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. 2017 Feb 28;119(5):885–899. doi: 10.1093/aob/mcw256

Table 2.

List of differentially expressed candidate genes potentially associated with Meloidogyne graminicola resistance in Oryza glaberrima TOG5681. Means of normalized reads counts obtained by edgeR are indicated for susceptible plants (Oryza sativa ‘Nipponbare’) and TOG5681 resistant plants in the RNA-Seq columns. Differential gene expression (log fold change, Padj<0·05) between nematode-infected and control root tips and between Oryza species control root tips is shown by the colour code on the right. Results of quantitative RT-PCR assays are indicated in the Q-PCR column (OK, validation; nt, not tested). See Table S4 for Q-PCR details

Locus Pathway Function RNA-seq
 Q-PCR
‘Nipponbare’
 TOG5681
C 2 dpi 4 dpi 8 dpi C 2 dpi 4 dpi 8 dpi
LOC_Os04g15920 Lignin biosynthesis Dehydrogenase, CAD6 419 475 293 130 172 823 586 379 OK
LOC_Os08g38910 Lignin biosynthesis Caffeoyl-CoA O-methyltransferase, CCoAOMT 12 13 67 309 26 112 297 788 nt
LOC_Os08g38920 Lignin biosynthesis Caffeoyl-CoA O-methyltransferase, CCoAOMT 17 8 5 6 192 339 381 196 nt
LOC_Os04g01354 Chalcones Chalcone synthase 5 6 15 2 31 544 288 21 nt Log FC
LOC_Os10g40880 Flavonols Flavonol synthase/flavanone 3-hydroxylase 2 3 0 0 746 485 613 747 OK  < −2
LOC_Os04g09900 Terpenoids Ent-kaurene synthase, chloroplast precursor 16 134 1158 62 1063 8902 3501 503 OK  < −1
LOC_Os04g10060 Terpenoids Ent-kaurene synthase, chloroplast precursor 3 11 186 10 3 465 221 43 OK >1
LOC_Os11g28530 Terpenoids Terpene synthase 265 635 1289 276 554 2604 1106 308 nt >2
LOC_Os02g41670 SA biosynthesis Phenylalanine ammonia lyase, OsPAL3 83 195 748 84 148 1009 819 217 nt
LOC_Os02g41680 SA biosynthesis Phenylalanine ammonia lyase, OsPAL4 242 368 976 491 251 1411 1474 988 OK Tog/Nip
LOC_Os04g43800 SA biosynthesis Phenylalanine ammonia lyase, OsPAL6 12 97 170 58 119 1001 1117 394 nt >2
LOC_Os09g25070 SA response WRKY62 604 425 647 180 206 1805 2504 1377 OK
LOC_Os03g12500 JA biosynthesis Allene oxide synthase 2 6 16 98 26 12 406 629 297 OK
LOC_Os08g39840 JA biosynthesis Lipoxygenase 7, chloroplast precursor 12 32 195 21 9 243 140 48 nt
LOC_Os11g08380 Ethylene biosynthesis 1-Aminocyclopropane-1-carboxylate oxidase 296 229 138 144 1819 870 1151 955 OK
LOC_Os06g31280 PR THION1, plant thionin family protein precursor 7 20 1 24 6339 2410 2528 783 OK
LOC_Os06g31800 PR THION2, plant thionin family protein precursor 83 15 5 105 278829 104220 66448 50602 OK
LOC_Os06g31890 PR THION3, plant thionin family protein precursor 60 26 0 9 761 312 173 106 nt
LOC_Os06g32240 PR THION9, plant thionin family protein precursor 0 1 0 4 733 288 195 118 nt
LOC_Os07g33780 Resistance Pleiotropic drug resistance protein 5 677 587 1364 1031 752 3914 4156 1338 OK
LOC_Os09g34160 Resistance Resistance protein 21 26 77 30 53 543 575 199 OK
LOC_Os11g37860 Resistance and QTL Stripe rust-resistance protein Yr10 395 439 1067 1997 318 1435 6272 5256 OK
LOC_Os01g73604 QTL LSM domain containing protein 3 4 3 7 310 252 324 335 nt
LOC_Os03g45740 QTL Transferase family protein 62 20 1 5 551 339 179 233 OK
LOC_Os03g45960 QTL Thaumatin 35 57 53 42 146 954 1050 1312 OK
LOC_Os03g46040 QTL Expressed protein 0 0 0 1 488 471 573 441 OK
LOC_Os03g46060 QTL Thaumatin family domain containing protein 91 121 549 732 55 479 1278 612 OK
LOC_Os03g46070 QTL Thaumatin 111 158 474 128 34 1280 746 168 OK
LOC_Os04g01470 QTL O-methyltransferase 1 2 91 12 14 753 1248 147 OK
LOC_Os04g04240 QTL Sterol 3-β-glucosyltransferase 0 0 0 0 177 161 168 143 nt
LOC_Os05g03920 QTL DUF26 9 14 119 132 38 124 314 393 OK
LOC_Os12g28710 QTL ATPase 3 3 5 5 5 70 239 437 194 OK