烟草生物碱性状的QTL定位

doi:10.3724/SP.J.1006.2024.34047

Abstract

Abstract:

Alkaloids are important chemical components in tobacco. In order to understand the genetic architecture of alkaloids in tobacco and identify major effect loci controlling alkaloids related traits, QTL mapping on tobacco alkaloids was performed. A set of 271 recombinant inbred lines (RIL) were constructed with Y3 and K326 as the parents. The RIL population was planted in Yanhe, Yuxi, Yunnan province and Shilin, Kunming, Yunnan province in 2018, 2019, and 2020, respectively. Five alkaloid phenotypes including total plant alkali (TPA), nicotine (NIC), nornicotine (NOR), anabasine (ANAB), and anatabine (ANAT) were measured. A linkage map of 46,129 markers was constructed by genome sequencing of the population. QTL mapping was performed by the software QTLNetwork 2.0 which was developed based on the mixed linear model. A total of 15 QTLs with significant additive effects were identified. The contribution rate of additive effect to the corresponding phenotypes varied from 0.58% to 11.57%. Four major QTLs, qTPA14 for total plant alkali, qNIC14 for nicotine, qANAB14 for anabasine, and qANAT14 for anatabine, accounted for more than 10% of phenotypic variation of the corresponding traits, which were located in linkage group 14. Six QTLs with significant additive-by-environment interaction effects were detected, their additive-by-environment interaction effects explained the phenotypic variation of 0.80%-1.81%. Five pairs of QTLs with significant additive-by-additive epistasis effects were detected, accounting for phenotypic variation from 0.15% to 2.31%, while two pairs of QTLs were detected with significant epistasis-by-environment interaction effects, which explaining the proportion of phenotypic variation from 0.81% to 1.16%. The results pave a foundation for further isolation of candidate genes, the dissection of genetic mechanism, and the molecular improvement of tobacco alkaloid traits.

Key words: tobacco, the recombinant inbred line, alkaloids, complex traits, gene by environment interaction

LIU Ying-Chao, FANG Dun-Huang, XU Hai-Ming, TONG Zhi-Jun, XIAO Bing-Guang. QTL mapping of alkaloids in tobacco[J].Acta Agronomica Sinica, 2024, 50(1): 42-54.

Figures/Tables 7

Table 1

Fig. 1

Fig. 2

Table 2

Table 3

Additive effect and additive-by-environment interaction effects of detected QTLs for alkaloids"

性状 Trait	位点 QTL	连锁群 LG	左侧标记 M-	右侧标记 M+	位置 Position (cM)	区间范围 Support interval (cM)	加性效应 a	加性与环境互作效应				贡献率
性状 Trait	位点 QTL	连锁群 LG	左侧标记 M-	右侧标记 M+	位置 Position (cM)	区间范围 Support interval (cM)	加性效应 a	ae₁	ae₂	ae₃	ae₄	h_a²(%)	h_ae²(%)
总植物碱TPA (%)	qTPA6	6	Nitab4.5_0026397_260_SNP	Nitab4.5_0468967_662_SNP	38.3	34.0-40.7	0.1626^***	0.1265^**				3.21	1.25
	qTPA9-1	9	Nitab4.5_0171306_975_SNP	Nitab4.5_0000110_495033_SNP	1.0	0.0-3.0	0.1212^***					2.28	0.00
	qTPA14	14	Nitab4.5_0286260_185_SNP	Nitab4.5_0007629_107938_SNP	112.5	110.0-114.6	-0.3037^***					10.97	0.00
烟碱NIC (%)	qNIC6	6	Nitab4.5_0095945_611_SNP	Nitab4.5_0000743_512482_SNP	36.1	32.9-39.7	0.1789^***	0.0924^*	-0.1017^*		-	3.70	0.89
	qNIC14	14	Nitab4.5_0007629_107938_SNP	Nitab4.5_0121404_652_SNP	113.6	111.0-115.6	-0.2933^***				-	10.04	0.00
降烟碱NOR (μg g^-1)	qNOR6	6	Nitab4.5_0468967_662_SNP	Nitab4.5_0384377_155_SNP	38.4	35.1-39.4	16.2771^***	12.8686^**	-10.7226^*	11.6036^**	-13.9089^*	2.38	1.26
	qNOR7	7	Nitab4.5_0318723_531_SNP	Nitab4.5_0008152_101211_SNP	72.0	70.3-73.0	-10.5465^***					1.92	0.00
	qNOR11	11	Nitab4.5_0558151_555_SNP	Nitab4.5_0484178_611_SNP	151.1	150.0-156.5	6.5518^**			12.0254^**		0.58	0.80
	qNOR14	14	Nitab4.5_0092225_197_SNP	Nitab4.5_0286260_185_SNP	111.0	108.9-113.6	-19.2023^***					3.28	0.00
假木贼碱ANAB (μg g^-1)	qANAB6	6	Nitab4.5_0026397_260_SNP	Nitab4.5_0468967_662_SNP	37.3	35.1-39.4	12.7296^***	10.2749^***	-6.1859^*			4.80	1.64
	qANAB9-1	9	Nitab4.5_0171306_975_SNP	Nitab4.5_0000110_495033_SNP	1.0	0.0-2.5	8.7332^***					2.91	0.00
	qANAB14	14	Nitab4.5_0286260_185_SNP	Nitab4.5_0007629_107938_SNP	112.5	110.0-114.6	-20.1681^***					11.57	0.00
新烟草碱ANAT (μg g^-1)	qANAT6	6	Nitab4.5_0026397_260_SNP	Nitab4.5_0468967_662_SNP	37.3	36.2-39.4	33.035^***	22.9189^***			-21.5076^*	6.49	1.81
	qANAT9	9	Nitab4.5_0171306_975_SNP	Nitab4.5_0000110_495033_SNP	0	0.0-1.5	17.95^***					1.85	0.00
	qANAT14	14	Nitab4.5_0286260_185_SNP	Nitab4.5_0007629_107938_SNP	111.5	110.0-114.6	-41.9745^***					10.77	0.00

Table 3

Table 4

Table 5

List of candidate genes for major QTLs"

位点 QTL	物理位置 Position (bp)	候选基因ID Gene ID	起始位置 Start position (bp)	终止位置 End position (bp)	基因功能描述 Gene function
qTPA14 qANAB14 qANAT14	chr8: 7243916-7447394	Nt08g00269	7307457	7315038	类似ADP-核糖基化因子GTP酶激活蛋白AGD8 Probable ADP-ribosylation factor GTPase-activating protein AGD8
		Nt08g00270	7315990	7323983	类泛素羧基末端水解酶21 Ubiquitin carboxyl-terminal hydrolase 21-like
		Nt08g00271	7331412	7334559	未鉴定蛋白LOC104211529 Uncharacterized protein LOC104211529
		Nt08g00272	7335169	7337638	未鉴定蛋白LOC109242621亚型X2 Uncharacterized protein LOC109242621 isoform X2
		Nt08g00273	7406451	7416964	类含有锚蛋白重复序列蛋白At5g02620 Ankyrin repeat-containing protein At5g02620-like
		Nt08g00274	7430649	7431218	未鉴定蛋白LOC107790963 Uncharacterized protein LOC107790963
qNIC14	chr8: 6624235-7243916	Nt08g00249	6655849	6662737	类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
		Nt08g00250	6664408	6681005	类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
		Nt08g00251	6819300	6826090	类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
		Nt08g00252	6827921	6832618	类叶绿体蛋白ABCI7 Protein ABCI7, chloroplastic-like
		Nt08g00253	6857681	6858055	未鉴定蛋白LOC104089357 Uncharacterized protein LOC104089357
		Nt08g00254	6867626	6872883	类铝激活苹果酸转运蛋白12 Aluminum-activated malate transporter 12-like
		Nt08g00255	6875043	6879809	MND1-相互作用蛋白1 MND1-interacting protein 1
		Nt08g00256	6885824	6888724	类植物细胞内Ras组相关LRR蛋白5 Plant intracellular Ras-group-related LRR protein 5-like
		Nt08g00257	6949292	6960262	类AP-2复合体亚基mu AP-2 complex subunit mu-like
		Nt08g00258	6963535	6969302	部分类AT-hook基序核定位蛋白10 AT-hook motif nuclear-localized protein 10-like, partial
		Nt08g00259	6971645	6972022	未鉴定蛋白LOC107812243 Uncharacterized protein LOC107812243
		Nt08g00260	6978849	6981270	类AT-hook基序核定位蛋白23 AT-hook motif nuclear-localized protein 23-like
		Nt08g00261	7068807	7069085	未鉴定蛋白LOC104241148 Uncharacterized protein LOC104241148
		Nt08g00262	7077078	7083605	未鉴定蛋白LOC104246313 Uncharacterized protein LOC104246313
		Nt08g00263	7089737	7091966	未鉴定蛋白LOC107821627 Uncharacterized protein LOC107821627
		Nt08g00264	7124300	7125049	未鉴定蛋白LOC104246315 Uncharacterized protein LOC104246315
		Nt08g00265	7128787	7129137	未鉴定蛋白LOC107817882 Uncharacterized protein LOC107817882
		Nt08g00266	7133456	7135411	类转录因子MYC2 Transcription factor MYC2-like
		Nt08g00267	7222657	7230856	未鉴定蛋白LOC109206945 Uncharacterized protein LOC109206945
		Nt08g00268	7231266	7233911	未鉴定蛋白LOC109207164 Uncharacterized protein LOC109207164

Table 5

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性状 Trait	环境 Environment	平均值 Mean	标准差 SD	最小值 Min.	最大值 Max.	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)	遗传率 h²(%)
总植物碱TPA (%)	E₁	2.91	0.88	1.09	5.62	0.24	-0.39	30.18	31.13
	E₂	1.96	0.51	0.95	3.53	0.62	0.36	26.23
	E₃	3.05	0.86	1.09	5.67	0.44	0.03	28.15
	E₄	2.75	0.68	1.29	4.80	0.30	-0.24	24.75
	BLUP	2.67	0.32	1.99	3.50	0.30	-0.43	11.90
烟碱NIC (%)	E₁	2.66	0.88	0.77	5.26	0.21	-0.42	33.14	31.05
	E₂	1.80	0.50	0.52	3.45	0.46	0.36	27.71
	E₃	2.96	0.84	0.78	5.41	0.27	-0.10	28.50
	E₄	—	—	—	—	—	—	—
	BLUP	2.47	0.31	1.76	3.27	0.23	-0.43	12.47
降烟碱NOR (μg g^-1)	E₁	323.24	92.82	113.16	586.11	0.15	-0.52	28.72	24.04
	E₂	197.69	50.33	74.67	356.27	0.54	0.36	25.46
	E₃	390.08	92.74	137.16	673.68	-0.04	-0.10	23.78
	E₄	312.18	64.27	154.84	467.82	0.14	-0.36	20.59
	BLUP	305.66	26.84	240.70	387.73	0.09	-0.14	8.78
假木贼碱ANAB (μg g^-1)	E₁	184.86	55.88	71.62	378.56	0.21	-0.31	30.23	32.87
	E₂	131.14	33.32	66.45	248.40	0.56	0.35	25.41
	E₃	201.90	56.25	60.71	364.08	0.48	0.10	27.86
	E₄	185.95	46.73	95.35	307.93	0.24	-0.64	25.13
	BLUP	175.91	21.59	128.49	233.97	0.29	-0.51	12.28
新烟草碱ANAT (μg g^-1)	E₁	423.22	123.71	152.32	845.40	0.12	-0.24	29.23	33.09
	E₂	278.98	85.46	110.45	570.15	0.46	0.27	30.63
	E₃	438.77	123.22	160.60	896.84	0.68	0.98	28.08
	E₄	358.88	95.42	139.84	604.16	0.25	-0.60	26.59
	BLUP	374.94	48.42	264.46	528.55	0.36	-0.06	12.92

连锁群 Linkage group	标记总数 Number of markers	SNP数 Number of SNPs	InDel数 Number of InDels	Bin数 Number of bin markers	遗传距离 Genetic distance (cM)	平均遗传距离 Average genetic distance (cM)	最大间距 Maximum interval (cM)
LG1	4992	4878	114	335	122.53	0.366	3.51
LG2	4654	4422	232	393	148.74	0.378	2.77
LG3	4150	3987	163	459	182.63	0.398	12.42
LG4	3119	2940	179	399	133.28	0.334	7.82
LG5	2939	2819	120	315	110.54	0.351	4.07
LG6	2865	2786	79	440	201.11	0.457	17.47
LG7	2839	2698	141	270	112.76	0.418	3.89
LG8	2177	2054	123	322	180.90	0.562	9.90
LG9	1969	1892	77	304	141.53	0.466	22.87
LG10	1915	1826	89	315	123.29	0.391	4.81
LG11	1833	1742	91	326	156.48	0.480	16.23
LG12	1513	1409	104	253	148.98	0.589	27.35
LG13	1509	1416	93	388	166.83	0.430	4.25
LG14	1496	1417	79	283	133.81	0.473	4.07
LG15	1262	1203	59	403	198.03	0.491	4.07
LG16	1235	1172	63	344	168.90	0.491	5.94
LG17	1054	993	61	184	111.99	0.609	10.09
LG18	877	828	49	288	150.04	0.521	4.44
LG19	873	829	44	195	101.54	0.521	4.81
LG20	862	812	50	253	141.20	0.558	14.41
LG21	802	755	47	270	164.38	0.609	7.24
LG22	620	587	33	244	153.23	0.628	5.00
LG23	290	275	15	203	191.41	0.943	9.33
LG24	284	272	12	106	55.75	0.526	5.18
总计Total	46,129	44,012	2117	7292	3499.88	0.480	27.35

性状 Trait	位点i QTL_i	位点i的两侧标记 Interval_i	位置 Position_i (cM)	区间范围 Range_i (cM)	位点j QTL_j	位点j的两侧标记 Interval_j	位置 Position_j (cM)	区间范围 Range_j (cM)	上位性效应 aa	上位性与环境互作效应				贡献率
性状 Trait	位点i QTL_i	位点i的两侧标记 Interval_i	位置 Position_i (cM)	区间范围 Range_i (cM)	位点j QTL_j	位点j的两侧标记 Interval_j	位置 Position_j (cM)	区间范围 Range_j (cM)	上位性效应 aa	aae₁	aae₂	aae₃	aae₄	$\mathrm{h}_{\mathrm{asa}}^{2}$ (%)	$\mathrm{h}_{\cos }^{2}$ (%)
总植物碱TPA (%)	qTPA1	Nitab4.5_0001423_298079_SNP-Nitab4.5_0007238_116369_SNP	55.4	52.6-57.5	qTPA9-2	Nitab4.5_0652147_514_SNP-Nitab4.5_0000051_663607_SNP	128.2	127.1-129.5		-0.1093^*			0.1711^**	0.00	1.16
烟碱NIC (%)	qNIC9	Nitab4.5_0104939_1831_SNP-Nitab4.5_0477966_676_SNP	137.4	134.8-139.5	qNIC12	Nitab4.5_0000615_20115_Indel-Nitab4.5_0108357_1594_SNP	103.4	101.0-104.4	-0.1455^***				-	2.31	0.00
降烟碱NOR (μg g^-1)	qNOR12-1	Nitab4.5_0389330_419_SNP-Nitab4.5_0002082_72841_SNP	89.4	87.7-90.4	qNOR21-1	Nitab4.5_0006357_88789_SNP-Nitab4.5_0006203_164411_SNP	75.8	73.6-76.8	-7.5006^**					1.03	0.00
	qNOR12-2	Nitab4.5_0047695_600_Indel-Nitab4.5_0013671_17800_Indel	98.6	95.3-99.6	qNOR21-2	Nitab4.5_0002795_109963_SNP-Nitab4.5_0051563_356_SNP	81.3	78.9-83.6	-5.2883^*					0.15	0.00
假木贼碱ANAB (μg g^-1)	qANAB9-2	Nitab4.5_0104939_1831_SNP-Nitab4.5_0477966_676_SNP	136.4	134.8-137.5	qANAB12	Nitab4.5_0002161_245575_SNP-Nitab4.5_0000615_20115_Indel	103.3	101.0-104.4	-7.7137^***					1.76	0.00
新烟草碱ANAT (μg g^-1)	qANAT3	Nitab4.5_0020528_167_SNP-Nitab4.5_0001196_316885_SNP	17.2	16.0-18.4	qANAT7	Nitab4.5_0130803_641_SNP-Nitab4.5_0010558_34998_SNP	20.4	13.2-23.2	-8.8321^**		12.2295^**			0.51	0.81

QTL mapping of alkaloids in tobacco

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