Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

Bhandari, Aditi; Sandhu, Nitika; Bartholome, Jérôme; Cao-Hamadoun, Tuong-Vi; Ahmadi, Nourollah; Kumari, Nilima; Kumar, Arvind

doi:10.1186/s12284-020-00406-3

Rice

Table 1 Summary statistics and sources of variation for the ten phenotypic traits under three different environments and two seasons for the diverse set of 280 lines

From: Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

Trait	Env	Wet Season					Dry Season
		Mean (SD)	Phenotypic variance				Mean (SD)	Phenotypic variance
			Fixed	Random		H²		Fixed	Random		H²
			Fixed	Genotype	Residual	H²		Fixed	Genotype	Residual	H²
DTF	LL_N	90.4 (8.69)	0.36	22.55^NS	52.22	0.34	87.83 (9.53)	0.12	76.31^d	23.49	0.75
	LL_S	79.66 (6.7)	2.29	37.89^d	6.02	0.90	88.09 (16.68)	5.96	212.92^d	68.03	0.85
	UL_S	80.28 (9.64)	0.01	55.82^d	39.41	0.72	93.07 (20.09)	4.78	357.44^d	51.19	0.93
PH	LL_N	113.79 (24.23)	1.18	579.55^d	42.06	0.93	108.63 (21.2)	0.08	538.47^d	21.62	0.96
	LL_S	102.42 (26.61)	8.70	605.08^d	104.52	0.92	69.09 (16.67)	3.34E-15	191.30^d	90.86	0.79
	UL_S	110.23 (29.58)	20.55	241.92^NS	616.22	0.43	71.03 (15.55)	8.56	196.20^d	46.21	0.88
PL	LL_N	21.75 (3.41)	0.01	1042^d	1.86	0.91	22.15 (3.16)	0.02	9.29^d	2.05	0.81
	LL_S	20.05 (3.12)	0.07	5.65^d	4.13	0.79	17.87 (3.35)	0.04	5.19^d	5.88	0.63
	UL_S	20.41 (3.22)	0.64	1.64^NS	8.13	0.16	16.45 (2.09)	0.41	1.45^d	2.58	0.50
FlgLA	LL_N	36.0 (10.92)	0.02	83.89^d	36.74	0.68	36.73 (9.74)	0.09	98.77^d	12.34	0.89
	LL_S	40.19 (13.46)	1.31	79.15^d	101.37	0.68	29.85 (9.81)	1.65	43.95^d	50.54	0.71
	UL_S	37.77 (11.95)	6.51	24.81^NS	111.33	0.19	22.96 (6.04)	1.67	17.56^d	17.99	0.63
BMDW	LL_N	15.57E + 03 (92E + 02)	0.05	3.13E + 07^d	5.48E + 08	0.34	14.78E + 03 (67.81E + 02)	1.92E + 05	4.23E + 07^d	9.9E + 06	0.82
	LL_S	36.13E + 02 (14.4E + 02)	1.11E + 05	4.86E + 05^a	15.06E + 05	0.40	36.50E + 02 (15.49E + 02)	3.37E + 04	6.6E + 05^d	1.75E + 06	0.50
	UL_S	54.61E + 02 (56.5E + 02)	2.07E + 05	5.87E + 07^NS	3.18E + 07	0.35	55.29E + 02 (18.14E + 02)	3.65E + 05	7.29E + 05^NS	2.34E + 06	0.42
NBP	LL_N	46.99 (18.24)	0.03	214.91^b	126.33	0.70	54.81 (17.02)	1.93	130.23^c	162.03	0.44
	LL_S	20.38 (14.57)	2.38	15.81^NS	211.05	0.20	14.99 (13.59)	2.91	102.80^d	83.08	0.76
	UL_S	23.32 (16.38)	11.35	0.22^NS	255.78	0.23	24.84 (14.38)	2.9	136.37^d	73.28	0.78
GY	LL_N	16.66E + 02 (10.03E + 02)	0.05	7.94E + 05^d	2.28E + 05	0.84	5.21E + 02 (16.8E + 02)	2.41E + 04	3.92E + 06^d	1.55E + 06	0.68
	LL_S	5.73E + 02 (6.28E + 02)	7.79E + 03	3.68E + 04^NS	3.52E + 05	0.20	1.58E + 02 (2.89 E + 02)	1.4E + 03	4.91E + 04^d	3.49E + 04	0.74
	UL_S	9.42E + 02 (9.24E + 02)	0.02	3.26E + 04^NS	8.23E + 05	0.13	3.36E + 02 (6.1 E + 02)	2.29E + 09	8.12E + 09^d	2.52E+ 04	0.91
TGW	LL_N	198.13 (77.77)	79.37	2221.13^b	3824.46	0.37	218.53 (39.82)	112.63	1528.06^d	191.65	0.89
	LL_S	149.2 (80.97)	75.33	0.01^NS	6481.26	0.20	113.26 (79.5)	158.25	2139.19^d	4015.32	0.52
	UL_S	177.96 (84.55)	96.99	0.01^NS	7100.32	0.10	83.69 (78.41)	138.69	4111.16^d	1870.32	0.81
HI	LL_N	0.17 (0.15)	0.01	0.001^NS	0.02	0.30	0.39 (0.11)	2.4E-04	0.006^d	0.005	0.61
	LL_S	0.15 (0.17)	4.8E-06	2.03E-03^NS	0.03	0.21	0.05 (0.08)	5.2E-05	0.004^d	0.003	0.76
	UL_S	0.11 (0.1)	0.001	8E-05^NS	0.01	0.14	0.05 (0.09)	8.2E-05	0.006^d	0.003	0.82
SPKFT	LL_N	86.81 (9.64)	0.02	27.88^a	64.19	0.80	96.41 (3.25)	0.51	6.83^d	4.22	0.78
	LL_S	57.49 (29.94)	29.36	106.46^NS	762.52	0.22	47.03 (31.33)	81.07	315.92^d	615.27	0.60
	UL_S	61.19 (29.59)	0.01	86.21^NS	892.48	0.15	25.19 (34.85)	27.01	809.67^d	349.53	0.81

SD standard deviation, Env environment (lowland non-stress, LL_N; lowland stress, LL_S and upland stress, UL_S), Fixed effects block (rep), Random effects genotype and residual, H² broad sense heritability for single environment analysis, DTF days to 50% flowering, PH plant height (cm), PL panicle length (cm), FlgLA flag leaf area (cm²), BMDW biomass dry weight at maturity (kg ha⁻¹), NBP number of effective panicles, GY grain yield (kg ha⁻¹), TGW 1000 grain weight (g), HI harvest index and SPKFT spikelet fertility from each of the six experiments in two seasons (wet and dry). ^asignificant at 5%, ^bsignificant at 1%, ^c significant at 0.1%, ^dsignificant at 0.01% levels and NS- Non-significant

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