Table 4 Functional annotation of loci harboring significant SNPs/ present in LD-region of significant SNPs

S1_1931325

LOC_Os01g04330, LOC_Os01g04340

OsCML16—Calmodulin-related calcium sensor protein, expressed; hsp20/alpha crystallin family protein, putative, expressed

S1_35199996

LOC_Os01g60870

Expressed protein

S2_21858276

LOC_Os02g36220

Terpene synthase, putative, expressed

S3_15,462,193

LOC_Os03g27003, LOC_Os02g36220

Expressed protein

S6_16,241,331

LOC_Os06g28550

nmrA-like family domain containing protein

S7_1,592,572

LOC_Os07g03810

Lectin-like receptor kinase 7

S7_18,874,511

LOC_Os07g31770

Chalcone synthase gene

S7_24,536,919

LOC_Os07g41014

Glycosyl hydrolases family 17 protein

S9_21,545,679

LOC_Os09g37280

Peroxisomal multifunctional enzyme type 2 protein

S11_21,499,010

LOC_Os11g36460, LOC_Os11g36470

SMC-related protein MSS2; ubiquitin carboxyl-terminal hydrolase 21

S2_30,762,305

LOC_Os02g50370

Helicase domain-containing protein

S3_32,359,666

LOC_Os03g56784

Expressed protein

S4_34,899,389

LOC_Os04g58690, LOC_Os04g58700

tRNA-specific adenosine deaminase 1; expressed protein

S6_6,597,022

LOC_Os06g12260, LOC_Os06g12250, LOC_Os06g12280

N-rich protein; sphingolipid C4-hydroxylase SUR2; glycosyl transferase 8 domain containing protein

S6_11,174,827

LOC_Os06g19590, LOC_Os06g19600, LOC_Os06g19610

Estradiol 17-beta-dehydrogenase 12, expressed protein; oxidoreductase, short chain dehydrogenase/reductase family

S8_11,774,122

LOC_Os08g19650, LOC_Os08g19670, LOC_Os08g19680

Homeobox protein knotted-1; expressed protein; expressed protein

S9_4,933,781

LOC_Os09g09220, LOC_Os09g09210

Protein kinase domain containing protein, expressed; expressed protein

S10_14,320,467

LOC_Os10g27170, LOC_Os10g27174, LOC_Os10g27180, LOC_Os10g27160

Calmodulin-binding protein; 40S ribosomal protein S28; expressed protein; hypothetical protein

S10_16,385,834

LOC_Os10g31240, LOC_Os10g31250

Plant protein of unknown function domain containing protein; expressed protein

S11_7,438,223

LOC_Os11g13570, LOC_Os11g13540, LOC_Os11g13560, LOC_Os11g13580

Gibberellin receptor GID1L2; serpin domain containing protein, putative, expressed; serpin domain containing protein, putative, expressed; expressed protein

S4_30,721,851

LOC_Os04g51809, LOC_Os04g51820

Expressed protein; OsHKT1;1—Na + transporter, expressed

S7_24,282,724

LOC_Os07g40520

Formin-like protein 20, putative, expressed

S6_24,807,445

LOC_Os06g41380, LOC_Os06g41384, LOC_Os06g41390

Expressed protein; zinc finger C- × 8-C- × 5-C- × 3-H type family protein, expressed; N-terminal asparagine amidohydrolase

S8_5,775,398

LOC_Os08g09990, LOC_Os08g10000

Expressed protein; expressed protein

S1_40,142,074

LOC_Os01g69070, LOC_Os01g69050, LOC_Os01g69060, LOC_Os01g69080

Auxin efflux carrier component; lysine ketoglutarate reductase trans-splicing related 1; hydrolase, alpha/beta fold family domain containing protein; acyl-desaturase chloroplast precursor

S2_7,048,091

LOC_Os02g13220

F-box family protein

S2_22,216,515

LOC_Os02g36830, LOC_Os02g36820

Cytokinin-O-glucosyltransferase2; expressed protein

S3_7,917,671

LOC_Os03g14590, LOC_Os03g14570, LOC_Os03g14580

Calcium-binding EF hand family protein; expressed protein (conserved gene of known function); expressed protein (in ortholog, conserved gene of known function)

S4_12,374,542

LOC_Os04g21820, LOC_Os04g21830, LOC_Os04g21840, LOC_Os04g21850

OsWAK33—OsWAK receptor-like protein OsWAK-RLP, expressed; hypothetical protein; expressed protein; expressed protein

S4_34,598,600

LOC_Os04g58080, LOC_Os04g58090, LOC_Os04g58100, LOC_Os04g58110

Polygalacturonase inhibitor 3 precursor; harpin-induced protein 1 domain containing protein, Arabidopsis-LEA (LEA) hydroxyproline-rich glycoprotein family/ other ortho NHL25; Expressed Protein; pyruvate kinase

S5_19,130,617

LOC_Os05g32680, LOC_Os05g32660, LOC_Os05g32670, LOC_Os05g32690

Pale Cress Protein (PCP); leucine-rich repeat family protein,; pentatricopeptide repeat-containing protein (ortho-60S ribosomal protein L34); expressed protein

S5_23,720,696

LOC_Os05g40370, LOC_Os05g40384

Expressed protein; cytochrome P450

S5_28,157,471

LOC_Os05g49100

WRKY49

S8_20,423,775

LOC_Os08g32930, LOC_Os08g32920, LOC_Os08g32940

Expressed protein (n ortho-chaperonin like RbcX protein); dynamin-2B; endoglucanase

S8_24,621,885

LOC_Os08g38960, LOC_Os08g38950

Expressed protein (conserved gene of unknown function); EP

S10_111,061

LOC_Os10g01110, LOC_Os10g01134

OsSCP44—Putative Serine Carboxypeptidase homologue; OsSCP46—Putative Serine Carboxypeptidase homologue

S10_19,109,511

LOC_Os10g35750, LOC_Os10g35720, LOC_Os10g35760

Pentatricopeptide; OsGrx_S17—glutaredoxin subgroup II (Pistil); pentatricopeptide

S10_19,238,621

LOC_Os10g35980, LOC_Os10g35990, LOC_Os10g36000

Tetraspanin family protein; DEAD-box ATP-dependent RNA helicase; remorin C-terminal domain containing protein

S1_38,370,584

–

–

S2_2,875,772

LOC_Os02g05820, LOC_Os02g05830, LOC_Os02g05840

Protein kinase domain containing protein; ribulose bisphosphate carboxylase small chain, chloroplast precursor; VIL2 protein

S2_3,873,759

LOC_Os02g07480, LOC_Os02g07490, LOC_Os02g07495

Transglycosylase SLT domain containing protein, expressed; glyceraldehyde-3-phosphate dehydrogenase; expressed protein (pistil)

S4_4,499,266

LOC_Os04g08390, LOC_Os04g08410

Leucine Rich Repeat family protein, expressed (NBS LRR orthologs in brachypodium, Sorghum); ELM2 domain containing protein, putative, expressed

S4_26,914,103

LOC_Os04g45480, LOC_Os04g45460, LOC_Os04g45470, LOC_Os04g45490, LOC_Os04g45500

Heat shock protein STI, putative; cysteine-rich repeat secretory protein precursor; vacuolar-processing enzyme precursor; elongation factor, putative; expressed protein

S4_31,316,844

LOC_Os04g52630, LOC_Os04g52640, LOC_Os04g52614

Leucine-rich repeat-containing protein kinase family protein; SHR5-receptor-like kinase, putative; SHR5-receptor-like kinase

S4_35,115,087

LOC_Os04g59010, LOC_Os04g59020, LOC_Os04g59040, LOC_Os04g59030

F-box domain containing protein; integral membrane protein; soluble inorganic pyrophosphatase, putative; expressed protein

S5_24,316,574

LOC_Os05g41530, LOC_Os05g41510, LOC_Os05g41520, LOC_Os05g41540, LOC_Os05g41550

ZOS5-11—C2H2 zinc finger protein, expressed; SH2 motif, putative, expressed; zinc finger, C3HC4 type domain containing protein, expressed; bZIP transcription factor domain containing protein, expressed; expressed protein

S11_19,062,952

LOC_Os11g32260, LOC_Os11g32250, LOC_Os11g32270

Lysosomal alpha-mannosidase precursor, putative, expressed; expressed protein; N-rich protein, putative, expressed