S1 Table. Summary of Regions and Annotated Genes with Significant Differences in Chromosome

S1 Table. Summary of regions and annotated genes with significant differences in chromosome 3 of -rl mutant compared to QHZ.

Region number / Base position on Chromosome 3 / log2 fold change (CGH) / Accession of annotated gene / Description / log2 fold change (RNA-seq) / log2 fold change (qPCR)
1 / 841–47564 / 0.260 / OsI_09589 / Hypothetical protein / Undetected
OsI_09593 / Hypothetical protein / Undetected
OsI_09594 / Hypothetical protein / Undetected
2 / 47629–51700 / 2.978 / OsI_09595 / Putative iron ion binding protein / 0.722(0.000049) / 0.660
3 / 51775–60113 / 1.329 / None
4 / 60188–65632 / 0.540 / None
5 / 3814021–3819439 / −2.837 / OsI_10125
(LOC_Os03g06654) / Flavin-containing monooxygenase# / −2.857(0.000042) / −4.718**
6 / 3820942–3824327 / −3.111 / None
7 / 3824392–3825570 / −1.592 / None
8 / 5289971–5294556 / 0.598 / OsI_10359 / Hypothetical protein / −2.826(0) / 0.184
9 / 7599146–7602230 / −0.327 / OsI_10659
(LOC_03g13190) / Hypothetical protein / Undetected
10 / 9695319–9700339 / −0.612 / OsI_10794
LOC_Os03g14950 / Putative lipid transfer/seed storage protein / 1.367(0) / 2.250**
OsI_10922
(LOC_Os03g16320) / Hypothetical protein / Undetected
11 / 11391842–11392970 / −0.849 / None
12 / 13189440–13213173 / 0.268 / OsI_11379 / Putative zinc ion binding protein / 0.957(0.230698) / −0.045
OsI_11381 / Hypothetical protein / 0.387(0.103524) / 0.539
OsI_11382 / Endoglucanase 11-like protein / 0.615(0.000047) / 0.474
OsI_11384
(LOC_Os03g20900) / Putative Myb family transcription factor / 0.130(0.475186) / 0.170
OsI_11412
(LOC_Os03g21250) / plant peroxidase-like protein / 1.036(0.001348) / 1.227**
13 / 19738559–19739594 / 3.720 / None
14 / 19739774–19745515 / 1.647 / OsI_12111 / Hypothetical protein / Undetected
15 / 23753929–23755711 / 0.345 / None
16 / 24681426–24682550 / 0.281 / OsI_12423
(LOC_Os03g39160) / Hypothetical protein / 0.087(0.466303) / 0.193
17 / 25062829–25065249 / 2.678 / None
18 / 25065429–25071132 / 2.360 / None
19 / 29074267–29077014 / −0.668 / None
20 / 30940982–30942412 / −0.476 / OsI_13020
(LOC_Os03g47580) / Hypothetical protein / Undetected
21 / 35807684–35809329 / −0.366 / None
22 / 36680837–36682720 / 3.031 / OsI_13780 / Probable serine/threonine-protein kinase / 1.173(0) / 0.366
23 / 36682785–36698367 / 0.934 / OsI_13781 / Putative protein serine/threonine kinase / Undetected
24 / 36698427–36701360 / 2.552 / OsI_13782 / Putative receptor protein kinase / Undetected
25 / 36874708–36878842 / 1.837 / OsI_13806 / Putative receptor-like protein kinase / −0.125(0.763648) / 0.406
26 / 36878907–36881019 / 2.389 / None
27 / 37120488–37125068 / −0.398 / OsI_13846
(LOC_Os03g57740) / Putative copper ion binding protein / −0.223(0.631121) / −0.047
28 / 38299829–38368870 / −0.293 / OsI_14024
(LOC_Os03g59680) / Putative peptidyl-prolyl cis-trans isomerase H / 0.189(0.143047) / 0.181
OsI_14025
(LOC_Os03g59720) / Putative 50S ribosomal protein L36 / −0.013(0.84014) / 0.341
OsI_14026
(LOC_Os03g59690) / Hypothetical protein / −0.193(0.015167) / −0.569
OsI_14027
(LOC_Os03g59700) / Putative peptidyl-prolyl cis-trans isomerase H / Undetected
OsI_14028
(LOC_Os03g59710) / Putative splicing factor 3B subunit 6 / 1.541(0) / 0.562
OsI_14030
(LOC_Os03g59720) / Putative 50S ribosomal protein L36 / Undetected
OsI_14031
(LOC_Os03g59730) / Putative NAC transcription factor 29 / −0.223(0.386265) / −0.370
OsI_14032
(LOC_Os03g59740) / Putative ADP-ribosylation factor / −0.103(0.587476) / −0.022
OsI_14033 / Putative DNA gyrase subunit A / Undetected
OsI_14036
(LOC_Os03g59760) / Putative zinc ion binding protein / Undetected
OsI_14037
(LOC_Os03g59770) / Putative calmodulin-like protein 4 / Undetected
29 / 38368945–38387057 / −0.698 / OsI_14038
(LOC_Os03g59790) / Putative calmodulin-like protein 5 / Undetected
OsI_14039
(LOC_Os03g59830) / Hypothetical protein / −0.766(0.058771) / 0.016
OsI_14040
(LOC_Os03g59840) / Hypothetical protein / Undetected
30 / 38387142–38446176 / 0.344 / OsI_14041
(LOC_Os03g59850) / Hypothetical protein / −0.766(0.052235) / 0.016
OsI_14042
(LOC_Os03g59860) / Putative heat shock protein / −0.050(0.494857) / −0.097
OsI_14043
(LOC_Os03g59870) / Probable calcium-binding protein CML45 / Undetected
OsI_14044
(LOC_Os03g59880) / Hypothetical protein / −0.766(0.014985) / 0.031
OsI_14045
LOC_Os03g62490 / Hypothetical protein / −1.149(0.002257) / −1.644**
OsI_14046 / Hypothetical protein / Undetected
OsI_14047 / Hypothetical protein / Undetected
OsI_14049
(LOC_Os03g59770) / Probable calcium-binding protein CML45 / Undetected
31 / 39070043–39100499 / 0.356 / OsI_14152
LOC_Os03g61360 / Putative bifunctional epoxide hydrolase 2 / 1.194(0) / 1.379**
OsI_14153
(LOC_Os03g61340) / Putative bifunctional epoxide hydrolase 3 / −0.803(0.00054) / −0.206
OsI_14154
(LOC_Os03g61330) / Putative fumarylacetoacetate hydrolase domain-containing protein 1 / Undetected
32 / 39101319–39113028 / 0.734 / OsI_14155
(LOC_Os03g61319) / Probable NAC domain-containing protein 76 / 1.194 (0) / 0.678
OsI_14156
(LOC_Os03g61260) / Putative 50S ribosomal protein L18 / 1.443 (0) / 0.429
OsI_14157
(LOC_Os03g61270) / Putative mannan endo-1,4-beta-mannosidase 3 / 0.422(0.004718) / 0.543
33 / 39113113–39121211 / 0.966 / None
34 / 39765924–39770691 / −2.257 / OsI_14270
(LOC_Os03g62600) / Ras-related protein RABA2a-like protein / undetected
OsI_14271
(LOC_Os03g62670) / Putative thiopurine S-methyltransferase / 0.184(0.223736) / 0.362
OsI_14272
(LOC_Os03g62680) / Poly(ADP-ribose) glycohydrolase 1-like protein / 0.197(0.131691) / 0.345
35 / 39771236–39816235 / 0.307 / OsI_14273
(LOC_Os03g62570) / Putative uncharacterized protein OSJNBa0075M12.26 / 0.131(0.733918) / 0.474
OsI_14274
(LOC_Os03g62580) / Putatvie vacuolar protein sorting-associated protein 9a / 0.634(0.039929) / −0.347
OsI_14276
(LOC_Os03g62590) / Hydroxysteroid 11-beta-dehydrogenase 1-like protein / 1.183(0.000532) / 0.726
OsI_14277
(LOC_Os03g62600) / Ras-related protein RABA2a-like protein / undetected
OsI_14278
(LOC_Os03g62610) / hypothetical protein / 0.239(0.220142) / −0.236
OsI_14279 (LOC_Os03g62620) / Putative late embryogenesis abundant protein Lea14-A / −0.943(0) / −1.012**
OsI_14280
(LOC_Os03g62630) / 30S ribosomal protein S6 alpha-like protein / 0.198(0.000116) / 0.431
OsI_14281
(LOC_Os03g62640) / Putative RNA-binding protein Luc7-like 2 / 0.103(0.582509) / 0.401
OsI_14282
(LOC_Os03g62650) / Probable ion channel DMI1-like protein / Undetected
36 / 39816310–39827698 / 1.359 / OsI_14283
(LOC_Os03g62660) / Putative zinc ion binding protein / 0.580(0.01815) / 0.472
OsI_14284
(LOC_Os03g62670) / Putative thiopurine S-methyltransferase / Undetected
OsI_14285
(LOC_Os03g62680) / Poly(ADP-ribose) glycohydrolase 1-like protein / Undetected
OsI_14286
(LOC_Os03g62690) / Putative pentatricopeptide repeat-containing protein / 0.409(0.001763) / −0.158
37 / 39998032–39999635 / −1.852 / None
38 / 39999725–40000910 / −3.260 / None
39 / 40003196–40006939 / 1.837 / None
40 / 40062494–40069490 / −2.152 / OsI_14326(LOC_Os03g63250) / hypothetical protein / −0.935(0.011386) / −3.095**
41 / 40069550–40071642 / −2.887 / None
42 / 40142137–40143482 / 2.119 / None
43 / 40183687–40185626 / 1.989 / OsI_14340
(LOC_Os03g63330) / Aspartate kinase 1-like protein / 0.051(0.508304) / −0.637
44 / 40185786–40196975 / −2.172 / OsI_14341
(LOC_Os03g63330) / Aspartate kinase 2-like protein / undetected
OsI_14342 / hypothetical protein / Undetected
45 / 40197065–40199624 / −1.865 / None
46 / 40220496–40222035 / 2.177 / None
47 / 40222100–40224005 / 4.049 / OsI_14347
(LOC_Os03g63400) / Putative nascent polypeptide-associated complex subunit beta / 0.064(0.857196) / 0.111
48 / 40736709–40738538 / −0.273 / OsI_14436
(LOC_Os03g64290) / Myosin-like protein / 0.436(0.00499) / 0.697
49 / 41350477–41354135 / −0.415 / None

None: no annotated gene is present within the region. Undetected: gene not detected in RNA-seq data. #previouslyidentified as OsFMO(t) (Yi et al., 2007 & 2013).“OsI_xx” represents the gene or locus in the indica rice genome ( “LOC_xx”in brackets represents corresponding gene or locus in the japonica rice genome ( Log2 fold change: The ratio of Log2-rl/QHZ (number in brackets represents P-value).A log2 ratio of 1.0 is equivalent to a 2.0 fold relative change in expression.**P ≤ 0.01.