Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (10): 1857-1869.doi: 10.3864/j.issn.0578-1752.2024.10.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Evaluation of Drought Resistance in Soybean Germplasm and Identification of Candidate Drought-Resistant Genes

LI ShengYou(), WANG ChangLing, YAN ChunJuan, ZHANG LiJun, SUN XuGang, CAO YongQiang(), WANG WenBin(), SONG ShuHong   

  1. Institute of Crop Research, Liaoning Academy of Agricultural Sciences, Shenyang 100161
  • Received:2023-12-19 Accepted:2024-01-08 Online:2024-05-16 Published:2024-05-23
  • Contact: CAO YongQiang, WANG WenBin

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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

Table 1

Primers of qRT-PCR for the candidate genes"

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

Fig. 1

Pearson's correlation coefficients describing associations of drought resistance index (DI), improved drought resistance index (IDI), weighted drought resistance coefficient (WDC), and weighted drought resistance index (WDI) for 188 soybean germplasm under different environments The diagonal shows the distribution of four parameters in different environments. The scatter plot shows below the diagonal. Above the diagonal is the correlation coefficient, *** represents significant difference at P<0.001"

Table 2

Grading standards of drought resistance for soybean germplasm and the number of germplasm at each level"

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)

Table 3

A total of 39 soybean accessions showing the same drought grade in different drought parameter methods"

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

Fig. 2

Manhattan plot and QQ plot of soybean drought resistance index (A), improved drought resistance index (B), weighted drought resistance coefficient (C) and weighted drought resistance index (D) by genome-wide association analysis"

Fig. 3

Expression profiles of 32 annotated genes after drought treatment Selected candidate genes marked in red font"

Fig. 4

Expression analysis of 8 candidate drought-resistant genes after drought treatment by qRT-PCR"

Table 4

Significant SNP loci and candidate drought-resistant genes in soybean"

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
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