Biodiv Sci ›› 2011, Vol. 19 ›› Issue (4): 485-493. DOI: 10.3724/SP.J.1003.2011.09232
Special Issue: 土壤生物与土壤健康
• Original Papers • Previous Articles Next Articles
Chunnan Li1,2, Hairui Cui1,*(), Weibo Wang1
Received:
2010-09-25
Accepted:
2011-02-19
Online:
2011-07-20
Published:
2011-07-29
Contact:
Hairui Cui
Chunnan Li, Hairui Cui, Weibo Wang. Genetic diversity in rhizosphere soil microbes detected with SRAP markers[J]. Biodiv Sci, 2011, 19(4): 485-493.
编号 Code | 植物 Plant species |
---|---|
A 区 Zone A | |
OS | 水稻 Rice (Oryza sativa) |
B 区 Zone B | |
AG | 芹菜 Celery (Apium graveolens) |
AS | 大蒜 Garlic (Allium sativum) |
AT | 韭菜 Chinese chives (Allium tuberosum) |
BC | 白菜 Chinese cabbage (Brassica campestris ssp. pekinensis) |
BN | 油菜 Rapeseed (Brassica napus) |
CS | 茶树 Tea plant (Camellia sinensis) |
GM | 大豆 Soybean (Glycine max) |
LE | 番茄 Tomato (Lycopersicon esculentum) |
LS | 莴苣 Lettuce (Lactuca sativa) |
PS | 豌豆 Pea (Pisum sativum) |
RS | 萝卜 Radish (Raphanus sativus) |
SM | 茄子 Eggplant (Solanum melongena) |
ST | 马铃薯 Potato (Solanum tuberosum) |
TA | 普通小麦 Wheat (Triticum aestivum) |
ZM | 玉米 Maize (Zea mays) |
C 区 Zone C | |
BO | 甘蓝 Cabbage (Brassica oleracea) |
FA | 高羊茅 Tall fescue (Festuca arundinacea) |
HV | 大麦 Barley (Hordeum vulgare) |
VF | 蚕豆 Broad bean (Vicia faba) |
Table 1 Codes of rhizosphere soils sampled from 20 plant species
编号 Code | 植物 Plant species |
---|---|
A 区 Zone A | |
OS | 水稻 Rice (Oryza sativa) |
B 区 Zone B | |
AG | 芹菜 Celery (Apium graveolens) |
AS | 大蒜 Garlic (Allium sativum) |
AT | 韭菜 Chinese chives (Allium tuberosum) |
BC | 白菜 Chinese cabbage (Brassica campestris ssp. pekinensis) |
BN | 油菜 Rapeseed (Brassica napus) |
CS | 茶树 Tea plant (Camellia sinensis) |
GM | 大豆 Soybean (Glycine max) |
LE | 番茄 Tomato (Lycopersicon esculentum) |
LS | 莴苣 Lettuce (Lactuca sativa) |
PS | 豌豆 Pea (Pisum sativum) |
RS | 萝卜 Radish (Raphanus sativus) |
SM | 茄子 Eggplant (Solanum melongena) |
ST | 马铃薯 Potato (Solanum tuberosum) |
TA | 普通小麦 Wheat (Triticum aestivum) |
ZM | 玉米 Maize (Zea mays) |
C 区 Zone C | |
BO | 甘蓝 Cabbage (Brassica oleracea) |
FA | 高羊茅 Tall fescue (Festuca arundinacea) |
HV | 大麦 Barley (Hordeum vulgare) |
VF | 蚕豆 Broad bean (Vicia faba) |
取样地点 Sites | pH | 有机质 Organic matter (g/kg) | 全氮 Total N (g/kg) | 速效P Available phosphorus (mg/kg) | 速效K Available potassium (mg/kg) |
---|---|---|---|---|---|
A区 | 6.47 | 18.59 | 1.13 | 18.40 | 43.80 |
B区 | 7.20 | 16.70 | 1.44 | 52.54 | 61.76 |
C区 | 7.15 | 15.10 | 1.80 | 48.52 | 58.10 |
Table 2 Physical and chemical properties of soil in the three sampling zones
取样地点 Sites | pH | 有机质 Organic matter (g/kg) | 全氮 Total N (g/kg) | 速效P Available phosphorus (mg/kg) | 速效K Available potassium (mg/kg) |
---|---|---|---|---|---|
A区 | 6.47 | 18.59 | 1.13 | 18.40 | 43.80 |
B区 | 7.20 | 16.70 | 1.44 | 52.54 | 61.76 |
C区 | 7.15 | 15.10 | 1.80 | 48.52 | 58.10 |
编号 Code | 正向引物序列 Forward primer (5'-3') | 编号 Code | 反向引物序列 Reverse primer (5′-3′) |
---|---|---|---|
F1 | TGAGTCCAAACCGGATA | R1 | GACTGCGTACGAATTAAT |
F2 | TGAGTCCAAACCGGAGC | R2 | GACTGCGTACGAATTTGC |
F3 | TGAGTCCAAACCGGAAT | R3 | GACTGCGTACGAATTGAC |
F4 | TGAGTCCAAACCGGACC | R4 | GACTGCGTACGAATTTGA |
F5 | TGAGTCCAAACCGGAAG | R5 | GACTGCGTACGAATTAAC |
F6 | TGAGTCCAAACCGGTAA | R6 | GACTGCGTACGAATTGCA |
F7 | TGAGTCCAAACCGGTCC | R7 | GACTGCGTACGAATTCAA |
F8 | TGAGTCCAAACCGGTGC | R8 | GACTGCGTACGAATTAGC |
Table 3 Sequences of SRAP forward and reverse primers used in the present study
编号 Code | 正向引物序列 Forward primer (5'-3') | 编号 Code | 反向引物序列 Reverse primer (5′-3′) |
---|---|---|---|
F1 | TGAGTCCAAACCGGATA | R1 | GACTGCGTACGAATTAAT |
F2 | TGAGTCCAAACCGGAGC | R2 | GACTGCGTACGAATTTGC |
F3 | TGAGTCCAAACCGGAAT | R3 | GACTGCGTACGAATTGAC |
F4 | TGAGTCCAAACCGGACC | R4 | GACTGCGTACGAATTTGA |
F5 | TGAGTCCAAACCGGAAG | R5 | GACTGCGTACGAATTAAC |
F6 | TGAGTCCAAACCGGTAA | R6 | GACTGCGTACGAATTGCA |
F7 | TGAGTCCAAACCGGTCC | R7 | GACTGCGTACGAATTCAA |
F8 | TGAGTCCAAACCGGTGC | R8 | GACTGCGTACGAATTAGC |
引物组合 Primer combination | 扩增片段大小 Fragment size (bp) | 位点总数 Total fragments | 多态位点比例 PPL (%) | 等位基因单体型 Ah | 多态信息含量 PIC | 遗传杂合度 He |
---|---|---|---|---|---|---|
F1/R3* | 110-310 | 14 | 92.86 | 20 | 0.95 | 0.9127 |
F1/R6* | 180-300 | 9 | 88.89 | 18 | 0.94 | 0.8732 |
F1/R7* | 120-290 | 7 | 85.71 | 13 | 0.90 | 0.9909 |
F1/R8 | 70-280 | 17 | 76.47 | 19 | 0.95 | 0.9137 |
F2/R3* | 90-300 | 13 | 100.00 | 20 | 0.95 | 0.9921 |
F2/R4* | 50-300 | 16 | 87.50 | 19 | 0.95 | 0.9975 |
F2/R7* | 100-300 | 10 | 100.00 | 17 | 0.94 | 0.9527 |
F3/R2 | 120-280 | 9 | 100.00 | 19 | 0.95 | 0.8854 |
F3/R3* | 100-290 | 11 | 81.82 | 16 | 0.93 | 0.9770 |
F3/R8* | 110-270 | 8 | 75.00 | 15 | 0.91 | 0.9944 |
F4/R2 | 90-310 | 7 | 100.00 | 12 | 0.90 | 0.8884 |
F4/R4 | 130-480 | 9 | 100.00 | 18 | 0.94 | 0.9912 |
F5/R1 | 140-280 | 11 | 100.00 | 19 | 0.95 | 0.9077 |
F5/R2 | 130-500 | 10 | 100.00 | 19 | 0.95 | 0.8878 |
F5/R3 | 60-310 | 12 | 91.67 | 19 | 0.95 | 0.8651 |
F5/R6 | 130-290 | 10 | 100.00 | 20 | 0.95 | 0.8368 |
F5/R7 | 80-480 | 15 | 93.33 | 20 | 0.95 | 0.8909 |
F6/R1 | 130-400 | 9 | 100.00 | 20 | 0.95 | 0.8732 |
F6/R7* | 110-450 | 10 | 90.00 | 16 | 0.93 | 0.8979 |
F6/R8 | 100-470 | 8 | 100.00 | 18 | 0.94 | 0.8872 |
F8/R5* | 80-460 | 12 | 100.00 | 20 | 0.95 | 0.9222 |
F8/R7* | 120-470 | 10 | 100.00 | 20 | 0.95 | 0.8668 |
Table 4 Polymorphic information of rhizosphere soil microbes from 20 plant species with 22 SRAP primer combinations
引物组合 Primer combination | 扩增片段大小 Fragment size (bp) | 位点总数 Total fragments | 多态位点比例 PPL (%) | 等位基因单体型 Ah | 多态信息含量 PIC | 遗传杂合度 He |
---|---|---|---|---|---|---|
F1/R3* | 110-310 | 14 | 92.86 | 20 | 0.95 | 0.9127 |
F1/R6* | 180-300 | 9 | 88.89 | 18 | 0.94 | 0.8732 |
F1/R7* | 120-290 | 7 | 85.71 | 13 | 0.90 | 0.9909 |
F1/R8 | 70-280 | 17 | 76.47 | 19 | 0.95 | 0.9137 |
F2/R3* | 90-300 | 13 | 100.00 | 20 | 0.95 | 0.9921 |
F2/R4* | 50-300 | 16 | 87.50 | 19 | 0.95 | 0.9975 |
F2/R7* | 100-300 | 10 | 100.00 | 17 | 0.94 | 0.9527 |
F3/R2 | 120-280 | 9 | 100.00 | 19 | 0.95 | 0.8854 |
F3/R3* | 100-290 | 11 | 81.82 | 16 | 0.93 | 0.9770 |
F3/R8* | 110-270 | 8 | 75.00 | 15 | 0.91 | 0.9944 |
F4/R2 | 90-310 | 7 | 100.00 | 12 | 0.90 | 0.8884 |
F4/R4 | 130-480 | 9 | 100.00 | 18 | 0.94 | 0.9912 |
F5/R1 | 140-280 | 11 | 100.00 | 19 | 0.95 | 0.9077 |
F5/R2 | 130-500 | 10 | 100.00 | 19 | 0.95 | 0.8878 |
F5/R3 | 60-310 | 12 | 91.67 | 19 | 0.95 | 0.8651 |
F5/R6 | 130-290 | 10 | 100.00 | 20 | 0.95 | 0.8368 |
F5/R7 | 80-480 | 15 | 93.33 | 20 | 0.95 | 0.8909 |
F6/R1 | 130-400 | 9 | 100.00 | 20 | 0.95 | 0.8732 |
F6/R7* | 110-450 | 10 | 90.00 | 16 | 0.93 | 0.8979 |
F6/R8 | 100-470 | 8 | 100.00 | 18 | 0.94 | 0.8872 |
F8/R5* | 80-460 | 12 | 100.00 | 20 | 0.95 | 0.9222 |
F8/R7* | 120-470 | 10 | 100.00 | 20 | 0.95 | 0.8668 |
样品编号 Sample codes | 位点总数 Total fragments | 多态位点数 No. of polymorphic loci | 多态位点比例 PPL (%) | Shannon多样性指数 I |
---|---|---|---|---|
水稻 OS | 116 | 99 | 85.34 | 0.2558 |
芹菜 AG | 118 | 101 | 85.59 | 0.2579 |
大蒜 AS | 149 | 132 | 88.59 | 0.3156 |
韭菜 AT | 129 | 112 | 86.82 | 0.2774 |
白菜 BC | 152 | 135 | 88.82 | 0.3205 |
油菜 BN | 144 | 127 | 88.19 | 0.3019 |
茶树 CS | 149 | 132 | 88.59 | 0.3144 |
大豆 GM | 145 | 128 | 88.28 | 0.3086 |
番茄 LE | 157 | 140 | 89.17 | 0.3281 |
莴苣 LS | 166 | 149 | 89.76 | 0.3457 |
豌豆 PS | 156 | 139 | 89.10 | 0.3258 |
萝卜 RS | 138 | 121 | 87.68 | 0.2945 |
茄子 SM | 132 | 115 | 87.12 | 0.2823 |
马铃薯 ST | 154 | 137 | 88.96 | 0.3240 |
普通小麦 TA | 125 | 108 | 86.40 | 0.2714 |
玉米 ZM | 144 | 127 | 88.19 | 0.3066 |
甘蓝 BO | 154 | 137 | 88.96 | 0.3243 |
高羊茅 FA | 126 | 109 | 86.51 | 0.2728 |
大麦 HV | 141 | 124 | 87.94 | 0.2993 |
蚕豆 VF | 131 | 114 | 87.02 | 0.2817 |
Table 6 SRAP amplification and Shannon diversity index of rhizosphere soil microbes from 20 plant species
样品编号 Sample codes | 位点总数 Total fragments | 多态位点数 No. of polymorphic loci | 多态位点比例 PPL (%) | Shannon多样性指数 I |
---|---|---|---|---|
水稻 OS | 116 | 99 | 85.34 | 0.2558 |
芹菜 AG | 118 | 101 | 85.59 | 0.2579 |
大蒜 AS | 149 | 132 | 88.59 | 0.3156 |
韭菜 AT | 129 | 112 | 86.82 | 0.2774 |
白菜 BC | 152 | 135 | 88.82 | 0.3205 |
油菜 BN | 144 | 127 | 88.19 | 0.3019 |
茶树 CS | 149 | 132 | 88.59 | 0.3144 |
大豆 GM | 145 | 128 | 88.28 | 0.3086 |
番茄 LE | 157 | 140 | 89.17 | 0.3281 |
莴苣 LS | 166 | 149 | 89.76 | 0.3457 |
豌豆 PS | 156 | 139 | 89.10 | 0.3258 |
萝卜 RS | 138 | 121 | 87.68 | 0.2945 |
茄子 SM | 132 | 115 | 87.12 | 0.2823 |
马铃薯 ST | 154 | 137 | 88.96 | 0.3240 |
普通小麦 TA | 125 | 108 | 86.40 | 0.2714 |
玉米 ZM | 144 | 127 | 88.19 | 0.3066 |
甘蓝 BO | 154 | 137 | 88.96 | 0.3243 |
高羊茅 FA | 126 | 109 | 86.51 | 0.2728 |
大麦 HV | 141 | 124 | 87.94 | 0.2993 |
蚕豆 VF | 131 | 114 | 87.02 | 0.2817 |
地点 Location | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
华家池 HJC | 0.0907-0.1771 | 16.66 | 0.0207 | 0.1243A |
建德 JD | 0.0256-0.0821 | 29.27 | 0.0160 | 0.0546B |
Table 7 Parameters of genetic distance of rice rhizosphere soil microbes at Huajiachi (HJC) and Jiande (JD)
地点 Location | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
华家池 HJC | 0.0907-0.1771 | 16.66 | 0.0207 | 0.1243A |
建德 JD | 0.0256-0.0821 | 29.27 | 0.0160 | 0.0546B |
品种/地点 Variety/location | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
明恢63/华家池 Minghui 63/HJC | 0.0958-0.1438 | 15.45 | 0.0189 | 0.1226 A |
嘉早935/华家池 Jiazao 935/HJC | 0.1002-0.1339 | 11.04 | 0.0128 | 0.1157A |
明恢63/建德 Minghui 63/JD | 0.0256-0.0520 | 25.24 | 0.0104 | 0.0412B |
嘉早935/建德 Jiazao 935/JD | 0.0334-0.0455 | 10.82 | 0.0044 | 0.0404 B |
Table 8 Parameters of genetic distance between Jiazao 935 and Minghui 63 at Huajiachi (HJC) and Jiande (JD)
品种/地点 Variety/location | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
明恢63/华家池 Minghui 63/HJC | 0.0958-0.1438 | 15.45 | 0.0189 | 0.1226 A |
嘉早935/华家池 Jiazao 935/HJC | 0.1002-0.1339 | 11.04 | 0.0128 | 0.1157A |
明恢63/建德 Minghui 63/JD | 0.0256-0.0520 | 25.24 | 0.0104 | 0.0412B |
嘉早935/建德 Jiazao 935/JD | 0.0334-0.0455 | 10.82 | 0.0044 | 0.0404 B |
取样时期 Stage | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
华家池 Huajiachi | ||||
成熟期 Maturation | 0.1050-0.1771 | 15.56 | 0.0215 | 0.1381A |
抽穗期 Heading | 0.1002-0.1580 | 15.01 | 0.0185 | 0.1232B |
分蘖期 Tillering | 0.0907-0.1620 | 17.20 | 0.0205 | 0.1189B |
灌浆期 Filling | 0.0958-0.1548 | 14.94 | 0.0175 | 0.1171B |
建德 Jiande | ||||
成熟期 Maturation | 0.0256-0.0821 | 34.05 | 0.0195 | 0.0573C |
灌浆期 Filling | 0.0404-0.0821 | 25.12 | 0.0142 | 0.0565C |
分蘖期 Tillering | 0.0333-0.0800 | 30.99 | 0.0165 | 0.0532C |
抽穗期 Heading | 0.0256-0.0701 | 28.03 | 0.0144 | 0.0515C |
Table 9 Parameters of genetic distance of rice rhizosphere soil microbes at different developmental stages in Huajiachi (HJC) and Jiande (JD)
取样时期 Stage | 变化范围 Range | 变异系数 CV (%) | 标准差 SD | 平均 Average |
---|---|---|---|---|
华家池 Huajiachi | ||||
成熟期 Maturation | 0.1050-0.1771 | 15.56 | 0.0215 | 0.1381A |
抽穗期 Heading | 0.1002-0.1580 | 15.01 | 0.0185 | 0.1232B |
分蘖期 Tillering | 0.0907-0.1620 | 17.20 | 0.0205 | 0.1189B |
灌浆期 Filling | 0.0958-0.1548 | 14.94 | 0.0175 | 0.1171B |
建德 Jiande | ||||
成熟期 Maturation | 0.0256-0.0821 | 34.05 | 0.0195 | 0.0573C |
灌浆期 Filling | 0.0404-0.0821 | 25.12 | 0.0142 | 0.0565C |
分蘖期 Tillering | 0.0333-0.0800 | 30.99 | 0.0165 | 0.0532C |
抽穗期 Heading | 0.0256-0.0701 | 28.03 | 0.0144 | 0.0515C |
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