野生大豆染色体片段代换系群体中与百粒重关联的野生片段及其候选基因

doi:10.3724/SP.J.1006.2022.14140

Abstract

Abstract:

Annual wild soybean is the ancestor of cultivated soybean. The 100-seed weight gradually increases in the long-term domestication process. Clarifying the genetic basis of this change is of great significance to the evolutionary research and variety improvement of soybean. In order to analyze the genetic basis of 100-seed weight during soybean domestication, a wild soybean chromosome segment substitution line population (SojaCSSLP5) composed of 177 whole-genome resequencing lines were used in this study. 13 QTLs/segments of 100-seed weight were detected by phenotypic evaluation in three different environments. All of 13 wild chromosome segments had the additive effect of reducing 100-seed weight, ranging from -0.49 g to -1.19 g, which was consistent with the smaller 100-seed weight of wild soybeans. These detected domesticated segments from 11 chromosomes explained 76.70% of the phenotypic variation, and the phenotypic contribution rate of a single segment ranged from 2.45% to 15.14%. The contribution rate of segments Gm03_LDB_15 and Gm12_LDB_46 exceeded 10%, which were major influence on the evolution of 100-seed weight of wild soybeans. Combined the transcriptome data and genome data of parental cultivated soybean Nannong 1138-2 and wild soybean N24852, a total of 13 candidate genes were predicted in these segments, and were involved in the pathways of plant seed size, including ubiquitin protein kinase regulatory pathway, G protein signal pathway, mitogen-activated protein kinase pathway, plant hormone pathway, transcription regulator pathway, and IKU (HAIKU) pathway. Compared with previous QTLs mapping results with cultivated soybeans, 4 of the 13 QTLs/segments were newly detected in this study, indicating that 9 wild chromosome segments might be passed to cultivated soybeans during domestication, and the corresponding cultivated segments of these 4 wild segments may be unique evolutionary segments of cultivated soybean.

Key words: wild soybean, chromosome segment substitution line, 100-seed weight, QTLs

LIU Cheng, ZHANG Ya-Xuan, CHEN Xian-Lian, HAN Wei, XING Guang-Nan, HE Jian-Bo, ZHANG Jiao-Ping, ZHANG Feng-Kai, SUN Lei, LI Ning, WANG Wu-Bin, GAI Jun-Yi. Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population[J].Acta Agronomica Sinica, 2022, 48(8): 1884-1893.

Figures/Tables 5

Table 1

Table 2

Table 3

Fig. 1

Table 4

Predicted candidate genes for 100-seed weight based on their sequence and expression differences between Nannong 1138-2 and N24852"

基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	差异表达 Expression difference (FPKM)
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	14 seed	21 seed	28 seed	35 seed	Leaf
Glyma.02G125200	qSW2.1	bHLH转录因子^[39] bHLH transcription factor^[39]	南农1138-2 Nannong 1138-2	TCGG	0.45	0.40	2.19	5.37	2.57
		bHLH转录因子^[39] bHLH transcription factor^[39]	N24852	CAAT	13.79	6.11	8.71	21.03	91.63
Glyma.03G066200	qSW3.1	ABA受体调节因子(IKU) Regulatory components of ABA receptor (IKU)	南农1138-2 Nannong 1138-2	GA	1.25	0.63	3.91	10.63	0.69
		ABA受体调节因子(IKU) Regulatory components of ABA receptor (IKU)	N24852	AG	3.16	1.39	3.48	20.33	2.93
Glyma.04G080800	qSW4.1	RNA聚合酶I相关因子 RNA polymerase I-associated factor	南农1138-2 Nannong 1138-2	G	48.56	53.32	13.06	16.68	16.63
		RNA聚合酶I相关因子 RNA polymerase I-associated factor	N24852	C	39.16	18.85	35.88	108.75	14.82
Glyma.04G078900	qSW4.2	裂原活化蛋白激酶 Mitogen-activated protein kinase	南农1138-2 Nannong 1138-2	G	0.80	0.42	2.21	2.27	0.93
		裂原活化蛋白激酶 Mitogen-activated protein kinase	N24852	C	11.43	5.44	5.54	9.74	7.88
Glyma.04G116700	qSW4.3	对生长素的反应 Response to auxin	南农1138-2 Nannong 1138-2	AACACGC	1.11	0.71	3.82	7.24	1.01
		对生长素的反应 Response to auxin	N24852	CGTCGAT	10.27	5.20	17.85	45.44	10.32
Glyma.06G146700	qSW6.1	调节发育的G蛋白^[40] G protein that regulates development^[40]	南农1138-2 Nannong 1138-2	TTCTTTC	0.41	0.68	2.28	4.90	0.77
		调节发育的G蛋白^[40] G protein that regulates development^[40]	N24852	CCTACCA	11.03	11.03	17.77	41.99	11.34
Glyma.09G194200	qSW9.1	丝氨酸/苏氨酸磷酸酶 Serine/threonine phosphatase	南农1138-2 Nannong 1138-2	CCCCTTCTCT	1.44	0.39	0.80	0.50	1.26
		丝氨酸/苏氨酸磷酸酶 Serine/threonine phosphatase	N24852	TTATCATAGC	19.75	6.88	9.99	4.78	11.35
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	差异表达 Expression difference (FPKM)
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	14 seed	21 seed	28 seed	35 seed	Leaf
Glyma.11G063500	qSW11.1	E3泛素连接酶^[41⇓-43] E3 ubiquitin ligase^[41⇓-43]	南农1138-2 Nannong 1138-2	C	0.31	1.42	1.93	3.45	0.78
		E3泛素连接酶^[41⇓-43] E3 ubiquitin ligase^[41⇓-43]	N24852	G	6.33	8.77	6.09	17.65	7.58
Glyma.12G216100	qSW12.1	GRAS类转录因子 GRAS transcription factors	南农1138-2 Nannong 1138-2	TCG	1.49	1.84	12.80	30.95	1.17
		GRAS类转录因子 GRAS transcription factors	N24852	GGA	1.61	2.14	20.70	73.39	1.99
Glyma.13G167900	qSW13.1	核糖体生物合成蛋白 Ribosomal biosynthetic protein	南农1138-2 Nannong 1138-2	AGG	28.37	39.78	17.86	19.92	22.40
		核糖体生物合成蛋白 Ribosomal biosynthetic protein	N24852	GAA	33.04	12.85	39.50	104.52	15.60
Glyma.16G084300	qSW16.1	生长素响应因子 Auxin response factor	南农1138-2 Nannong 1138-2	G	0.31	0.46	0.88	0.11	3.24
		生长素响应因子 Auxin response factor	N24852	C	30.59	10.86	3.63	0.44	39.27
Glyma.18G200100	qSW18.1	E3泛素连接酶 E3 ubiquitin ligase	南农1138-2 Nannong 1138-2	GTATTAC	0.59	1.41	1.15	0.92	1.45
		E3泛素连接酶 E3 ubiquitin ligase	N24852	ACCCCGT	2.80	3.46	5.14	2.68	4.40
Glyma.19G004200	qSW19.1	亲环蛋白 Cyclophilin	南农1138-2 Nannong 1138-2	TGCACG	14.24	9.18	8.69	5.45	4.90
			N24852	AAAGTT	8.19	5.47	17.04	34.60	7.26

Table 4

References 51

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变异来源 Source of variation	自由度 DF	均方 MS	F值 F-value	P
环境 Environment	2	417.90	398.00	<0.0001
环境内重复 Repeat (Environment)	6	8.03	7.65	<0.0001
家系 Line	176	29.31	12.06	<0.0001
家系×环境Line×Environment	356	2.43	2.31	<0.0001
误差 Error	1007	1.05
总和 Total	1549

QTL	连锁标记 Marker	染色体区间 Genome region	区间大小 Size of region (Mb)	显著性 LOD	贡献率 PVE (%)	加性效应 Add	已报道QTL Reported QTL
qSW2.1	Gm02_LDB_27	12586195-13747176	1.16	9.11	6.97	-0.77	Seed weight 49-8^[32]
qSW3.1	Gm03_LDB_15	12466486-13017335	0.55	17.63	15.14	-1.19	新位点New
qSW4.1	Gm04_LDB_13	2601664-2650056	0.05	5.62	4.10	-0.62	Seed weight 47-3^[33]
qSW4.2	Gm04_LDB_25	6482923-6818956	0.34	6.22	4.58	-0.58	Seed weight 54-1^[34] Seed weight 47-3^[33]
qSW4.3	Gm04_LDB_39	12291313-15488343	3.20	4.30	3.09	-0.57	Seed weight 50-9^[6] Seed weight 47-3^[33]
qSW6.1	Gm06_LDB_34	11933129-12135714	0.20	5.11	3.71	-0.49	新位点New
qSW9.1	Gm09_LDB_54	41753666-41795135	0.04	9.10	6.96	-0.59	Seed weight 27-3^[33]
qSW11.1	Gm11_LDB_21	4680921-4726090	0.05	8.95	6.83	-0.77	Seed weight 37-9^[35]
qSW12.1	Gm12_LDB_46	37389148-37916269	0.53	12.59	10.10	-1.08	新位点New
qSW13.1	Gm13_LDB_27	28160461-28502188	0.34	6.96	5.17	-0.67	Seed weight 50-7^[6] Seed weight 19-2^[36] Seed weight 15-3^[37] Seed weight 49-14^[32] Seed weight 2-4^[38]
qSW16.1	Gm16_LDB_38	8724531-9795523	1.07	5.31	3.86	-0.67	新位点New
qSW18.1	Gm18_LDB_24	43990050-47921961	3.93	3.45	2.45	-0.50	Seed weight 27-1^[33]
qSW19.1	Gm19_LDB_3	223110-353922	0.13	5.16	3.74	-0.49	Seed weight 3-6^[33]

Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population

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环境 Environment	亲本 Parents		染色体片段代换系群体 Chromosome segment substitution line population (SojaCSSLP5)
	南农1138-2 Nannong 1138-2	N24852	组中值Class mid-value (g)													变幅 Range	均值 Mean	变异系数 CV (%)	遗传率 h² (%)
	南农1138-2 Nannong 1138-2	N24852				10	11	12	13	14	15	16	17	18	19	变幅 Range	均值 Mean	变异系数 CV (%)	遗传率 h² (%)	20	21	Σ
2016JP	18.07	1.84	1	3	4	9	30	43	47	31	7	2	0	0	177	10.49-18.85	15.34	6.45	84.2
2017JP	19.22	1.79	2	2	4	8	21	30	40	36	24	8	1	1	177	10.00-21.18	15.91	6.52	89.0
2018DT	19.56	1.74	0	0	2	2	12	16	26	36	40	34	8	1	177	12.10-20.78	17.14	6.08	86.6
平均Mean	18.95	1.73	0	1	3	6	12	28	46	54	23	4	0	0	177	11.15-18.96	16.14	6.36	91.8

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