Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Du, Xiongming; Liu, Shouye; Sun, Junling; Zhang, Gengyun; Jia, Yinhua; Pan, Zhaoe; Xiang, Haitao; He, Shoupu; Xia, Qiuju; Xiao, Songhua; Shi, Weijun; Quan, Zhiwu; Liu, Jianguang; Ma, Jun; Pang, Baoyin; Wang, Liru; Sun, Gaofei; Gong, Wenfang; Jenkins, Johnie N.; Lou, Xiangyang; Zhu, Jun; Xu, Haiming

doi:10.1186/s12864-018-4837-0

Table 2 Genome-wide significant QTSs associated with the protein content and the oil content at -log₁₀p > 7 (at least one kind of effect of QTS)

From: Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Trait	QTS	^aChr.	^bAllele	^cEffect type	Predicted effect	−log₁₀p	h²(%)
Protein	A3_115443958	A3	T/A	a	1.302	69.59	5.14
	A6_29542325	A6	G/A	a	0.408	8.16	0.50
	A6_29542325	A6	G/A	d	−0.477	1.33	0.34
	A7_1504479	A7	A/G	a	0.363	6.59	0.40
	A7_1504479	A7	A/G	d	1.019	4.83	1.57
	A11_27630663	A11	A/G	a	0.535	14.64	0.87
	A11_115510024	A11	A/G	a	0.541	14.95	0.89
	D1_616439	D1	C/T	a	−0.909	32.58	2.50
	D2_383581	D2	A/C	d	−1.842	8.56	5.14
	D3_35705563	D3	T/C	a	−0.418	8.83	0.53
	D6_58640083	D6	G/A	a	0.323	5.36	0.32
	D6_58640083	D6	G/A	d	−1.362	7.57	2.81
	D8_18888997	D8	G/A	a	0.38	7.23	0.44
	D8_18888997	D8	G/A	d	−0.513	1.35	0.40
	A3_115443958 & D2_383581	A3 & D2	T/A & A/C	aa	−0.297	4.15	0.53
		A3 & D2	T/A & A/C	ad	−2.579	11.98	20.16
		A3 & D2	T/A & A/C	da	−0.784	4.74	1.86
		A3 & D2	T/A & A/C	dd	1.516	1.94	3.48
	A6_29542325 & D8_18888997	A6 & D8	G/A & G/A	dd	3.167	8.44	15.19
	A7_1504479 & D2_383581	A7 & D2	A/G & A/C	aa	−0.142	1.31	0.12
		A7 & D2	A/G & A/C	da	1.512	9.17	6.93
		A7 & D2	A/G & A/C	dd	−2.902	3.2	12.76
Oil	A2_58832915	A2	G/A	a	0.24	2.5	0.16
	A2_58832915	A2	G/A	d	−0.854	7.79	0.99
	A6_124107263	A6	G/A	a	0.517	11.41	0.73
	A6_124107263	A6	G/A	d	−1.277	5.81	2.22
	A7_110987422	A7	A/C	a	−0.256	3.25	0.18
	A9_85081637	A9	T/C	a	−0.555	13.04	0.84
	A9_85081637	A9	T/C	d	0.563	1.47	0.43
	A13_83121382	A13	T/C	a	0.763	24.58	1.58
		A13	T/C	d	−3.057	18.52	12.71
		A13	T/C	de2	−1.956	3.25	5.20
		A13	T/C	de3	1.262	1.59	2.17
	D3_35705563	D3	T/C	a	0.163	1.57	0.07
	D3_35705563	D3	T/C	d	−1.834	8.06	4.57
	D6_54108367	D6	G/A	d	1.639	8.42	3.65
	D10_18219333	D10	C/T	a	−0.98	40.02	2.61
	D12_3388946	D12	A/G	a	−0.405	7.39	0.45
	D12_3388946	D12	A/G	d	−0.608	1.37	0.50
	D12_41865508	D12	G/A	a	0.526	12.01	0.75
	D12_41865508	D12	G/A	d	0.911	2.49	1.13
	A3_100487624 & D10_18219333	A3 & D10	G/A & C/T	aa	−1.208	44.59	7.94
	A3_100487624 & D10_18219333	A3 & D10	G/A & C/T	da	1.718	32.67	8.03
	A11_34775904 & D9_37961611	A11 & D9	G/A & C/T	aa	−0.565	12.61	1.74
		A11 & D9	G/A & C/T	ad	− 0.608	1.48	1.00
		A11 & D9	G/A & C/T	da	0.741	1.95	1.49
	A7_110987422 & A13_83121382	A7 & A13	A/C & T/C	aa	0.367	5.95	0.73
		A7 & A13	A/C & T/C	ad	−1.483	3.63	5.98
		A7 & A13	A/C & T/C	da	1.332	4.79	4.83
		A7 & A13	A/C & T/C	dd	2.138	3.1	6.21
		A7 & A13	A/C & T/C	ade2	−1.688	2.02	7.76

^aChromosome. A and D represent A genome and D genome of cotton. ^b(Major allele/minor allele). ^ca and d represent the additive effect and the dominant effect respectively; aa, ad, da and dd denote the epistasis effects of the additive × additive, the additive × dominance, the dominance × additive, the dominance × dominance respectively; de2 and de3 denote the interaction effects of the dominance with the second and the third environments respectively; h² is the heritability in percentage due to genetic effect of significant QTS

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