An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

Su, Junji; Wang, Caixiang; Ma, Qi; Zhang, Ai; Shi, Chunhui; Liu, Juanjuan; Zhang, Xianliang; Yang, Delong; Ma, Xiongfeng

doi:10.1186/s12870-020-02613-y

BMC Plant Biology

Table 1 The significant SNPLDB loci associated with three yield-related traits in upland cotton

From: An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

Traits	Locus	Chr.	Position	-log₁₀(P)	PVE(%)	Common environments ^a
BN	LDB_10_108252822	A10	108,252,822	16.46	0.58	E2(7.68)
	LDB_8_80957905_80958114	A08	80,957,905	9.87	0.97	E2(3.30)
	LDB_9_38930641	A09	38,930,641	9.52	0.51	E2(2.58)
	LDB_18_53807715	D05	53,807,715	8.38	0.37	E3(2.32)
	LDB_3_42046528_42046540	A03	42,046,528	6.52		E2(4.92)
	LDB_16_4143574	D03	4,143,574	5.94	0.38	E2(4.39)
	LDB_5_32745305	A05	32,745,305	2.80		E1(3.07)
	LDB_5_30624560	A05	30,624,560	1.84	0.22	E2(5.03)
BW	LDB_25_61293136^b	D12	61,293,136	28.02	1.05	E1(5.75), E2(7.39), E4(9.79)
	LDB_7_11434307	A07	11,434,307	19.97	3.12	E3(13.44)
	LDB_18_60784,945	D05	60,784,945	19.01	2.68	E1(4.96)
	LDB_8_117999939	A08	117,999,939	18.24	0.97	E3(9.25)
	LDB_24_62501704_62501749	D11	62,501,704	14.84	0.56	E1(6.03)
	LDB_18_62137879	D05	62,137,879	14.07	1.31	E4(10.43)
	LDB_1_27714781	A01	27,714,781	13.53	2.33	E1(1.71)
	LDB_23_7162905	D10	7,162,905	12.59	0.58	E4(3.13)
	LDB_3_101231660	A03	101,231,660	8.52	0.20	E3(11.57)
	LDB_5_2524535	A05	2,524,535	7.65	1.00	E1(1.69)
	LDB_15_21962239	D02	21,962,239	2.02		E4(2.61)
	LDB_13_31802375	A13	31,802,375	1.31		E1(8.65)
LP	LDB_2_98957055_98957100^b	A02	98,957,055	46.97	0.98	E3(21.27), E4(17.27)
	LDB_20_52488458^b	D07	52,488,458	40.68	5.09	E2(10.18), E3(12.10)
	LDB_6_81838215_81856977	A06	81,838,215	39.14	3.67	E4(13.50)
	LDB_19_62926589^b	D06	62,926,589	29.91	2.60	E2(14.57), E3(4.25),
	LDB_15_33683466_33683486^b	D02	33,683,466	22.99	0.19	E3(8.76), E4(8.64)
	LDB_6_87041656_87041922^b	A06	87,041,656	21.47	2.01	E1(4.66), E2(3.48)
	LDB_22_5519816_5520088	D09	5,519,816	17.17	2.12	E3(10.04)
	LDB_5_6292927	A05	6,292,927	16.95	1.20	E4(17.58)
	LDB_13_14883849_14884035	A13	14,883,849	6.83	0.35	E2(7.38)
	LDB_15_6072794	D02	6,072,794	6.01	0.77	E3(2.25)
	LDB_15_58321721	D02	58,321,721	3.90		E1(1.66)
	LDB_12_92891416_92891433	A12	92,891,416	1.61	0.08	E1(2.93)

^a Figures in brackets denote -log₁₀(P) values in the planting environments. ^b labels the six stable SNPLDB loci
BN Boll number, BW Boll weight, LP Lint percentage, Chr. Chromosome, PVE Phenotypic variation explanation

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ISSN: 1471-2229

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