Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.)

Guo, Jie; Shi, Weiping; Zhang, Zheng; Cheng, Jingye; Sun, Daizhen; Yu, Jin; Li, Xinlei; Guo, Pingyi; Hao, Chenyang

doi:10.1186/s12870-018-1234-4

BMC Plant Biology

Table 3 Favored alleles and genetic effects of 76 SNP loci significantly (P < 3.06 × 10^− 4) associated with six phenotypic traits

From: Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.)

Trait	SNP Name	Chr.	Position	Favored allele	Freq. (%)	Allele effect
Trait	SNP Name	Chr.	Position	Favored allele	Freq. (%)	09TA	09YL	09YZ	10TA	10YL	10YZ	BLUP
PH	wsnp_Ra_c16846_25598885	3A	54.99	GG	93.56	−1.50^*
	wsnp_Ex_c13802_21639096	3A	56.74	TT	93.56			−1.57^*
	wsnp_BF292596A_Ta_1_1	3A	119.09	CC	74.29						−1.49^*
	wsnp_JD_c8158_9193784	3B	69.01	CC	82.52	−2.69^*
	wsnp_CAP8_c4989_2410261	3B	97.05	CC	94.37					−1.10^*
	wsnp_CAP8_c1419_836050	3B	97.26	GG	94.37				−1.24^*
	wsnp_Ex_c33463_41948471	3B	97.72	GG	94.37					−1.21^*
	wsnp_Ex_c12048_19288999	5B	71.11	TT	85.78	−4.93^**	−1.68^*	− 1.87^*			−1.53^*	− 1.36^*
	wsnp_Ku_c99567_87349060	5B	163.25	CC	90.73		−8.82^**	−6.91^**			−5.90^**
	wsnp_Ex_c34597_42879693	6A	180.19	TT	79.02		−6.88^**	−6.07^**
	wsnp_Ra_rep_c69821_67403173	6B	82.68	TT	43.28				−3.06^*
	wsnp_Ex_c15458_23737002	7B	65.56	GG	61.43	−3.46^**			−3.32^*
SL	wsnp_JD_c6974_8084752	3B	95.50	GG	93.49	0.80^*
	wsnp_CAP8_c4989_2410261	3B	97.05	CC	94.37				1.05^*
	wsnp_CAP8_c1419_836050	3B	97.26	GG	94.37					1.10^**		1.09^**
	wsnp_Ex_c33463_41948471	3B	97.72	GG	94.37			0.76^*
	wsnp_Ex_c1563_2987002	4A	136.22	GG	93.95					0.64^*		0.72^*
	wsnp_Ex_c28092_37240192	4A	140.47	GG	95.10				0.58^*
	wsnp_Ex_rep_c67779_66463916	4A	141.36	CC	94.84		0.40^*	0.37^*		0.49^*		0.62^*
	wsnp_Ex_c2266_4247520	4A	141.80	AA	94.81					0.38^*		0.49^*
	wsnp_Ex_c12_21212	4A	143.00	TT	94.84			0.49^*
	wsnp_Ex_c3463_6348659	4A	144.11	GG	94.81				0.48^*	0.45^*	0.60^*
	wsnp_Ex_c13942_21820758	5A	102.41	GG	91.63							0.89^*
	wsnp_Ex_c49211_53875575	5A	108.64	GG	60.47	0.32^**	0.42^**	0.30^**	0.27^**	0.62^**	0.52^**
	wsnp_Ex_c10127_16635328	5A	108.92	TT	64.19	0.18^*
	wsnp_Ex_c19647_28632894	5A	123.92	GG	53.49						0.48^*
	wsnp_Ex_c1630_3105100	5B	161.77	AA	94.81					1.34^**
	wsnp_Ex_c2459_4591695	5B	212.53	AA	94.88					0.97^**		0.68^**
	wsnp_Ex_c8510_14306239	6A	175.39	AA	94.39					1.02^**		0.74^**
	wsnp_Ex_c46061_51675853	7B	25.00	GG	19.34						0.89^*
	wsnp_Ex_rep_c101269_86664147	7B	132.23	AA	23.27		0.57^**				0.78^**
SNPS	wsnp_BM140362B_Ta_1_1	1B	76.37	AA	93.84				1.08^*
	wsnp_Ku_rep_c68484_67499824	3A	99.60	TT	66.67			0.46^*
	wsnp_Ex_rep_c67136_65617520	4B	108.15	CC	87.25			0.73^*
	wsnp_Ku_c21275_31007309	5A	85.17	CC	36.28		0.45^*
	wsnp_RFL_Contig3939_4369467	5A	94.73	CC	88.37		1.08^**
	wsnp_Ex_c7713_13153321	6B	127.53	CC	89.47	1.48^**
KNPS	wsnp_JD_c6974_8084752	3B	95.50	GG	93.49				2.79^*
	wsnp_Ex_c6129_10723019	3B	97.26	CC	91.59			2.71^**			2.50^**
	wsnp_Ku_c29102_39008953	3B	123.29	AA	74.04	3.18^**	3.84^**					3.45^**
	wsnp_Ku_c31407_41142340	3B	125.61	AA	76.64					1.23^*
	wsnp_Ex_c11837_18996495	3B	126.24	GG	77.25		3.97^**					3.27^**
	wsnp_Ex_c12781_20280445	3B	126.61	GG	76.64					3.25^**	3.27^**
	wsnp_Ex_c13154_20784674	3B	127.87	CC	76.92	3.59^**	4.18^**					3.73^**
	wsnp_Ex_c13154_20785032	3B	127.87	AA	76.56	3.44^**						3.55^**
	wsnp_Ex_c13953_21831752	4A	13.89	CC	81.43			4.27^**	3.45^**
	wsnp_Ex_c16551_25060833	5A	190.95	CC	19.53	2.01^*
	wsnp_Ex_c1630_3105100	5B	161.77	AA	94.81				2.49^*
	wsnp_Ex_c1302_2489542	5B	184.33	TT	89.37						2.62^*
	wsnp_Ku_c56917_60245833	5B	185.06	CC	89.47						2.74^*
	wsnp_Ku_c19037_28455905	7B	57.38	GG	80.90			0.88^*
KWPS	wsnp_Ex_rep_c106111_90308719	1A	12.73	TT	6.10		0.11^*					0.10^*
	wsnp_Ex_c1130_2166731	1D	54.49	GG	6.05							0.20^*
	wsnp_Ex_rep_c69919_68881108	3A	117.88	AA	70.48				0.03^*
	wsnp_Ex_rep_c104327_89077792	3A	118.07	AA	70.48			0.03^*
	wsnp_Ra_c19079_28210937	3A	123.35	AA	47.85		0.02^*
	wsnp_Ex_c12341_19693570	3A	127.51	CC	57.21	0.14^**			0.20^**		0.21^**
	wsnp_Ku_c29102_39008953	3B	123.29	CC	25.96			0.10^*
	wsnp_Ex_c13154_20785032	3B	127.87	GG	23.44	0.11^*
	wsnp_Ex_rep_c67136_65617520	4B	108.15	CC	87.25			0.05^*
	wsnp_JD_rep_c49046_33288885	5A	116.00	CC	92.56			0.31^**				0.15^**
	wsnp_Ku_c14275_22535693	5A	116.57	AA	90.70				0.15^*
	wsnp_Ku_c14275_22535576	5A	116.83	TT	90.70						0.17^*
	wsnp_Ex_c43578_49857984	5A	130.98	TT	72.56		0.20^**					0.20^**
	wsnp_Ex_rep_c101757_87064771	5A	133.01	CC	97.21			0.18^*
	wsnp_Ex_rep_c101757_87065169	5A	133.17	CC	90.70	0.18^*
	wsnp_Ex_c57667_59284398	5B	125.89	CC	56.59	0.07^*
	wsnp_Ex_c1050_2009301	6A	45.73	TT	85.10				0.19^*
	wsnp_Ex_c19467_28423197	6B	50.70	AA	7.62	0.26^*
	wsnp_Ex_c65899_64135487	7D	1.12	AA	95.12		0.01^*
TKW	wsnp_Ex_c3685_6723631	2A	9.91	GG	34.11							1.07^*
	wsnp_BE406351A_Ta_2_2	2A	112.62	TT	66.03	0.83^*
	wsnp_RFL_Contig2914_2757372	2B	211.84	AA	61.46					1.19^*
	wsnp_Ku_rep_c69511_68887456	3A	59.73	TT	55.77	1.41^**	1.01^**	1.48^**				1.33^**
	wsnp_CAP12_c4769_2174195	4B	106.45	CC	89.76				1.26^*
	wsnp_BF291478B_Ta_2_1	6B	80.00	CC	84.21	1.18^*

^*indicates significant at P < 0.05 ^**indicates significant at P < 0.01

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