大豆种质抗旱性评价及抗旱候选基因的挖掘

doi:10.3864/j.issn.0578-1752.2024.10.002

摘要/Abstract

摘要：

【目的】综合运用不同抗旱评价指标，筛选大豆优异抗旱种质，发掘重要抗旱基因，为大豆抗旱分子育种提供理论基础。【方法】利用188份大豆种质资源，于2018、2019、2020和2021年测定正常供水和干旱胁迫下的单株荚数、单株生物量和单株产量，利用抗旱指数、改进抗旱指数、加权抗旱系数和加权抗旱指数等参数鉴定大豆种质的抗旱性，通过全基因组关联分析（genome-wide association study，GWAS）检测与大豆抗旱参数显著相关的SNP（single nucleotide polymorphisms）标记，并结合干旱胁迫下大豆幼苗叶片基因表达谱分析，筛选抗旱候选基因。【结果】188份大豆种质资源的抗旱指数、改进抗旱指数、加权抗旱系数和加权抗旱指数存在广泛变异，分别利用逐级分类法将供试材料划分为5个等级。其中，辽豆15、辽豆69、辽豆14、金杖子黄豆、中黄606、科新3号、Koreane 4等7份种质在不同评价方法中均被鉴定为一级抗旱。对抗旱指数、改进抗旱指数、加权抗旱系数和加权抗旱指数进行GWAS分析，共定位到15个显著关联的SNP位点能够在多环境下稳定表达，这些位点对表型变异的贡献率为12.46%—25.60%。在显著SNP位点上、下游各200 kb区间内共有注释基因226个。通过对抗旱品种辽豆14和干旱敏感型品种辽豆21在干旱胁迫下进行转录组测序和实时荧光定量PCR分析，鉴定出32个注释基因受干旱胁迫诱导显著差异表达。其中，Glyma.02G182900、Glyma.04G012400、Glyma.06G258900、Glyma.15G100900、Glyma.01G172600、Glyma.04G012300、Glyma.01G172200和Glyma.04G010300等8个候选基因分别编码钙依赖性蛋白激酶、通用应激蛋白A、G型凝集素S受体样丝氨酸/苏氨酸蛋白激酶、蛋白磷酸酶2C、异黄酮还原酶、异黄酮还原酶同源物、生长素蛋白和bZIP转录因子。【结论】综合运用不同抗旱参数，在188份大豆种质资源中筛选出7份抗旱种质资源，鉴定了15个与抗旱参数显著关联的SNP位点，并鉴定出抗旱候选基因8个。

关键词: 大豆, 种质资源, 抗旱性评价, 全基因组关联分析, 候选基因

Abstract:

【Objective】 In order to provide theoretical basis for molecular breeding of soybean drought resistance, the different evaluation indexes of drought resistance were comprehensively used to screen soybean germplasm with drought-resistance, and the candidate drought-tolerant genes were identified. 【Method】 In 2018, 2019, 2020 and 2021, a total of 188 soybean germplasm were used to determine pod number per plant, biomass per plant and yield per plant under well-watered and drought stressed conditions. Drought resistance index (DI), improved drought resistance index (IDI), weighted drought resistance coefficient (WDC) and weighted drought resistance index (WDI) were used to identify drought resistance of soybean germplasm. The single nucleotide polymorphisms (SNP) loci significantly associated with these parameters were detected by genome-wide association study (GWAS), and the candidate genes for drought resistance were screened by RNA-seq and qRT-PCR analysis of soybean seedling leaves under drought stress. 【Result】 The DI, IDI, WDC and WDI of 188 soybean germplasm varied widely, and five classification criteria for each drought resistance parameter were determined by hierarchical classification method. Among them, Liaodou 15, Liaodou 69, Liaodou 14, Jinzhangzi Huangdou, Zhonghuang 606, Kexin 3 and Koreane 4 were identified as first-grade drought resistant by all evaluation methods. By using GWAS for DI, IDI, WDC and WDI, a total of 15 significantly SNP loci were detected under multiple environments, and the contribution rate of these loci to phenotypic variation ranged from 12.46% to 25.60%. There are 226 annotated genes within 200 kb intervals of upstream and downstream for the significant SNP loci. According to RNA-seq and qRT-PCR analysis of drought-resistant cultivar Liaodou 14 and drought-sensitive cultivar Liaodou 21 under drought stress, a total of 32 annotated genes were significantly differentially expressed by drought stress. Among them, eight genes including Glyma.02G182900, Glyma.04G012400, Glyma.06G258900, Glyma.15G100900, Glyma.01G172600, Glyma.04G012300, Glyma.01G172200 and Glyma.04G010300, encodes calcium-dependent protein kinase, universal stress protein A-like protein, G-type lectin S-receptor-like serine/threonine-protein kinase, protein phosphatase 2C, isoflavone reductase, isoflavone reductase homolog, auxin-like protein, and bZIP transcription factor, respectively. 【Conclusion】 Seven germplasm were identified from 188 soybean germplasm by comprehensive application of different drought tolerance parameters. A total of 15 SNP loci significantly associated with drought tolerance parameters were identified by GWAS, and eight candidate genes were identified.

Key words: soybean, germplasm, drought resistance evaluation, genome-wide association analysis, candidate genes

李盛有, 王昌陵, 闫春娟, 张立军, 孙旭刚, 曹永强, 王文斌, 宋书宏. 大豆种质抗旱性评价及抗旱候选基因的挖掘[J]. 中国农业科学, 2024, 57(10): 1857-1869.

LI ShengYou, WANG ChangLing, YAN ChunJuan, ZHANG LiJun, SUN XuGang, CAO YongQiang, WANG WenBin, SONG ShuHong. Evaluation of Drought Resistance in Soybean Germplasm and Identification of Candidate Drought-Resistant Genes[J]. Scientia Agricultura Sinica, 2024, 57(10): 1857-1869.

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大豆抗旱显著相关的SNP位点和抗旱候选基因"

性状 Trait	位置 Position	基因 Gene	注释 Annotation
加权抗旱系数 WDC	Chr.1:50851116	Glyma.01G169000	锌指CCCH结构域含蛋白44 Zinc finger CCCH domain-containing protein 44
		Glyma.01G169500	富亮氨酸重复受体丝氨酸/苏氨酸蛋白激酶At3g53590 Leucine-rich repeat receptor-like serine/threonine-protein kinase At3g53590
		Glyma.01G169900	CDK5RAP1蛋白 CDK5RAP1-like protein
		Glyma.01G170200	半乳糖苷酶3 Beta-galactosidase 3
		Glyma.01G171400	AAA-ATP酶At5g17760 AAA-ATPase At5g17760
		Glyma.01G171900	甘露聚糖内嵌体-1,4-甘露糖苷酶7 Mannanendo-1,4-beta-mannosidase 7
		Glyma.01G172200	生长素蛋白1 Auxin-like protein 1
		Glyma.01G172600	异黄酮还原酶Isoflavone reductase
	Chr.6:44505365	Glyma.06G258900	G型凝集素S受体丝氨酸/苏氨酸蛋白激酶At4g27290 G-type lectin S-receptor-like serine/threonine-protein kinase At4g27290
		Glyma.06G259400	TMV抗性蛋白N TMV resistance protein N
		Glyma.06G260000	转录因子bHLH 123 Transcription factor bHLH 123
		Glyma.06G260100	TMV抗性蛋白N TMV resistance protein N
抗旱指数DI	Chr.2:31492269	Glyma.02G182900	钙依赖性蛋白激酶32 Calcium-dependent protein kinase 32
	Chr.3:16108362	Glyma.03G070100	依赖于NADPH的醛酮还原酶，叶绿体 NADPH-dependentaldo-ketoreductase, chloroplastic
	Chr.16:5063353	Glyma.16G050700	GEM蛋白5 GEM-like protein 5
		Glyma.16G050900	锌指蛋白Constans-like14 Zinc finger protein Constans-like 14
		Glyma.16G051300	酰基转移酶样蛋白，叶绿体 Acyltransferase-like protein At3g26840, chloroplastic
		Glyma.16G052000	甘油磷酸二酯磷酸二酯酶GDPD 2 Glycero phosphodiester phosphodiesterase GDPD 2
改进抗旱指数 IDI	Chr.4:935137	Glyma.04G009400	脱氢蛋白ERD14 Dehydrin ERD 14
		Glyma.04G009900	胚胎细胞蛋白40 Embryogenic cell protein 40
		Glyma.04G010300	转录因子bZIP11 Transcription factor bZIP11
		Glyma.04G012300	异黄酮还原酶同源物Isoflavone reductase homolog
		Glyma.04G012400	通用应激蛋白A蛋白 Universal stress protein A-like protein
		Glyma.04G013000	葡聚糖内切酶1,3-d-葡萄糖苷酶 Glucanendo-1,3-beta-D-glucosidase
		Glyma.04G013400	器官特异性蛋白P4 Organ-specific protein P4
		Glyma.04G013500	含BURP结构域蛋白3 BURP domain-containing protein 3
	Chr.8:35316814	Glyma.08G270600	肉桂酰辅酶A还原酶SNL6 Cinnamoyl-CoA reductase-like SNL6
	Chr.15:7739713	Glyma.15G097100	磷脂酶A1-Igamma 2，叶绿体 Phospholipase A1-Igamma 2, chloroplastic
		Glyma.15G097700	二乙烯叶绿素一种8-乙烯还原酶，叶绿体 Divinyl chlorophyll idea8-vinyl-reductase, chloroplastic
		Glyma.15G100700	肽蛋氨酸亚砜还原酶B5 Peptide methionine sulfoxide reductase B5
		Glyma.15G100900	蛋白磷酸酶2C 35 Protein phosphatase 2C 35
加权抗旱指数WDI	Chr.17:38770868	Glyma.17G230700	液泡生产酶Vacuolar-processing enzyme

表4

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基因 Gene	正向引物 Forward primers (5′-3′)	反向引物 Reverse primers (5′-3′)
Glyma.02G182900	ATGGGTAACTGTTGCGTTTT	ACTTCGACGATGGTTCTG
Glyma.04G012400	TTGTCTCTTATTGTGGAA	ACAATACTTGTGGCCAAATT
Glyma.06G258900	TTCACTCTCATACTTGCTAT	AGAAGGATCATCCCAGTTCT
Glyma.15G100900	AAGCACATTCTCACTCAGA	TCAGGAATGCAGAAGTGTA
Glyma.01G172600	ACTTTGCTCCCTTTTATTGTA	CACTTGGGATTAATTACCTTT
Glyma.04G012300	TATGACCGTATGATTATTT	AACCAGCAAAGAAGTTGCTT
Glyma.01G172200	AATGACTTTGATTTGAGGGA	TAGCTGAGTCATGTGAGTTTT
Glyma.04G010300	ATGTATTCAATTCTGAGTGAAAT	TCATGAAACGTAGTAGAGCCA
18S	TGATTAGACCGAAACCAATGC	GGCAGAAACTTGAATGAAACG

抗旱等级 Drought grade	抗旱指数 DI	改进抗旱指数 IDI	加权抗旱系数 WDC	加权抗旱指数 WDI
一级Grade1	≥1.503 (26)	≥2.132 (30)	≥0.764 (31)	≥1.947 (27)
二级Grade2	≥1.011<1.503 (28)	≥1.568<2.132 (29)	≥0.746<0.764 (26)	≥1.453<1.947 (26)
三级Grade3	≥0.193<1.011 (97)	≥0.216<1.568 (97)	≥0.530<0.746 (71)	≥0.617<1.453 (86)
四级Grade4	≥0.074<0.193 (29)	≥0.125<0.216 (25)	≥0.475<0.530 (27)	≥0.417<0.617 (27)
五级Grade5	<0.074 (8)	<0.125 (7)	<0.475 (38)	<0.417 (22)

抗旱等级 Drought grade	种质名称 Germplasm name	抗旱指数 DI	改进抗旱指数 IDI	加权抗旱系数 WDC	加权抗旱指数 WDI
一级Grade1	辽豆15 LD15	3.05	4.32	0.79	3.55
	辽豆69 LD69	2.96	6.48	0.83	3.33
	金杖子黄豆JZZHD	2.76	3.32	0.80	3.11
	辽豆14 LD14	2.40	5.59	0.82	3.13
	科新3号KX3	1.73	2.92	0.80	2.40
	Koreane 4	1.60	2.42	0.83	2.39
	中黄606 ZH606	1.55	2.23	0.82	2.60
二级Grade2	Conrad	1.33	2.12	0.74	1.77
三级Grade3	铁丰33 TF33	0.88	0.91	0.66	1.14
	郑92116 Z92116	0.87	0.93	0.68	1.16
	白脐大豌豆BQDWD	0.85	1.17	0.65	1.08
	IOA2020	0.79	0.85	0.68	1.09
	沈农6号SN6	0.76	1.23	0.69	1.17
	Son won	0.65	0.63	0.68	1.29
	蒙豆13 MD13	0.64	0.51	0.69	0.81
	平顶黄PDX	0.61	0.46	0.61	0.75
	伊通满仓金YTMCJ	0.58	0.49	0.64	0.74
	辽豆21 LD21	0.55	1.04	0.65	1.09
	北水泉乡黄豆BSQXHD	0.53	0.56	0.66	0.77
	百日熟BRS	0.51	0.48	0.65	0.89
	Corsoy	0.49	1.00	0.59	1.04
	吉育86 JY86	0.48	0.79	0.58	0.77
	黑农26 HN26	0.47	0.40	0.64	0.65
	吉林36 JL36	0.46	0.47	0.70	1.03
	满仓金MCJ	0.46	0.54	0.61	0.70
	绥农6号SuiN6	0.44	0.58	0.65	0.68
	吉原引3号JYY3	0.41	0.54	0.65	0.92
	克山1号KS1	0.40	0.85	0.56	0.73
	吉育67 JY67	0.37	0.39	0.63	0.62
	压破车YPC	0.37	0.43	0.57	0.69
	PI196160	0.37	1.05	0.61	1.11
	吉林3号JL3	0.36	0.48	0.62	0.64
	垦丰16 KF16	0.30	0.51	0.67	0.78
	PSB543	0.27	0.38	0.61	0.80
	中黄13 ZH13	0.26	0.53	0.63	0.76
四级Grade4	龙品10-217 LP10-217	0.15	0.32	0.51	0.60
五级Grade5	龙垦330 LK330	0.05	0.11	0.36	0.17
	AVELINE CH21715	0.03	0.04	0.43	0.34
	黑河5号HH5	0.02	0.08	0.41	0.40