: biological process, cellular component, and molecular function.

    • Figure 3. 

      KEGG pathway classification of the up-regulated DEGs identified in (a) CM vs NM and (b) CV vs NV comparisons.

    • Figure 4. 

      Heat map of partial candidate acclimation response genes that were identified both in the QTL regions previously reported in Brown et al.[15] and the differentially expressed genes reported here. Color bar shows the log2(Fold Change) value, red color indicates up-regulation, blue color indicates down-regulation, and white color indicates no significant change.

    • Figure 5. 

      Heat map of Late embryogenesis abundant protein (LEA) genes that were identified as differentially expressed after cold acclimation in Z. japonica, which were also differentially expressed in protein abundance in a previous study[16]. Color bar shows the log2(Fold Change) value, red color indicates up-regulation, blue color indicates down-regulation, and white color indicates no significant change.

    • SampleRaw readsClean readsClean basesError rate (%)Q20 (%)Q30 (%)GC content (%)
      NM149,475,25448,077,3827.2G0.0397.9294.1557.25
      NM251,183,83650,010,4727.5G0.0397.8493.9957.49
      NM350,168,62849,079,3967.4G0.0397.8894.0457.49
      CM159,804,05658,665,4468.8G0.0397.3792.9552.47
      CM267,204,25865,599,3809.8G0.0397.3592.9451.48
      CM353,728,04652,608,8147.9G0.0397.1192.4852.52
      NV171,039,90269,474,29610.4G0.0397.4793.1953.68
      NV246,536,82445,397,7126.8G0.0397.3993.0352.99
      NV355,073,38453,918,0228.1G0.0397.0892.4153.03
      CV161,931,4586,0855,1049.1G0.0397.4393.1252.9
      CV251,018,63449,819,7847.5G0.0397.2892.8452.43
      CV367,843,32466,500,25210.0G0.0397.4993.2352.78
      *NM: 'Meyer' genotype under non-cold acclimated conditions; CM: 'Meyer' genotype under cold acclimated conditions; NV: 'Victoria' genotype under non-cold acclimated conditions; CV: 'Victoria' genotype under cold acclimated conditions.

      Table 1. 

      Summary of reads following Illumina sequencing.

    • QTL
      region
      Gene_idlog2FoldChange 'Meyer'log2FoldChange 'Victoria'Blast gene accessionBlast gene name
      QTL1Zjn_sc00044.1.g05080.1.sm.mk−1.2035NSQ9C5Q2AI5L3_ARATH ABSCISIC ACID-INSENSITIVE 5-like protein 3
      QTL1Zjn_sc00044.1.g04640.1.sm.mkhc2.78124.4685Q7X996CIPK2_ORYSJ CBL-interacting protein kinase 2
      QTL1Zjn_sc00044.1.g04620.1.am.mkNS1.7587Q7XIW5CIPKT_ORYSJ CBL-interacting protein kinase 29
      QTL1Zjn_sc00044.1.g03340.1.am.mk3.9076NSQ7XHZ0HFB4B_ORYSJ Heat stress transcription factor B-4b
      QTL1Zjn_sc00044.1.g05110.1.sm.mkNS3.422A3AHG5LEA17_ORYSJ Late embryogenesis abundant protein 17
      QTL1Zjn_sc00044.1.g05130.1.sm.mkhc3.3773NSQ10MB4MYB2_ORYSJ Transcription factor MYB2
      QTL1Zjn_sc00044.1.g04960.1.sm.mk5.4299NSA0SPJ6NAMB2_TRITD NAC transcription factor NAM-B2
      QTL1Zjn_sc00044.1.g04580.1.am.mkhc−1.0768NSP42736RAP23_ARATH Ethylene-responsive transcription factor RAP2-3
      QTL1Zjn_sc00044.1.g04450.1.sm.mkhcNS1.8656Q9SW70SRP_VITRI Stress-related protein
      QTL2Zjn_sc00036.1.g01730.1.am.mk3.16174.869Q6VBA4HFC1A_ORYSJ Heat stress transcription factor C-1a
      QTL2Zjn_sc00036.1.g01650.1.am.mkhc3.3333NSQ93WV4WRK71_ARATH WRKY transcription factor 71
      QTL6Zjn_sc00007.1.g01680.1.am.mk4.04152.6034Q6K846IAA9_ORYSJ Auxin-responsive protein IAA9
      QTL8Zjn_sc00004.1.g04500.1.sm.mkhc−2.3169NSQ7XBH4MYB4_ORYSJ Transcription factor MYB4
      QTL8Zjn_sc00004.1.g04560.1.sm.mkhc1.3851−1.3166P14717PAL1_ORYSJ Phenylalanine ammonia-lyase
      QTL8Zjn_sc00004.1.g04570.1.sm.mkhc7.72815.9998A2X7F7PAL2_ORYSI Phenylalanine ammonia-lyase
      QTL10Zjn_sc00122.1.g00870.1.am.mk−1.0261NSO80341EF102_ARATH Ethylene-responsive transcription factor 5
      *log2FoldChange, positive value indicates up-regulation after cold acclimation, negative value indicates down-regulation after cold acclimation, NS indicates non-significant.

      Table 2. 

      Partial list of candidate acclimation response genes that were identified both in the QTL regions previously reported in Brown et al.[15] and differential expression genes reported in this study. Full gene list and QTL information are provided in Supplemental File 4.

    • Gene_idlog2FoldChange
      'Meyer'
      log2FoldChange
      'Victoria'
      Blast gene
      accession
      Blast gene name
      Protein spot 64[16]6.7NSLate embryogenesis abundant protein 3 (LEA3)
      Zjn_sc00027.1.g00580.1.am.mk−1.34351.2295P46518LEA14_GOSHI Late embryogenesis abundant protein Lea14-A
      Zjn_sc00011.1.g01110.1.sm.mkNSInfQ94JF2LEA14_ORYSJ Late embryogenesis abundant protein 14
      Zjn_sc00011.1.g01130.1.sm.mk11.6469.6458Q94JF2LEA14_ORYSJ Late embryogenesis abundant protein 14
      Zjn_sc00044.1.g05110.1.sm.mkNS3.422A3AHG5LEA17_ORYSJ Late embryogenesis abundant protein 17
      Zjn_sc00002.1.g03150.1.am.mk3.80762.7007A3AHG5LEA17_ORYSJ Late embryogenesis abundant protein 17
      Zjn_sc00003.1.g02040.1.sm.mkhc7.5978.8459A3AHG5LEA17_ORYSJ Late embryogenesis abundant protein 17
      Zjn_sc00004.1.g08640.1.sm.mkInf9.7227Q96273LEA18_ARATH Late embryogenesis abundant protein 18
      Zjn_sc00027.1.g03080.1.am.mkhc4.28474.8089Q42376LEA3_MAIZE Late embryogenesis abundant protein, group 3
      Zjn_sc00012.1.g02810.1.sm.mkhcInf8.9382Q42376LEA3_MAIZE Late embryogenesis abundant protein, group 3
      Zjn_sc00081.1.g00290.1.sm.mk6.50693.7991Q9LJ97LEA31_ARATH Late embryogenesis abundant protein 31
      Zjn_sc00003.1.g11730.1.am.mkNSInfP09444LEA34_GOSHI Late embryogenesis abundant protein D-34
      Zjn_sc00108.1.g00280.1.sm.mkInf4.7263P09444LEA34_GOSHI Late embryogenesis abundant protein D-34
      Zjn_sc00023.1.g01980.1.am.mk−2.0172NSF4KFM8LEA65_ARATH Late embryogenesis abundant protein At5g17165
      Zjn_sc00004.1.g08970.1.am.mk−1.2806NSF4KFM8LEA65_ARATH Late embryogenesis abundant protein At5g17165
      * log2FoldChange, positive value indicates up-regulation after cold acclimation, negative value indicates down-regulation after cold acclimation, NS indicates non-significant, Inf indicates infinite value.

      Table 3. 

      List of Late embryogenesis abundant protein (LEA) genes that were identified as differentially expressed after cold acclimation in Z. japonica, which were also differentially expressed in protein abundance in a previous study[16].