Table 1.

Gene-set analysis using GWAS of candidates identified within the hotspot genomic regions on chromosomes 3, 6, 8, and 11 associated with head rice yield.

Gene ID†	No. of SNPs	SNP positions		Percent head rice			Weight head rice			Annotation
		Start	End	Z-Score	P-value	Corrected P-value‡	Z-Score	P-value	Corrected P-value‡
Chromosome 3
LOC_Os03g53990	32	30954587	30959201	2.79	0.0026	0.0784	2.82	0.0024	0.0726	Development unspecified
Chromosome 6
LOC_Os06g45550	16	27572045	27573452	4.10	2.09E−5	0.0006	4.10	2.0E−5	0.0006	Unclassified
LOC_Os06g45560	91	27583949	27590245	3.60	0.0002	0.0047	3.60	0.0002	0.0046	Unclassified
LOC_Os06g45570	2	27595301	27595529	3.35	0.0004	0.0116	3.35	0.0004	0.0117	Unclassified
LOC_Os06g45580	4	27598795	27599239	3.57	0.0002	0.0051	3.58	0.0002	0.0049	Protein degradation ubiquitin E3 RING
LOC_Os06g45590	5	27601517	27603740	3.84	0.0001	0.0018	3.86	0.0001	0.0017	Plastid branch 3-phosphoglycerate kinase
LOC_Os06g45600	4	27608612	27609181	3.87	0.0001	0.0016	3.89	0.0001	0.0015	Unclassified
LOC_Os06g45610	4	27614080	27614765	3.65	0.0001	0.0039	3.66	0.0001	0.0036	Unclassified
Chromosome 8
LOC_Os08g39590	6	25060904	25062898	2.08	0.0189	0.5484	2.06	0.0199	0.5777	Signalling receptor kinases
LOC_Os08g39600	14	25064684	25066661	1.82	0.0342	0.9929	1.81	0.0354	1.0000	RNA processing
LOC_Os08g39610	5	25068294	25068437	2.40	0.0081	0.2356	2.38	0.0086	0.2501	Unclassified
LOC_Os08g39620	57	25070901	25076423	1.68	0.0466	1.0000	1.67	0.0477	1.0000	Transcription factor
LOC_Os08g39640	53	25102192	25105599	2.33	0.0099	0.2867	2.32	0.0102	0.2953	Cytochrome P450
LOC_Os08g39650	48	25107131	25109344	3.46	0.0003	0.0078	3.45	0.0003	0.0081	Unclassified
LOC_Os08g39660	16	25110579	25111307	2.56	0.0052	0.1513	2.55	0.0053	0.1542	Cytochrome P450
LOC_Os08g39694	94	25121356	25134182	1.80	0.0357	1.0000	1.79	0.0364	1.0000	Cytochrome P450
LOC_Os08g39710	22	25138857	25142157	2.94	0.0016	0.0477	2.93	0.0017	0.0499	Signalling receptor kinases
LOC_Os08g39730	20	25155263	25156844	2.01	0.0220	0.6369	2.03	0.0213	0.6170	Cytochrome P450
LOC_Os08g39760	15	25174628	25179927	3.51	0.0002	0.0065	3.47	0.0003	0.0075	Signalling receptor kinases
LOC_Os08g39770	31	25185266	25186195	2.60	0.0047	0.1362	2.57	0.0051	0.1478	Unclassified
LOC_Os08g39780	36	25187198	25188563	2.35	0.0094	0.2734	2.33	0.0099	0.2882	Unclassified
LOC_Os08g39790	9	25189370	25189553	1.92	0.0273	0.7911	1.90	0.0289	0.8373	Unclassified
LOC_Os08g39800	10	25193197	25193799	1.72	0.0428	1.0000	1.68	0.0463	1.0000	Unclassified
Chromosome 11
LOC_Os11g42800	68	25775818	25778449	1.91	0.0278	0.8059	1.92	0.0272	0.7874	Cell organization

^†Genes showing P≤0.05 were included.

^‡ P-values subjected to Bonferroni correction.