Table 2.

List of genes identified from significantly associated SNPs for phenotypic traits.

Trait	SNP ID	Chr	Position	SNP effect	−Log10 (P)	Locus_ID	Description
Clum length	AX-281898346	7	29623752	6.79	23.60	Os07g0695100	OsPRR37; Heading date 2, PSEUDO-RESPONSE REGULATOR 37
	AX-95959478	9	16415391	4.95	22.51	Os09g0441900	OsDEP1; DENSE AND ERECT PANICLE 1
	AX-115865280	7	29529536	-2.74	12.32	Os07g0693700	WD40 repeat-like domain-containing protein.
	AX-154994951	9	18671171	2.90	9.23	Os09g0483400	Similar to Ubiquitin/ribosomal fusion protein (Fragment).
	AX-117368794	9	16535714	-4.27	8.98	Os09g0444100	Similar to Minus dominance protein.
	AX-95931544	9	17878923	3.07	7.06	Os09g0469900	Similar to Queuine tRNA-ribosyltransferase.
	AX-95938232	9	16543763	-5.44	7.04	Os09g0444200	Lecithin: cholesterol acyltransferase family protein.
Heading date	AX-115865280	7	29529536	-3.34	20.65	Os07g0693700	WD40 repeat-like domain-containing protein.
	AX-281898346	7	29623752	5.75	17.17	Os07g0695100	OsPRR37; Heading date 2, PSEUDO-RESPONSE REGULATOR 37
	AX-115788386	7	29623803	3.89	15.96	Os07g0695100	OsPRR37; Heading date 2, PSEUDO-RESPONSE REGULATOR 37
	AX-283557343	7	29632090	3.78	15.26	Os07g0695300	OsRLCK243: Receptor-like Cytoplasmic Kinase 243
	AX-117367125	6	10148113	-4.49	11.19	Os06g0285400	Similar to Serine/threonine-specific kinase-like protein.
	AX-154504166	6	10588394	3.99	10.86	Os06g0289900	UDP-glucuronosyl/UDP-glucosyltransferase family protein.
	AX-117355228	6	10377892	-4.46	10.66	Os06g0286500	Similar to NBS-LRR disease resistance protein homolog.
	AX-123161598	6	10347685	-4.45	10.66	Os06g0286351	Armadillo-type fold domain-containing protein
	AX-155742676	6	10480694	4.18	10.29	Os06g0288300	OsCGT; C-glucosyltransferase, Flavone-C-glycoside synthesis
	AX-155780256	6	10343235	4.04	10.27	Os06g0286310	Similar to Oxidoreductase-like protein.
	AX-116841734	6	8197078	3.94	9.98	Os06g0257200	Similar to Signal recognition particle 9 kDa protein.
	AX-154042176	6	10959896	4.02	9.77	Os06g0296700	C-type lectin, conserved site domain-containing protein.
	AX-154664097	6	8313556	3.80	9.54	Os06g0258900	NAD(P)-binding domain-containing protein.
	AX-155544336	6	10553998	3.96	9.47	Os06g0289200	UDP-glucuronosyl/UDP-glucosyltransferase family protein.
	AX-273967585	6	9319713	-2.58	9.34	Os06g0274500	OsSERL2; Somatic embryogenesis receptor kinase-like 2
	AX-117351923	6	10438340	3.82	8.75	Os06g0287500	CC-NBS-LRR protein, Blast resistance
	AX-154759957	6	10374435	3.55	7.87	Os06g0286375	Similar to Nitrate-induced NOI protein-like protein.
	AX-117364893	6	10131338	-3.16	7.79	Os06g0285100	OsFLA23; fasciclin-like arabinogalactan protein 23
	AX-117360522	6	10184468	-3.39	7.40	Os06g0285900	Similar to embryogenesis transmembrane protein.
Panicle length	AX-95959478	9	16415391	1.91	21.49	Os09g0441900	OsDEP1; DENSE AND ERECT PANICLE 1
	AX-95938232	9	16543763	-2.12	9.65	Os09g0444200	Lecithin: cholesterol acyltransferase family protein.
	AX-283693666	9	15591135	-1.35	8.62	Os09g0429000	OsGLR2.1; Glutamate receptor homolog 2.1.
	AX-115821718	9	17185419	-1.88	8.46	Os09g0456100	OsLP1; LONG PANICLE 1.
	AX-117360521	9	17109742	-1.91	8.39	Os09g0455200	OsHSF22; Heat stress transcription factor 22.
	AX-117388485	9	17290563	-1.91	8.23	Os09g0457400	OsEnS-129; Alpha-amylase3A.
	AX-155718545	9	17506122	-1.82	8.01	Os09g0462875	OsSCP42; Serine carboxypeptidase 42.
	AX-276235752	9	17081620	-1.86	7.90	Os09g0454600	OsPT19; Phosphate transporter 19
	AX-116843575	9	17185192	-1.81	7.43	Os09g0456100	OsLP1; LONG PANICLE 1.
	AX-154875030	9	17172676	-1.71	7.39	Os09g0455900	Alpha/beta hydrolase fold-3 domain-containing protein.
	AX-117388873	9	17184182	-1.77	7.23	Os09g0456100	OsLP1; LONG PANICLE 1.