Journal of Agricultural Science and Technology ›› 2023, Vol. 25 ›› Issue (9): 69-82.DOI: 10.13304/j.nykjdb.2022.1035
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Rui TIAN(), Hua ZHANG, Meihong HUANG, Zhenqi SHAO, Xihuan LI(), Caiying ZHANG()
Received:
2022-11-27
Accepted:
2022-12-26
Online:
2023-09-15
Published:
2023-09-28
Contact:
Xihuan LI,Caiying ZHANG
田蕊(), 张华, 黄玫红, 邵振启, 李喜焕(), 张彩英()
通讯作者:
李喜焕,张彩英
作者简介:
田蕊 E-mail:tianrui7726@163.com
基金资助:
CLC Number:
Rui TIAN, Hua ZHANG, Meihong HUANG, Zhenqi SHAO, Xihuan LI, Caiying ZHANG. Mining of Candidate Genes and Genetic Loci Conferring Drought Tolerance in Soybean[J]. Journal of Agricultural Science and Technology, 2023, 25(9): 69-82.
田蕊, 张华, 黄玫红, 邵振启, 李喜焕, 张彩英. 大豆抗旱遗传位点及候选基因发掘[J]. 中国农业科技导报, 2023, 25(9): 69-82.
环境 Environment | 均值 Mean | 标准差 SD | 最大值 Max. | 最小值 Min. | 变异系数 CV/% | 偏度 Skew. | 峰度 Kurt. | 显著性 Sig. | 遗传力 h2/% |
---|---|---|---|---|---|---|---|---|---|
E1 | 1.35 | 0.14 | 1.82 | 0.96 | 10.40 | 0.06 | 0.71 | ** | 81.44 |
E2 | 1.47 | 0.17 | 2.11 | 1.07 | 11.64 | 0.43 | 0.94 | ** | |
E3 | 1.48 | 0.12 | 1.68 | 0.98 | 8.71 | 0.14 | 0.21 | ** |
Table 1 Genetic variation analysis of drought resistance index in soybean natural population
环境 Environment | 均值 Mean | 标准差 SD | 最大值 Max. | 最小值 Min. | 变异系数 CV/% | 偏度 Skew. | 峰度 Kurt. | 显著性 Sig. | 遗传力 h2/% |
---|---|---|---|---|---|---|---|---|---|
E1 | 1.35 | 0.14 | 1.82 | 0.96 | 10.40 | 0.06 | 0.71 | ** | 81.44 |
E2 | 1.47 | 0.17 | 2.11 | 1.07 | 11.64 | 0.43 | 0.94 | ** | |
E3 | 1.48 | 0.12 | 1.68 | 0.98 | 8.71 | 0.14 | 0.21 | ** |
Fig. 1 Association analysis for chlorophyll drought resistance index in soybean populationA: Distribution, Manhattan and QQ plots of chlorophyll drought resistance index in E1; B: Distribution, Manhattan and QQ plots of chlorophyll drought resistance index in E2; C: Distribution, Manhattan and QQ plots of chlorophyll drought resistance index in E3; D: Distribution, Manhattan and QQ plots for mean values of chlorophyll drought resistance index; E: Distribution, Manhattan and QQ plots for BLUP values of chlorophyll drought resistance index
位点 Locus | 染色体 Chromosome | SNP区间 SNP interval/bp | SNP数目 SNP number | 最显著SNP Highest association SNP | -log10(P) | 环境 Environment |
---|---|---|---|---|---|---|
Locus 1 | Chr1 | 40 004 695~40 004 931 | 6 | Gm01:40004755 | 6.24 | Mean、BLUP、E1、E2、E3 |
Locus 2 | Chr2 | 687 623~688 028 | 5 | Gm02:687623 | 5.08 | Mean、E1、E2、E3 |
Locus 3 | Chr3 | 41 106 456 | 1 | Gm03:41106456 | 5.15 | Mean、E1 |
Locus 4 | Chr7 | 4 696 623 | 1 | Gm07:4696623 | 5.16 | BLUP |
Locus 5 | Chr10 | 348 939 | 1 | Gm10:348939 | 5.16 | Mean、BLUP、E1、E2、E3 |
Locus 6 | Chr10 | 656 486~694 780 | 5 | Gm10:656486 | 5.57 | Mean、BLUP、E1、E2、E3 |
Locus 7 | Chr10 | 703 703~707 681 | 15 | Gm10:703703 | 5.42 | Mean、E1、E2、E3 |
Locus 8 | Chr10 | 873 426 | 1 | Gm10:873426 | 5.07 | Mean、E1、E2、E3 |
Locus 9 | Chr10 | 987 325~1 087 932 | 5 | Gm10:1086041 | 5.20 | Mean、BLUP、E1 |
Locus 10 | Chr16 | 5 831 709~5 931 196 | 3 | Gm16:5931196 | 5.38 | E1、E2、E3 |
Locus 11 | Chr16 | 6 226 168~6 321 014 | 62 | Gm16:6302330 | 5.81 | Mean、BLUP、E1、E2、E3 |
Locus 12 | Chr16 | 6 329 004~6 419 081 | 83 | Gm16:6353406 | 7.11 | Mean、BLUP、E1、E2、E3 |
Locus 13 | Chr16 | 6 438 949~6 534 022 | 27 | Gm16:6472037 | 6.23 | Mean、BLUP、E1、E2、E3 |
Locus 14 | Chr16 | 6 564 434~6 651 708 | 6 | Gm16:6564434 | 5.31 | Mean、BLUP、E1、E2、E3 |
Locus 15 | Chr17 | 11 692 552~11 760 989 | 9 | Gm17:11711567 | 5.64 | Mean、BLUP、E1、E2、E3 |
Locus 16 | Chr18 | 39 040 317 | 1 | Gm18:39040317 | 5.85 | Mean、E1、E2、E3 |
Locus 17 | scaffold | 58 888 | 1 | scaffold_82:58888 | 6.24 | Mean、BLUP、E1、E2、E3 |
Locus 18 | scaffold | 14 534~15 780 | 5 | scaffold_288:14774 | 6.46 | Mean、BLUP、E1、E2、E3 |
Table 2 Associated genetic loci for drought resistance index in soybean natural population
位点 Locus | 染色体 Chromosome | SNP区间 SNP interval/bp | SNP数目 SNP number | 最显著SNP Highest association SNP | -log10(P) | 环境 Environment |
---|---|---|---|---|---|---|
Locus 1 | Chr1 | 40 004 695~40 004 931 | 6 | Gm01:40004755 | 6.24 | Mean、BLUP、E1、E2、E3 |
Locus 2 | Chr2 | 687 623~688 028 | 5 | Gm02:687623 | 5.08 | Mean、E1、E2、E3 |
Locus 3 | Chr3 | 41 106 456 | 1 | Gm03:41106456 | 5.15 | Mean、E1 |
Locus 4 | Chr7 | 4 696 623 | 1 | Gm07:4696623 | 5.16 | BLUP |
Locus 5 | Chr10 | 348 939 | 1 | Gm10:348939 | 5.16 | Mean、BLUP、E1、E2、E3 |
Locus 6 | Chr10 | 656 486~694 780 | 5 | Gm10:656486 | 5.57 | Mean、BLUP、E1、E2、E3 |
Locus 7 | Chr10 | 703 703~707 681 | 15 | Gm10:703703 | 5.42 | Mean、E1、E2、E3 |
Locus 8 | Chr10 | 873 426 | 1 | Gm10:873426 | 5.07 | Mean、E1、E2、E3 |
Locus 9 | Chr10 | 987 325~1 087 932 | 5 | Gm10:1086041 | 5.20 | Mean、BLUP、E1 |
Locus 10 | Chr16 | 5 831 709~5 931 196 | 3 | Gm16:5931196 | 5.38 | E1、E2、E3 |
Locus 11 | Chr16 | 6 226 168~6 321 014 | 62 | Gm16:6302330 | 5.81 | Mean、BLUP、E1、E2、E3 |
Locus 12 | Chr16 | 6 329 004~6 419 081 | 83 | Gm16:6353406 | 7.11 | Mean、BLUP、E1、E2、E3 |
Locus 13 | Chr16 | 6 438 949~6 534 022 | 27 | Gm16:6472037 | 6.23 | Mean、BLUP、E1、E2、E3 |
Locus 14 | Chr16 | 6 564 434~6 651 708 | 6 | Gm16:6564434 | 5.31 | Mean、BLUP、E1、E2、E3 |
Locus 15 | Chr17 | 11 692 552~11 760 989 | 9 | Gm17:11711567 | 5.64 | Mean、BLUP、E1、E2、E3 |
Locus 16 | Chr18 | 39 040 317 | 1 | Gm18:39040317 | 5.85 | Mean、E1、E2、E3 |
Locus 17 | scaffold | 58 888 | 1 | scaffold_82:58888 | 6.24 | Mean、BLUP、E1、E2、E3 |
Locus 18 | scaffold | 14 534~15 780 | 5 | scaffold_288:14774 | 6.46 | Mean、BLUP、E1、E2、E3 |
SNP | 石76368 Shi 76368 | 沧0719 Cang 0719 | 冀豆27 Jidou 27 | HN0906 | 石豆5号 Shidou 5 | HN1030 | 邯15-685 Han15-685 | 冀11B9 Ji 11B9 | 沧0627 Cang 0627 | 冀10B5 Ji 10B5 |
---|---|---|---|---|---|---|---|---|---|---|
Gm07:4696623 | AA | AA | AA | AA | AA | AA | — | |||
Gm10:348939 | CC | CC | CC | — | CC | |||||
Gm10:656486 | AA | AA | AA | AA | AA | |||||
Gm10:703703 | CC | CC | CC | CC | CC | |||||
Gm10:873426 | GG | GG | GG | GG | GG | |||||
Gm10:1086041 | GG | GG | GG | GG | GG | GG | ||||
Gm16:6302330 | TT | TT | TT | TT | TT | |||||
Gm16:6353406 | AA | AA | AA | AA | AA | |||||
Gm16:6564434 | GG | GG | GG | GG | GG | |||||
Gm17:11711567 | CC | CC | CC | CC | CC | |||||
scaffold_288:14774 | GG | — | GG | GG | GG | |||||
抗旱指数 Drought resistance index | 1.07 | 1.08 | 1.09 | 1.11 | 1.13 | 1.70 | 1.71 | 1.80 | 1.81 | 1.83 |
优异等位变异数量 Number of elite allele | 0 | 0 | 0 | 0 | 0 | 9 | 11 | 10 | 11 | 11 |
Table 3 Analysis of associated SNPs in different soybean accessions with different drought resistance index
SNP | 石76368 Shi 76368 | 沧0719 Cang 0719 | 冀豆27 Jidou 27 | HN0906 | 石豆5号 Shidou 5 | HN1030 | 邯15-685 Han15-685 | 冀11B9 Ji 11B9 | 沧0627 Cang 0627 | 冀10B5 Ji 10B5 |
---|---|---|---|---|---|---|---|---|---|---|
Gm07:4696623 | AA | AA | AA | AA | AA | AA | — | |||
Gm10:348939 | CC | CC | CC | — | CC | |||||
Gm10:656486 | AA | AA | AA | AA | AA | |||||
Gm10:703703 | CC | CC | CC | CC | CC | |||||
Gm10:873426 | GG | GG | GG | GG | GG | |||||
Gm10:1086041 | GG | GG | GG | GG | GG | GG | ||||
Gm16:6302330 | TT | TT | TT | TT | TT | |||||
Gm16:6353406 | AA | AA | AA | AA | AA | |||||
Gm16:6564434 | GG | GG | GG | GG | GG | |||||
Gm17:11711567 | CC | CC | CC | CC | CC | |||||
scaffold_288:14774 | GG | — | GG | GG | GG | |||||
抗旱指数 Drought resistance index | 1.07 | 1.08 | 1.09 | 1.11 | 1.13 | 1.70 | 1.71 | 1.80 | 1.81 | 1.83 |
优异等位变异数量 Number of elite allele | 0 | 0 | 0 | 0 | 0 | 9 | 11 | 10 | 11 | 11 |
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.01G114050 | 驱动蛋白类蛋白KIN-14U Kinesin-like protein KIN-14U | 细胞脂质代谢过程 Cellular lipid metabolic process |
Glyma.01G114300# | TIC蛋白Protein TIC | - |
Glyma.01G114050 | 驱动蛋白类蛋白KIN-14U Kinesin-like protein KIN-14U | 细胞脂质代谢过程 Cellular lipid metabolic process |
Glyma.02G006300# | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.03G188100∆ | C末端结构域蛋白 C-terminal domain-containing protein | 蛋白靶向膜 Protein targeting to membrane |
Glyma.07G053900# | Dof型结构域蛋白 Dof-type domain-containing protein | 转录负调控 Negative regulation of transcription |
Glyma.07G054000∆ | MYB转录因子 MYB transcription factor | 肉桂酸生物合成过程 Cinnamic acid biosynthetic process |
Glyma.10G010700 | Fe2O G加双氧酶结构域蛋白 Fe2O G dioxygenase domain-containing protein | 赤霉素分解代谢过程 Gibberellin catabolic process |
Glyma.10G010750 | - | - |
Glyma.10G010902 | mRNA剪接因子 Probable pre-mRNA-splicing factor | mRNA加工 mRNA processing |
Table 4 Candidate genes of drought resistance index in soybean
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.01G114050 | 驱动蛋白类蛋白KIN-14U Kinesin-like protein KIN-14U | 细胞脂质代谢过程 Cellular lipid metabolic process |
Glyma.01G114300# | TIC蛋白Protein TIC | - |
Glyma.01G114050 | 驱动蛋白类蛋白KIN-14U Kinesin-like protein KIN-14U | 细胞脂质代谢过程 Cellular lipid metabolic process |
Glyma.02G006300# | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.03G188100∆ | C末端结构域蛋白 C-terminal domain-containing protein | 蛋白靶向膜 Protein targeting to membrane |
Glyma.07G053900# | Dof型结构域蛋白 Dof-type domain-containing protein | 转录负调控 Negative regulation of transcription |
Glyma.07G054000∆ | MYB转录因子 MYB transcription factor | 肉桂酸生物合成过程 Cinnamic acid biosynthetic process |
Glyma.10G010700 | Fe2O G加双氧酶结构域蛋白 Fe2O G dioxygenase domain-containing protein | 赤霉素分解代谢过程 Gibberellin catabolic process |
Glyma.10G010750 | - | - |
Glyma.10G010902 | mRNA剪接因子 Probable pre-mRNA-splicing factor | mRNA加工 mRNA processing |
Fig. 4 Identification of candidate gene Glyma.16G063600A:GWAS signal on chromosome 16 (top) in the region from 6.0~6.5 Mb and LD heatmap (bottom) for this region; B:Haplotypes of Glyma.16G063600 in soybean natural population, statistical significance is determined by a two-tailed t-test; C:Gene structure and encoding protein conserved domain of Glyma.16G063600. Black rectangle— Exon; White rectangle—5’UTR;White pentagon—3’UTR; Vertical red line—SNP mutation
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.10G011000 | PlsC结构域蛋白 PlsC domain-containing protein | CDP甘油二酯生物合成 CDP-diacylglycerol biosynthetic process |
Glyma.10G011700∆ | EB_dh结构域蛋白 EB_dh domain-containing protein | - |
Glyma.10G011600 | - | - |
Glyma.10G003400# | VAN3结合蛋白 VAN3-binding protein | 韧皮部或木质部组织发生 Phloem or xylem histogenesis |
Glyma.10G003500# | CCR4非转录复合亚族 CCR4-NOT transcription complex subunit | 生物过程 Biological process |
Glyma.10G006600# | GmMYB29A1蛋白 GmMYB29A1 protein | 缺水反应 Response to water deprivation |
Glyma.10G006700∆ | 大豆磷转运蛋白 Soybean phosphate transporter protein | 磷酸盐离子转运 Phosphate ion transport |
Glyma.10G007000∆ # | AP2-EREBP转录因子 AP2-EREBP transcription factor | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.10G007100# | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.10G007200# | RING型结构域蛋白 RING-type domain-containing protein | 蛋白泛素化 Protein ubiquitination |
Glyma.10G009000 | 果胶酯酶 Pectinesterase | 细胞壁修饰 Cell wall modification |
Glyma.10G010400∆ # | MYB转录因子 MYB transcription factor | 缺水反应 Response to water deprivation |
Glyma.10G010501 | 果胶酯酶结构域蛋白 Pectinesterase domain-containing protein | 细胞壁修饰 Cell wall modification |
Glyma.16G059801# | 线粒体丙酮酸载体 Mitochondrial pyruvate carrier | 气孔运动的调节 Regulation of stomatal movement |
Glyma.16G060800 | 萌发素类蛋白 Germin-like protein | 胁迫反应 Response to stress |
Glyma.16G063600∆ # | F-box蛋白 F-box protein | 植物型过敏反应 Plant-type hypersensitive response |
Glyma.16G063700 | Myb 原癌基因蛋白 Myb proto-oncogene protein | DNA结合转录因子 DNA-binding transcription factor activity |
Glyma.16G063900∆ | 肽基丝氨酸-半乳糖转移酶 Peptidyl serine alpha-galactosyltransferase | 生物过程 Biological process |
Glyma.16G064000 | WVD2蛋白 Protein WVD2 | 生物过程 Biological process |
Glyma.16G064100# | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Table 4 Candidate genes of drought resistance index in soybean
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.10G011000 | PlsC结构域蛋白 PlsC domain-containing protein | CDP甘油二酯生物合成 CDP-diacylglycerol biosynthetic process |
Glyma.10G011700∆ | EB_dh结构域蛋白 EB_dh domain-containing protein | - |
Glyma.10G011600 | - | - |
Glyma.10G003400# | VAN3结合蛋白 VAN3-binding protein | 韧皮部或木质部组织发生 Phloem or xylem histogenesis |
Glyma.10G003500# | CCR4非转录复合亚族 CCR4-NOT transcription complex subunit | 生物过程 Biological process |
Glyma.10G006600# | GmMYB29A1蛋白 GmMYB29A1 protein | 缺水反应 Response to water deprivation |
Glyma.10G006700∆ | 大豆磷转运蛋白 Soybean phosphate transporter protein | 磷酸盐离子转运 Phosphate ion transport |
Glyma.10G007000∆ # | AP2-EREBP转录因子 AP2-EREBP transcription factor | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.10G007100# | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号通路 Ethylene-activated signaling pathway |
Glyma.10G007200# | RING型结构域蛋白 RING-type domain-containing protein | 蛋白泛素化 Protein ubiquitination |
Glyma.10G009000 | 果胶酯酶 Pectinesterase | 细胞壁修饰 Cell wall modification |
Glyma.10G010400∆ # | MYB转录因子 MYB transcription factor | 缺水反应 Response to water deprivation |
Glyma.10G010501 | 果胶酯酶结构域蛋白 Pectinesterase domain-containing protein | 细胞壁修饰 Cell wall modification |
Glyma.16G059801# | 线粒体丙酮酸载体 Mitochondrial pyruvate carrier | 气孔运动的调节 Regulation of stomatal movement |
Glyma.16G060800 | 萌发素类蛋白 Germin-like protein | 胁迫反应 Response to stress |
Glyma.16G063600∆ # | F-box蛋白 F-box protein | 植物型过敏反应 Plant-type hypersensitive response |
Glyma.16G063700 | Myb 原癌基因蛋白 Myb proto-oncogene protein | DNA结合转录因子 DNA-binding transcription factor activity |
Glyma.16G063900∆ | 肽基丝氨酸-半乳糖转移酶 Peptidyl serine alpha-galactosyltransferase | 生物过程 Biological process |
Glyma.16G064000 | WVD2蛋白 Protein WVD2 | 生物过程 Biological process |
Glyma.16G064100# | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.16G064200∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064300 | 驱动蛋白类蛋白KIN-4C Kinesin-like protein KIN-4C | 微管运动 Microtubule-based movement |
Glyma.16G064401 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064700# | 2-羧基-1,4萘醌转移酶 2-carboxy-1,4-naphthoquinone phytyltransferase | 光合电子传递 Photosynthetic electron transport |
Glyma.16G064800 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064900∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G065000 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065200∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G065300# | 蛋白Ycf2 Protein Ycf2 | 蛋白进入叶绿体基质 Protein import into chloroplast stroma |
Glyma.16G065400∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065500∆ | LRRNT_2结构域蛋白 LRRNT_2 domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065600 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导信号途径 Hormone-mediated signaling pathway |
Glyma.16G065900∆ | 胱氨酸 Cystinosin homolog | L-胱氨酸转运 L-cystine transport |
Glyma.16G066200∆ | 琥珀酸脱氢酶[泛醌]铁硫 Succinate dehydrogenase [ubiquinone] iron-sulfur | 三羧酸循环 Tricarboxylic acid cycle |
Glyma.16G066600 | 液泡加工酶 Vacuolar-processing enzyme | 液泡蛋白合成 Vacuolar protein processing |
Glyma.16G067400 | - | - |
Glyma.16G067500 | 水解酶_4结构域蛋白 Hydrolase_4 domain-containing protein | 生物过程 Biological process |
Glyma.16G067600 | 未知蛋白 Uncharacterized protein | - |
Glyma.16G067700 | 筛管封闭 Sieve element occlusion | 韧皮部发育 Phloem development |
Table 4 Candidate genes of drought resistance index in soybean
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.16G064200∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064300 | 驱动蛋白类蛋白KIN-4C Kinesin-like protein KIN-4C | 微管运动 Microtubule-based movement |
Glyma.16G064401 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064700# | 2-羧基-1,4萘醌转移酶 2-carboxy-1,4-naphthoquinone phytyltransferase | 光合电子传递 Photosynthetic electron transport |
Glyma.16G064800 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G064900∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G065000 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065200∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导的信号途径 Hormone-mediated signaling pathway |
Glyma.16G065300# | 蛋白Ycf2 Protein Ycf2 | 蛋白进入叶绿体基质 Protein import into chloroplast stroma |
Glyma.16G065400∆ | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065500∆ | LRRNT_2结构域蛋白 LRRNT_2 domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.16G065600 | 蛋白激酶结构域蛋白 Protein kinase domain-containing protein | 激素介导信号途径 Hormone-mediated signaling pathway |
Glyma.16G065900∆ | 胱氨酸 Cystinosin homolog | L-胱氨酸转运 L-cystine transport |
Glyma.16G066200∆ | 琥珀酸脱氢酶[泛醌]铁硫 Succinate dehydrogenase [ubiquinone] iron-sulfur | 三羧酸循环 Tricarboxylic acid cycle |
Glyma.16G066600 | 液泡加工酶 Vacuolar-processing enzyme | 液泡蛋白合成 Vacuolar protein processing |
Glyma.16G067400 | - | - |
Glyma.16G067500 | 水解酶_4结构域蛋白 Hydrolase_4 domain-containing protein | 生物过程 Biological process |
Glyma.16G067600 | 未知蛋白 Uncharacterized protein | - |
Glyma.16G067700 | 筛管封闭 Sieve element occlusion | 韧皮部发育 Phloem development |
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.17G143800 | 鞘磷脂磷酸二酯酶 Sphingomyelin phosphodiesterase 4 | 生物过程 Biological process |
Glyma.17G143900∆ # | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号途径 Ethylene-activated signaling pathway |
Glyma.17G144000 | 过氧化物酶体酰基辅酶A氧化酶 Peroxisomal acyl-coenzyme A oxidase | 茉莉酸生物合成 Jasmonic acid biosynthetic process |
Glyma.17G144100# | HTH MYB型结构域蛋白 HTH MYB-type domain-containing protein | ABA反应 Response to abscisic acid |
Glyma.17G144301 | Fe2O G加双氧酶结构域蛋白 Fe2O G dioxygenase domain-containing protein | - |
Glyma.18G167700 | F-box结构域蛋白 F-box domain-containing protein | 生物过程 Biological process |
Glyma.18G167833 | E1A结合蛋白 p400E1A-binding protein p400 | - |
Glyma.U024802 | 含有蛋白激酶结构域的蛋质 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.U043000 | 未知蛋白 Uncharacterized protein | - |
Table 4 Candidate genes of drought resistance index in soybean
候选基因 Candidate gene | 基因注释 Annotation | 生物过程描述 Biological process description |
---|---|---|
Glyma.17G143800 | 鞘磷脂磷酸二酯酶 Sphingomyelin phosphodiesterase 4 | 生物过程 Biological process |
Glyma.17G143900∆ # | AP2/ERF结构域蛋白 AP2/ERF domain-containing protein | 乙烯激活信号途径 Ethylene-activated signaling pathway |
Glyma.17G144000 | 过氧化物酶体酰基辅酶A氧化酶 Peroxisomal acyl-coenzyme A oxidase | 茉莉酸生物合成 Jasmonic acid biosynthetic process |
Glyma.17G144100# | HTH MYB型结构域蛋白 HTH MYB-type domain-containing protein | ABA反应 Response to abscisic acid |
Glyma.17G144301 | Fe2O G加双氧酶结构域蛋白 Fe2O G dioxygenase domain-containing protein | - |
Glyma.18G167700 | F-box结构域蛋白 F-box domain-containing protein | 生物过程 Biological process |
Glyma.18G167833 | E1A结合蛋白 p400E1A-binding protein p400 | - |
Glyma.U024802 | 含有蛋白激酶结构域的蛋质 Protein kinase domain-containing protein | 蛋白磷酸化 Protein phosphorylation |
Glyma.U043000 | 未知蛋白 Uncharacterized protein | - |
Fig. 5 Identification of candidate gene Glyma.10G007000A:GWAS signal on chromosome 10 (top) in the region from 0.0~0.9 Mb and LD heatmap (bottom) for this region; B:Haplotypes of Glyma.10G007000 in soybean natural population, statistical significance is determined by a two-tailed t-test; C:Gene structure and encoding protein conserved domain of Glyma.10G007000. Black rectangle— Exon; White rectangle— 5’UTR; White pentagon—3’UTR; Vertical red line— SNP mutation
Fig. 6 Identification of candidate gene Glyma.17G143900A:GWAS signal on chromosome 17 (top) in the region from 11.5 ~11.9 Mb and LD heatmap (bottom) for this region; B:Haplotypes of Glyma.17G143900 in soybean natural population, statistical significance is determined by a two-tailed t-test; C:Gene structure and encoding protein conserved domain of Glyma.17G143900. Black rectangle—Exon; White rectangle—5’UTR; White pentagon—3’UTR; Vertical red line—SNP mutation
基因型Genotype | 品种数量Variety number | 抗旱指数Drought resistance index |
---|---|---|
基因型Ⅰ (CCC)Genotype Ⅰ (CCC) | 70 | 0.97 d |
基因型Ⅱ (CCT)Genotype Ⅱ (CCT) | 36 | 1.03 c |
基因型Ⅲ (CAC)Genotype Ⅲ (CAC) | 17 | 1.10 abc |
基因型Ⅳ (CAT)Genotype Ⅳ (CAT) | 13 | 1.14 ab |
基因型Ⅴ (ACC)Genotype Ⅴ (ACC) | 35 | 1.03 c |
基因型Ⅵ (ACT)Genotype Ⅵ (ACT) | 17 | 1.04 c |
基因型Ⅶ (AAT)Genotype Ⅶ (AAT) | 7 | 1.20 a |
基因型Ⅷ (AAC)Genotype Ⅷ (AAC) | 4 | 1.18 ab |
Table 5 Analysis of soybean natural population based on the allele variations of three selected causal genes
基因型Genotype | 品种数量Variety number | 抗旱指数Drought resistance index |
---|---|---|
基因型Ⅰ (CCC)Genotype Ⅰ (CCC) | 70 | 0.97 d |
基因型Ⅱ (CCT)Genotype Ⅱ (CCT) | 36 | 1.03 c |
基因型Ⅲ (CAC)Genotype Ⅲ (CAC) | 17 | 1.10 abc |
基因型Ⅳ (CAT)Genotype Ⅳ (CAT) | 13 | 1.14 ab |
基因型Ⅴ (ACC)Genotype Ⅴ (ACC) | 35 | 1.03 c |
基因型Ⅵ (ACT)Genotype Ⅵ (ACT) | 17 | 1.04 c |
基因型Ⅶ (AAT)Genotype Ⅶ (AAT) | 7 | 1.20 a |
基因型Ⅷ (AAC)Genotype Ⅷ (AAC) | 4 | 1.18 ab |
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