大豆根部水压胁迫耐逆指数遗传体系解析

doi:10.3724/SP.J.1006.2021.04176

Abstract

Abstract:

Soybean is an important source of plant protein and vegetable oil in the world. Drought is one of the important environmental stress factors affecting soybean yield. To explore the genetic base of drought tolerance in soybean, a nested association mapping population composed of two sets of recombinant inbred lines with a common parent in a total of 429 lines was investigated for leaf proline content under PEG simulated drought stress. The genetic system of root hydraulic stress tolerance index (RHSTI) was analyzed using the RTM-GWAS (restrictive two-stage multilocus genome-wide association study). The results showed that there were significant differences in RHSTI among the three parents under two different environments in spring and summer, and among the nested association mapping population with the variation range of 0.11-2.94 and 0.03-1.93, respectively. The heritability values of Line and Line×Environment were 37.9% and 60.1%, respectively, indicating that the variation of RHSTI was greatly affected by the environment. Using the RHSTI data and 6137 SNPLDB markers, a total of 45 main effect QTLs were detected on 18 chromosomes, which could explain a total of 37.58% phenotypic variation, including 7 large contribution QTLs with R ² more than 1%. Among them, 34 QTLs with QTL×Environment effect explained 12.50% of the phenotypic variation. Combined with the transcriptome data under PEG stress, totally 38 differentially expressed genes were identified within a QTL ± 500 kb, which can be grouped into different biological categories, including ABA responders, stress responders, transcription factors, development factors, protein metabolism factors, unknown functions and others, with stress responses, transcription factors and development factors as the major parts. In summary, the results indicated that the drought tolerance of soybean was a complex quantitative trait, with the complex genetic basis controlling by multiple loci, multiple genes and interaction with the environment. The present results can lay the foundation of molecular breeding for drought tolerance in soybean.

Key words: soybean, root hydraulic stress tolerance index, proline content, QTL, nested association mapping population

WANG Wu-Bin, TONG Fei, KHAN Mueen-Alam, ZHANG Ya-Xuan, HE Jian-Bo, HAO Xiao-Shuai, XING Guang-Nan, ZHAO Tuan-Jie, GAI Jun-Yi. Detecting QTL system of root hydraulic stress tolerance index at seedling stage in soybean[J].Acta Agronomica Sinica, 2021, 47(5): 847-859.

Figures/Tables 8

Table 1

Table 2

Fig. 1

Table 3

Table 4

Identified QTLs conferring root hydraulic stress tolerance index (RHSTI) in MTZ population"

QTL	连锁不平衡区段 SNPLDB	染色体 Chr.	位置 Position	等位变异数目 AN	主效QTL Main effect QTL		QTL与环境互作 QTL×Env ^a		已报道位点 Reported QTLs
QTL	连锁不平衡区段 SNPLDB	染色体 Chr.	位置 Position	等位变异数目 AN	-lg P	R²(%)	-lg P	R²(%)	已报道位点 Reported QTLs
RHSTI1.1	Gm01_4742892	Gm01	4742892	2	15.4	0.57	12.2	0.44
RHSTI2.1	BLOCK_2_27517291_27687530	Gm02	27517291-27687530	3	18.1	0.72	4.0	0.15
RHSTI2.2	BLOCK_2_39672439_39870477	Gm02	39672439-39870477	3	40.6	1.66	4.4	0.17	mqCanopy wilt-018^[18]
RHSTI2.3	BLOCK_2_46859465_47055418	Gm02	46859465-47055418	3	22.0	0.88	NS
RHSTI2.4	BLOCK_2_51400285_51574802	Gm02	51400285-51574802	3	18.8	0.74	6.1	0.24
RHSTI3.1	BLOCK_3_2456930_2505542	Gm03	2456930-2505542	3	14.7	0.58	10.2	0.40
RHSTI3.2	BLOCK_3_43400584_43484318	Gm03	43400584-43484318	3	16.5	0.65	33.4	1.36
RHSTI4.1	BLOCK_4_41364990_41553577	Gm04	41364990-41553577	3	17.1	0.68	2.5	0.10
RHSTI6.1	BLOCK_6_4265210_4332096	Gm06	4265210-4332096	2	21.0	0.79	4.3	0.14
RHSTI6.2	BLOCK_6_4951013_5150438	Gm06	4951013-5150438	3	17.4	0.69	NS
RHSTI6.3	BLOCK_6_13682742_13879752	Gm06	13682742-13879752	3	15.1	0.59	NS
RHSTI7.1	BLOCK_7_945093_1143184	Gm07	945093-1143184	3	16.0	0.63	10.9	0.43
RHSTI7.2	Gm07_27902201	Gm07	27902201	2	35.3	1.39	NS
RHSTI7.3	BLOCK_7_37870093_38067672	Gm07	37870093-38067672	3	15.8	0.62	9.3	0.36
RHSTI8.1	Gm08_42822124	Gm08	42822124	2	18.8	0.70	14.6	0.54
RHSTI9.1	BLOCK_9_5045930_5095878	Gm09	5045930-5095878	3	21.4	0.85	11.9	0.47
RHSTI9.2	Gm09_5673327	Gm09	5673327	2	15.3	0.56	2.2	0.06
RHSTI9.3	BLOCK_9_7453368_7651586	Gm09	7453368-7651586	3	25.5	1.02	NS
RHSTI9.4	BLOCK_9_14835645_14840806	Gm09	14835645-14840806	2	18.5	0.69	3.5	0.11
RHSTI10.1	BLOCK_10_10109602_10137279	Gm10	10109602-10137279	3	18.1	0.72	NS
RHSTI10.2	BLOCK_10_39940500_40129301	Gm10	39940500-40129301	3	24.1	0.96	4.4	0.17	Drought tolerance 6-3^[13]
RHSTI10.3	BLOCK_10_40440079_40629141	Gm10	40440079-40629141	3	15.3	0.60	12.2	0.48	Drought tolerance 6-3^[13]
RHSTI10.4	BLOCK_10_47418374_47616648	Gm10	47418374-47616648	3	19.7	0.78	3.5	0.14
RHSTI11.1	BLOCK_11_26241368_26440039	Gm11	26241368-26440039	3	15.0	0.59	3.1	0.12	mqCanopy wilt-020^[18] mqCanopy wilt-009^[18]
RHSTI11.2	BLOCK_11_29079685_29279006	Gm11	29079685-29279006	3	20.1	0.80	16.6	0.66	mqCanopy wilt-020^[18]
RHSTI12.1	BLOCK_12_11206224_11381903	Gm12	11206224-11381903	3	16.3	0.64	11.6	0.45
RHSTI12.2	BLOCK_12_11687384_11857574	Gm12	11687384-11857574	2	73.0	3.09	NS
RHSTI13.1	BLOCK_13_3657693_3729944	Gm13	3657693-3729944	3	14.4	0.57	13.3	0.52
RHSTI13.2	BLOCK_13_35892463_36008531	Gm13	35892463-36008531	3	15.5	0.61	4.1	0.16
RHSTI13.3	BLOCK_13_41064207_41264076	Gm13	41064207-41264076	2	18.1	0.67	NS
RHSTI14.1	BLOCK_14_2645749_2661861	Gm14	2645749-2661861	3	19.9	0.79	5.8	0.22
RHSTI14.2	BLOCK_14_46766676_46936602	Gm14	46766676-46936602	3	20.9	0.83	4.7	0.18	Canopy wilt 2-5^[13]
RHSTI15.1	Gm15_38751520	Gm15	38751520	2	34.1	1.34	NS		Canopy wilt 2-5^[13]
RHSTI15.2	BLOCK_15_49313308_49446734	Gm15	49313308-49446734	2	18.0	0.67	42.6	1.70
RHSTI17.1	BLOCK_17_9162497_9323658	Gm17	9162497-9323658	3	11.7	0.46	5.7	0.22	Drought index 1-9^[14] Canopy wilt 1-3^[12] Canopy wilt 3-10^[13]
RHSTI17.2	BLOCK_17_10274061_10289190	Gm17	10274061-10289190	3	59.2	2.51	NS
RHSTI17.3	BLOCK_17_32103917_32299960	Gm17	32103917-32299960	3	14.1	0.55	NS
RHSTI18.1	BLOCK_18_1411394_1609397	Gm18	1411394-1609397	3	25.0	1.00	3.1	0.12
RHSTI18.2	BLOCK_18_4798286_4951218	Gm18	4798286-4951218	3	12.6	0.50	6.4	0.25
RHSTI18.3	BLOCK_18_13133051_13329765	Gm18	13133051-13329765	3	18.3	0.72	7.0	0.27
RHSTI19.1	BLOCK_19_1291865_1491855	Gm19	1291865-1491855	3	17.2	0.68	32.0	1.29
RHSTI19.2	Gm19_17194130	Gm19	17194130	2	12.9	0.47	3.2	0.10
RHSTI19.3	BLOCK_19_23574474_23596371	Gm19	23574474-23596371	2	15.4	0.56	NS
RHSTI19.4	BLOCK_19_35661675_35858974	Gm19	35661675-35858974	3	17.6	0.70	8.3	0.32
RHSTI20.1	BLOCK_20_35376980_35573994	Gm20	35376980-35573994	3	18.7	0.74	4.0	0.15
总计Total	45			123		37.58		12.50

Table 4

Fig. 2

Table 5

Analysis the candidate genes of root hydraulic stress tolerance index (RHSTI) combined the results of GWAS and RNA-seq"

基因 Gene	QTL	对照 Control	处理 Treatment	A	S	T	D	PM	UF	O
Glyma.01G044100	RHSTI1.1	4.63315	26.99810					√
Glyma.02G171100	RHSTI2.1	1.65710	35.83620		√
Glyma.02G196500	RHSTI2.2	13.39870	54.69290	√	√	√	√
Glyma.02G250200	RHSTI2.3	10.60250	154.59800	√	√			√
Glyma.02G308100	RHSTI2.4	20.68510	89.04400							√
Glyma.03G023900	RHSTI3.1	10.74360	39.75440						√
Glyma.03G202400	RHSTI3.2	46.58860	2.89863					√
Glyma.04G179500	RHSTI4.1	615.19900	78.03500	√	√			√
Glyma.06G054700	RHSTI6.1	0.27378	132.47900		√
Glyma.06G063500	RHSTI6.2	5.58627	26.31760				√
Glyma.06G165100	RHSTI6.3	16.17140	3.43912				√
Glyma.07G013900	RHSTI7.1	119.39400	5.21799					√
Glyma.07G208700	RHSTI7.3	59.19030	196.58300		√		√
Glyma.08G316700	RHSTI8.1	8.69897	187.91100							√
Glyma.09G051700	RHSTI9.1	0.00001	40.02450						√
Glyma.09G071600	RHSTI9.3	5.55258	142.93600	√	√		√
Glyma.10G081700	RHSTI10.1	18.56970	69.58230	√	√	√	√
Glyma.10G169300	RHSTI10.2	3.97157	66.91020					√
Glyma.10G179200	RHSTI10.3	32.64080	6.27830							√
Glyma.10G251900	RHSTI10.4	248.40400	501.60600					√
Glyma.11G171400	RHSTI11.1	8.60429	102.58700		√
Glyma.11G207000	RHSTI11.2	1.99196	20.33400		√
Glyma.12G112100	RHSTI12.1	64.63140	29.13040							√
基因 Gene	QTL	对照 Control	处理 Treatment	A	S	T	D	PM	UF	O
Glyma.12G117000	RHSTI12.2	3.83243	33.14560		√
Glyma.13G078400	RHSTI13.1	49.82870	14.74430			√
Glyma.13G272000	RHSTI13.2	56.77120	135.84100		√
Glyma.13G333100	RHSTI13.3	44.62830	847.65000		√
Glyma.14G190800	RHSTI14.2	36.08840	9.31428		√
Glyma.15G222200	RHSTI15.1	19.02410	1.79038		√
Glyma.15G267900	RHSTI15.2	2.69447	34.25220							√
Glyma.17G113100	RHSTI17.1	79.26370	26.09940				√
Glyma.17G122900	RHSTI17.2	46.38730	23.03860							√
Glyma.17G202600	RHSTI17.3	0.73104	40.50930							√
Glyma.18G018600	RHSTI18.1	9.17402	136.37000		√		√
Glyma.19G014800	RHSTI19.1	31.60140	7.32146		√
Glyma.19G100600	RHSTI19.3	53.01000	13.26570							√
Glyma.19G109400	RHSTI19.4	25.26790	129.41800					√
Glyma.19G112700	RHSTI20.1	119.13700	37.92940				√

Table 5

Table 6

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作图群体 Mapping population	评价指标 Indicator	QTL数目 QTL number	染色体(QTL数目)^a Chromosome (QTL number)	参考文献 Reference
Benning/PI 416937	萎蔫指数Canopy width	7	2(1) 4(1) 5(1) 12(1) 14(1) 17(1) 19(1)	[11]
KS4895/Jackson	萎蔫指数Canopy width	4	8(1) 13(1) 14(1) 17(1)	[12]
93705KS4895/Jackson	萎蔫指数Canopy width	13	2(3) 4(1) 5(2) 6(2) 8(1) 14(1) 17(3)	[13]
08705KS4895/Jackson	萎蔫指数Canopy width	7	9(1) 11(2) 12(1) 16(1) 17(2)	[13]
KS4895/ PI 424140	萎蔫指数Canopy width	4	11(1) 17(1) 19(2)	[13]
Benning/PI 416937	萎蔫指数Canopy width	4	2(3) 19(1)	[13]
NN1138-2/Kefeng 1	耐旱系数Drought index	10	1(1) 5(2) 6(1) 7(1) 12(1) 16(1) 17(2) 20(1)	[14]
Benning/PI 416937	叶片电导率Hydraulic conductance	4	3(1) 5(1) 10(1) 12(1)	[15]
S-100/Tokyo	水分利用率Water use efficiency	3	4(2) 19(1)	[16]
Young/PI 416937	水分利用率Water use efficiency	6	12(2) 16(3) 18(1)	[17]
QTL元分析Meta-QTL		26	2(10) 5(3) 11(4) 12(2) 17(6) 19(3)	[18]

变异来源 Source of variation	F值 F-value
家系 Line	50.54^**
环境 Environment	0.80
区组(环境) Block (Environment)	94.89^**
家系×环境 Line × Environment	30.38^**

序号 Order	QTL	染色体 Chr.	物理位置 Physical position	序号 Order	QTL	染色体 Chr.	物理位置 Physical position
1	RHSTI3.2/RRL3.5	Gm03	43400584-43484318	10	RRL14.1/RPDW14.2	Gm14	47717307-48064975
2	RSL4.2/RPL4.1	Gm04	44742587-45097286	11	RRL15.1/RSL15.1	Gm15	11105948-11421179
3	RHSTI6.3/RRL6.2	Gm06	13682742-13879752	12	RHSTI15.2/RRL15.4	Gm15	48985599-49446734
4	RHSTI7.3/RRL7.2	Gm07	37870093-38067672	13	RHSTI17.3/RRL17.2	Gm17	32103917-34132465
5	RHSTI10.3/RRL10.2	Gm10	40440079-40629141	14	RHSTI18.1/RPL18.1	Gm18	1411394-2099117
6	RRL10.3/RPDW10.1	Gm10	50470068-50478746	15	RHSTI19.2/RSL19.3	Gm19	16552234-17194130
7	RPL13.2/RPDW13.1	Gm 13	22001544-22395896	16	RHSTI19.4/RRL19.3	Gm19	35661675-35924257
8	RHSTI13.2/RSL13.1	Gm 13	35347991-36008531	17	RRL19.5/RPDW19.1	Gm19	37678898-38456131
9	RRL13.6/RPL13.1	Gm 13	43533843-43640816	18	RHSTI20.1/RPL20.1	Gm20	35319103-35573994

Detecting QTL system of root hydraulic stress tolerance index at seedling stage in soybean

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环境 Environment	M	Z	T	MTZ
				组中值(频数) Value of class mid-point (frequency)										变幅 Range	平均数 Mean	变异系数 CV (%)	遗传力 h²
				0.1	0.3	0.5	0.7	0.9	1.1	1.3	1.5	1.7	>1.9	变幅 Range	平均数 Mean	变异系数 CV (%)	遗传力 h²
春季Spring	0.35	1.05	0.95	1	24	159	128	57	15	9	2	1	9	0.11-2.94	0.69	13.2	97.2
夏季Summer	0.17	1.04	0.96	38	56	75	100	61	34	20	5	0	2	0.03-1.93	0.65	12.1	97.9
平均值Mean	0.26	1.05	0.95	2	41	115	159	55	19	5	6	0	5	0.09-2.80	0.68	12.7	37.9

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