Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.)

Ma, Jianjiang; Geng, Yanhui; Pei, Wenfeng; Wu, Man; Li, Xingli; Liu, Guoyuan; Li, Dan; Ma, Qifeng; Zang, XinShan; Yu, Shuxun; Zhang, Jinfa; Yu, Jiwen

doi:10.1186/s12864-018-5309-2

Table 4 Summary of SNPs significantly associated with FL traits at different developmental time-points

From: Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.)

QTL	SNP	Chr.	Site	-log10P	R² (%)	Traits	Reported previously
FL-QTL-1	i43923Gh	At8	6,889,977	4.70–7.91	20.54–43.50	25 DPA^a,b, Maturity^b,c	[16, 22]
	i47458Gh	At8	6,926,743	4.64–7.77	20.20–42.63	25 DPA^a,b, Maturity^b,c
	i46694Gh	At8	6,947,649	4.64–7.77	20.20–42.63	25 DPA^a,b, Maturity^b,c
FL-QTL-2	i55088Gb	At9	60,651,133	4.27–12.61	11.71–49.44	25 DPA^a,b, Maturity^a,b
FL-QTL-3	i06403Gh	At9	70,095,261	5.40–6.94	14.56–20.77	20 DPA^b, 25 DPA^a,b, Maturity^a,b,c
FL-QTL-3	i06405Gh	At9	70,132,917	5.40–6.94	14.56–20.77	20 DPA^b, 25 DPA^a,b, Maturity^a,b,c
FL-QTL-4	i07778Gh	At12	562,289	4.21–5.97	18.57–27.78	25 DPA^a,b, Maturity^b,c
FL-QTL-5	i16326Gh	At12	62,237,916	4.20–9.15	17.91–53.60	20 DPA^b,c, 25 DPA^a, Maturity^b,c	[20]
	i31671Gh	At12	62,374,407	4.21–8.99	18.03–52.56	20 DPA^b,c, 25 DPA^a, Maturity^b,c
	i34476Gh	At12	62,421,193	4.20–9.15	17.91–53.60	20 DPA^b,c, 25 DPA^a, Maturity^b,c
	i36493Gh	At12	62,584,169	4.20–9.15	17.91–53.60	20 DPA^b,c, 25 DPA^a, Maturity^b,c
	i63008Gt	At12	62,631,642	4.21–8.99	18.03–52.56	20 DPA^b,c, 25 DPA^a, Maturity^b,c
	i08069Gh	At12	62,823,942	4.20–9.15	17.91–53.60	20 DPA^b,c, 25 DPA^a, Maturity^b,c
	i46470Gh	At12	62,896,861	4.22–8.99	18.03–52.56	20 DPA^b,c, 25 DPA^a, Maturity^b,c
FL-QTL-6	i05769Gh	Dt2	67,113,037	5.38–8.75	14.59–28.90	15 DPA^c, 25 DPA^a,b, Maturity^b,c
FL-QTL-7	i60907Gt	Dt4	196,659	4.24–9.87	18.05–59.97	20 DPA^b, 25 DPA^a,b, Maturity^b,c
FL-QTL-7	i47681Gh	Dt4	200,376	4.24–9.87	18.05–59.97	20 DPA^b, 25 DPA^a,b, Maturity^b,c
FL-QTL-8	i27361Gh	Dt4	3,262,973	4.23–5.36	11.10–14.30	20 DPA^b,c, 25 DPA^a,b, Maturity^b
	i39155Gh	Dt4	3,280,556	4.23–5.36	11.10–14.30	20 DPA^b,c, 25 DPA^a,b, Maturity^b
	i36124Gh	Dt4	3,387,942	4.29–5.66	18.30–25.97	20 DPA^b,c, 25 DPA^a,b, Maturity^b,c
	i20432Gh	Dt4	3,496,432	4.45–6.57	19.22–31.58	20 DPA^b, 25 DPA^a,b, Maturity^b,c
	i17744Gh	Dt4	3,544,396	4.31–6.61	18.41–31.78	20 DPA^b, 25 DPA^a,b, Maturity^b,c
	i12503Gh	Dt4	3,551,693	4.29–5.66	18.30–25.97	20 DPA^b,c, 25 DPA^a,b, Maturity^b,c
	i24940Gh	Dt4	3,731,918	4.37–6.16	18.73–28.94	20 DPA^b, 25 DPA^a,b, Maturity^b,c
	i45150Gh	Dt4	3,735,149	4.37–6.16	18.73–28.94	20 DPA^b, 25 DPA^a,b, Maturity^b,c
FL-QTL-9	i56109Gb	Dt5	10,061,254	4.30–6.67	18.41–32.06	15 DPA^c, 20 DPA^b, 25 DPA^a,b
FL-QTL-10	i01791Gh	Dt7	20,011,717	5.08–9.01	13.59–30.13	20 DPA^b, 25 DPA^a,b, Maturity^b,c
FL-QTL-10	i01793Gh	Dt7	20,012,463	5.36–9.85	24.23–59.73	25 DPA^a,b, Maturity^b,c
FL-QTL-11	i25898Gh	Dt8	60,138,274	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b	[16]
	i39699Gh	Dt8	60,145,594	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i04589Gh	Dt8	60,209,167	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i52348Gb	Dt8	60,213,494	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i40219Gh	Dt8	60,283,929	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i25899Gh	Dt8	60,289,122	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i04592Gh	Dt8	60,327,275	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
	i47255Gh	Dt8	60,364,319	4.37–8.60	12.02–28.24	25 DPA^a,b, Maturity^a,b
FL-QTL-12	i36390Gh	Dt9	35,827,578	4.50–4.53	19.30–25.02	10 DPA^b, 15 DPA^c, 25 DPA^a,b
FL-QTL-13	i06490Gh	Dt9	47,021,366	4.19–7.72	11.44–24.40	25 DPA^a,b, Maturity^a,b
FL-QTL-13	i06491Gh	Dt9	47,021,806	4.19–7.72	11.44–24.40	25 DPA^a,b, Maturity^a,b
FL-QTL-14	i20045Gh	Dt10	13,951,286	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c	[20]
	i39524Gh	Dt10	13,996,422	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
	i35125Gh	Dt10	13,999,766	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
	i38078Gh	Dt10	14,128,474	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
	i37666Gh	Dt10	14,155,678	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
	i39425Gh	Dt10	14,181,220	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
	i27558Gh	Dt10	14,295,765	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
FL-QTL-15	i14259Gh	Dt10	55,580,911	4.86–6.62	22.11–33.94	25 DPA^a,b, Maturity^a,b	[9]
FL-QTL-15	i20114Gh	Dt10	55,589,792	4.86–6.62	22.11–33.94	25 DPA^a,b, Maturity^a,b	[9]
FL-QTL-16	i60963Gt	Dt11	8,678,122	4.59–12.82	19.89–60.01	25 DPA^a,b, Maturity^a,b,c
FL-QTL-17	i07222Gh	Dt11	16,662,698	5.14–12.16	13.74–46.69	10 DPA^b, 25 DPA^a,b, Maturity^a,b,c
FL-QTL-18	i60962Gt	Dt11	24,030,081	4.67–6.29	20.36–31.63	25 DPA^a,b, Maturity^b,c	[9, 10]
	i16034Gh	Dt11	24,059,057	4.67–6.29	20.36–31.63	25 DPA^a,b, Maturity^b,c
	i16035Gh	Dt11	24,059,152	4.67–6.29	20.36–31.63	25 DPA^a,b, Maturity^b,c
FL-QTL-19	i32896Gh	Dt12	7,215,751	4.53–9.15	19.56–53.61	25 DPA^a,b, Maturity^a,b,c
	i07931Gh	Dt12	7,261,923	4.53–9.15	19.56–53.61	25 DPA^a,b, Maturity^a,b,c
	i34663Gh	Dt12	7,263,333	4.53–9.15	19.56–53.61	25 DPA^a,b, Maturity^a,b,c
	i34662Gh	Dt12	7,378,095	4.53–9.15	19.56–53.61	25 DPA^a,b, Maturity^a,b,c
FL-QTL-20	i19464Gh	Dt12	46,546,520	4.23–7.99	17.96–44.08	25 DPA^a,b, Maturity^a,b,c
FL-QTL-21	i11417Gh	Dt13	54,844,478	4.68–6.79	12.43–19.07	15 DPA^c, 25 DPA^b, Maturity^a,b	[16]
FL-QTL-21	i33230Gh	Dt13	56,126,379	4.25–7.09	11.06–20.16	25 DPA^b,c, Maturity^a,b,c	[16]
AGR-QTL-1	i06955Gh	At11	6,536,455	4.27	19.45	10–15 DPA^c
AGR-QTL-1	i06960Gh	At11	6,631,727	4.19	18.83	10–15 DPA^c
AGR-QTL-2	i02910Gh	Dt1	58,316,772	5.02	22.61	10–15 DPA^c, 15–20 DPA^c
AGR-QTL-3	i36135Gh	Dt4	7,617,473	4.45	20.02	10–15 DPA^c
AGR-QTL-3	i33788Gh	Dt4	7,718,785	4.45	20.02	10–15 DPA^c
AGR-QTL-4	i08049Gh	Dt12	37,886,196	4.58	25.31	15–20 DPA^a
	i08062Gh	Dt12	38,398,622	4.46	28.99	15–20 DPA^a
	i08063Gh	Dt12	38,401,647	4.85	26.76	15–20 DPA^a
AGR-QTL-5	i11425Gh	Dt13	54,754,208	5.99	19.2	20–25 DPA^b	[16]
AGR-QTL-5	i11417Gh	Dt13	54,844,478	5.66	29.01	10–15 DPA^c	[16]

a, b and c indicate the 2014, 2015, and 2016 environments in Anyang, respectively
r² is the percentage of phenotypic variance explained by the SNP
Traits indicate the FL and AGR at different developmental time-point

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