Table 3.

GWAS results for final set of genetic loci detected for grain yield in non-stress and water-deficit stress conditions during 2013 and 2014. Detailed GWAS results for yield components and related traits across treatments and years are given in Supplementary Tables S3–S6 and S8

Treatment	Year (mean grain yield (g m−2))	Locus name	SNP posa	Chrb	Allele	MAFc	P CMLM d	P MLMM e	AEf (g m−2)	LD blockg		Size (kb)	Known genesh
										Start	End
Non-stress	2013 (451.1)	Q1	10101900	11	C:G	0.336	2.72 × 10−5	—	30.13	10101900	10173685	71	2
		Q2	30523925	2	G:A	0.070	—	5.78 × 10 −8	−175.90	30397910	30541202	143	16
	2014 (521.9)	Q3	13199901	12	C:T	0.468	6.84 × 10−5	—	30.04	12917853	13298195	380	8
		Q4	26796595	3k	C:T	0.097	9.91 × 10−5	2.20 × 10−6	−46.18	26756997	26978105	221	9
		Q5	29142398	2l	C:A	0.179	—	4.19 × 10−5	13.98	29122557	29261158	138	9
		Q6	19367031	10l	T:G	0.466	—	1.75 × 10−6	74.08	19280939	19474522	193	21
		Q7	5105627	12l	A:C	0.078	—	3.03 × 10−5	−186.24	5101105	5390949	289	12
		Q8	42643337	1l	A:G	0.347	—	6.58 × 10−5	−97.80	42587683	42643699	56	9
Water deficit	2013 (317.3)	Q9i	34815277	4	C:T	0.074	1.17 × 10−5	1.77 × 10−6	−81.29	34815277	34833179	17	5
		—	—	—	—	—	1.29 × 10 −6	3.05 × 10 −6
		Q10j	5113428	3k	T:C	0.424	3.55 × 10−5	5.17 × 10−6	−40.61	5 021 158	5167439.00	146	13
	2014 (319.5)	Q11	6934188	3k	A:G	0.397	8.26 × 10−5	8.73 × 10−6	31.47	6 908 684	7020707	112	7
		Q12	42144827	1l	T:C	0.366	—	1.86 × 10−7	6.10	42 123 552	42144993	21	2
		Q13	16038003	10l	T:C	0.358	—	5.46 × 10−6	−49.86	16 024 382	16110372	85	6
		Q14	23005301	11l	G:A	0.276	—	1.12 × 10−5	−23.54	22 976 390	23005386	28	0
		Q15	27115652	11l	G:A	0.075	—	4.92 × 10−5	33.65	27 115 609	27123090	7	1

^a Single nucleotide polymorphism (SNP) position.

^b Chromosome.

^c Minor allele frequency (MAF).

^d P-value of single-locus compressed mixed linear model (CMLM).

^e P-value of multi-locus mixed model (MLMM).

^f Allelic effect with respect to minor allele=(average traits value of genotypes carrying minor allele−average traits value of genotypes carrying major allele).

^g Linkage disequilibrium block.

^h Total number of known characterized genes in LD block.

ⁱ Genetic locus detected for non-corrected and corrected grain yield value.

^j Genetic locus detected for corrected grain yield value and coinciding with days to flowering.

^k Genetic locus detected through CMLM and MLMM methods.

^l Genetic locus detected through MLMM method only.

All the unmarked loci were detected through CMLM method. The italic P-value is for corrected grain yield value. The genetic locus marked in bold (Q2) overlaps with panicle weight (equivalent to grain yield) from Kikuchi et al. (2017) (Supplementary Table S10).