生物多样性 ›› 2013, Vol. 21 ›› Issue (3): 315-325. DOI: 10.3724/SP.J.1003.2013.11035
杜周和1,2, 刘俊凤1,*(), 刘彬斌1, 左艳春1, 吴建梅1, 陈义安1, 张剑飞1, 鲁成2,*(
)
收稿日期:
2013-02-04
接受日期:
2013-04-26
出版日期:
2013-05-20
发布日期:
2013-06-05
通讯作者:
刘俊凤,鲁成
基金资助:
Zhouhe Du1,2, Junfeng Liu1,*, Binbin Liu1, Yanchun Zuo1, Jianmei Wu1, Yi-an Chen1, Jianfei Zhang1, Cheng Lu2,*()
Received:
2013-02-04
Accepted:
2013-04-26
Online:
2013-05-20
Published:
2013-06-05
Contact:
Liu Junfeng,Lu Cheng
摘要:
为检测家蚕(Bombyx mori)地方品种间的遗传差异, 分析其遗传多样性和系统分化模式, 为家蚕的品种鉴定和杂交育种亲本选择提供分子依据, 本文对72个家蚕地方品种的淀粉酶基因(Bmamy2)片段进行测序, 采用DNA序列分析技术探究了家蚕地方品种在核苷酸序列水平上的遗传差异及其系统分化特征。结果显示, 家蚕地方品种在Bmamy2基因变异丰富, 碱基突变率为5.6-8.2%, 单倍型多样度为0.8294, 核苷酸多样度为0.0236±0.00122, 表明Bmamy2是一个具有丰富序列多样性的标记基因, 能够较好地区分家蚕地方品种间的遗传多样性。系统发育分析、分子方差分析和Network分析等多种分析方法均检测到家蚕地方品种不按地理系统或生态类型聚类, 各聚类种群均由来自不同地理系统或生态类型的品种构成, 而来自同一地理系统或生态类型的品种则分别归属于不同的聚类种群。推测在家蚕的进化过程中并没有形成按地理系统或生态类型归类的分化格局, 家蚕可能具有多种化性混合驯化起源的遗传背景和系统分化特征。
杜周和, 刘俊凤, 刘彬斌, 左艳春, 吴建梅, 陈义安, 张剑飞, 鲁成 (2013) 家蚕地方品种遗传多样性及其分子系统学研究. 生物多样性, 21, 315-325. DOI: 10.3724/SP.J.1003.2013.11035.
Zhouhe Du,Junfeng Liu,Binbin Liu,Yanchun Zuo,Jianmei Wu,Yi-an Chen,Jianfei Zhang,Cheng Lu (2013) Genetic diversity and molecular genealogy of local silkworm varieties. Biodiversity Science, 21, 315-325. DOI: 10.3724/SP.J.1003.2013.11035.
序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype | 序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype |
---|---|---|---|---|---|---|---|
1 | 小石丸 Xiaoshiwan | XSW | CV1 | 37 | 萨尼斯 Sanisi | SNS | EV1 |
2 | 二毛 Ermao | EM | CV1 | 38 | 罗尼7 Luoni7 | LN7 | EV1 |
3 | 土三虎斑 Tusanhuban | TSHB | CV1 | 39 | 法408 Fa408 | F408 | EV1 |
4 | 中土 Zhongtu | ZT | CV1 | 40 | 欧18 Ou18 | O18 | EV1 |
5 | 达县土种 Daxiantuzhong | DXTZ | CV1 | 41 | 意16 Yi16 | Y16 | EV1 |
6 | 土一肉黄圆 Tuyirouhuangyuan | TYRHY | CV1 | 42 | 乌D WuD | WD | EV2 |
7 | 土八 Tuba | Tba | CV1 | 43 | 乌G WuG | WG | EV2 |
8 | 鲁1 Lu1 | L1 | CV1 | 44 | 乌B WuB | WB | EV2 |
9 | Re黑 Rehei | RH | CV1 | 45 | 乌2 Wu2 | W2 | EV2 |
10 | 鲁10 Lu10 | L10 | CV1 | 46 | 日110 Ri110 | R110 | T |
11 | 土种01 Tuzhong01 | TZ01 | CV1 | 47 | 大造 Dazao | DZ | T |
12 | 诸桂 Zhugui | ZG | CV1 | 48 | 高花 Gaohua | GH | T |
13 | 温州种 Wenzhouzhong | WZZ | CV1 | 49 | 第五白卵 Diwubailuan | DWBL | T |
14 | 芙蓉灰卵 Furonghuiluan | FRHL | CV1 | 50 | 演金黄白 Yanjinhuangbai | YJHB | T |
15 | 灰色卵 Huiseluan | HSL | CV1 | 51 | 15-100 | 15-100 | T |
16 | 盱眙种 Xuyizhong | XYZ | CV1 | 52 | 07-310 | 07-310 | T |
17 | 余杭24 Yuhang24 | YH24 | CV1 | 53 | 高白 Gaobai | GB | T |
18 | 沛县种 Peixianzhong | PXZ | CV1 | 54 | 琼山海南 Qiongshanhainan | QSHN | T |
19 | 邯郸种 Handanzhong | HDZ | CV1 | 55 | 655 | 655 | T |
20 | 中4010 Zhong4010 | Z4010 | CV2 | 56 | 防四 Fangsi | FS | T |
21 | 泰 Tai | T | CV2 | 57 | 印度种 Yinduzhong | YDZ | T |
22 | 玉溪2号 Yuxi2hao | YX | CV2 | 58 | 加秋 Jiaqiu | JQ | T |
23 | 平 Ping | P | CV2 | 59 | 白夏B BaixiaB | BXB | T |
24 | C108 | C108 | CV2 | 60 | 天龙青白 Tianlongqingbai | TLQB | JV1 |
25 | 余杭2 Yuhang2 | YH2 | CV2 | 61 | 赤熟 Chishu | Cshu | JV1 |
26 | 土白 Tubai | Tbai | CV2 | 62 | 日9 Ri9 | R9 | JV1 |
27 | 松花形吴 Songhuaxingwu | SHXW | CV2 | 63 | 姬蚕 Jican | JC | JV1 |
28 | 保黄 Baohuang | BH | CVd | 64 | 黑子 Heizi | HZ | JV1 |
29 | MCH101 | MCH101 | CVd | 65 | 日10 Ri10 | R10 | JV1 |
30 | BT924 | BT924 | CVd | 66 | 绵蚕 Miancan | MC | JV1 |
31 | BH863 | BH863 | CVd | 67 | 日限2 Rixian2 | RX2 | JV2 |
表1 (续) Table 1 (continued) | |||||||
序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype | 序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype |
32 | 琼十 Qiongshi | QS | CVd | 68 | 赢纹形 Yingwenxing | YWX | JV2 |
33 | 四海 Sihai | SH | CVd | 69 | J115 | J115 | JV2 |
34 | 兰十 Lanshi | LanS | CVd | 70 | 830 | 830 | JV2 |
35 | 罗萨 Luosa | LuoS | EV1 | 71 | 春四 Chunsi | CS | JV2 |
36 | 阿利可斯 Alikesi | ALKS | EV1 | 72 | T8 | T8 | JV2 |
表1 供试的72个家蚕品种材料的来源及特性
Table 1 The origin and characters of 72 silkworm varieties used in this study
序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype | 序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype |
---|---|---|---|---|---|---|---|
1 | 小石丸 Xiaoshiwan | XSW | CV1 | 37 | 萨尼斯 Sanisi | SNS | EV1 |
2 | 二毛 Ermao | EM | CV1 | 38 | 罗尼7 Luoni7 | LN7 | EV1 |
3 | 土三虎斑 Tusanhuban | TSHB | CV1 | 39 | 法408 Fa408 | F408 | EV1 |
4 | 中土 Zhongtu | ZT | CV1 | 40 | 欧18 Ou18 | O18 | EV1 |
5 | 达县土种 Daxiantuzhong | DXTZ | CV1 | 41 | 意16 Yi16 | Y16 | EV1 |
6 | 土一肉黄圆 Tuyirouhuangyuan | TYRHY | CV1 | 42 | 乌D WuD | WD | EV2 |
7 | 土八 Tuba | Tba | CV1 | 43 | 乌G WuG | WG | EV2 |
8 | 鲁1 Lu1 | L1 | CV1 | 44 | 乌B WuB | WB | EV2 |
9 | Re黑 Rehei | RH | CV1 | 45 | 乌2 Wu2 | W2 | EV2 |
10 | 鲁10 Lu10 | L10 | CV1 | 46 | 日110 Ri110 | R110 | T |
11 | 土种01 Tuzhong01 | TZ01 | CV1 | 47 | 大造 Dazao | DZ | T |
12 | 诸桂 Zhugui | ZG | CV1 | 48 | 高花 Gaohua | GH | T |
13 | 温州种 Wenzhouzhong | WZZ | CV1 | 49 | 第五白卵 Diwubailuan | DWBL | T |
14 | 芙蓉灰卵 Furonghuiluan | FRHL | CV1 | 50 | 演金黄白 Yanjinhuangbai | YJHB | T |
15 | 灰色卵 Huiseluan | HSL | CV1 | 51 | 15-100 | 15-100 | T |
16 | 盱眙种 Xuyizhong | XYZ | CV1 | 52 | 07-310 | 07-310 | T |
17 | 余杭24 Yuhang24 | YH24 | CV1 | 53 | 高白 Gaobai | GB | T |
18 | 沛县种 Peixianzhong | PXZ | CV1 | 54 | 琼山海南 Qiongshanhainan | QSHN | T |
19 | 邯郸种 Handanzhong | HDZ | CV1 | 55 | 655 | 655 | T |
20 | 中4010 Zhong4010 | Z4010 | CV2 | 56 | 防四 Fangsi | FS | T |
21 | 泰 Tai | T | CV2 | 57 | 印度种 Yinduzhong | YDZ | T |
22 | 玉溪2号 Yuxi2hao | YX | CV2 | 58 | 加秋 Jiaqiu | JQ | T |
23 | 平 Ping | P | CV2 | 59 | 白夏B BaixiaB | BXB | T |
24 | C108 | C108 | CV2 | 60 | 天龙青白 Tianlongqingbai | TLQB | JV1 |
25 | 余杭2 Yuhang2 | YH2 | CV2 | 61 | 赤熟 Chishu | Cshu | JV1 |
26 | 土白 Tubai | Tbai | CV2 | 62 | 日9 Ri9 | R9 | JV1 |
27 | 松花形吴 Songhuaxingwu | SHXW | CV2 | 63 | 姬蚕 Jican | JC | JV1 |
28 | 保黄 Baohuang | BH | CVd | 64 | 黑子 Heizi | HZ | JV1 |
29 | MCH101 | MCH101 | CVd | 65 | 日10 Ri10 | R10 | JV1 |
30 | BT924 | BT924 | CVd | 66 | 绵蚕 Miancan | MC | JV1 |
31 | BH863 | BH863 | CVd | 67 | 日限2 Rixian2 | RX2 | JV2 |
表1 (续) Table 1 (continued) | |||||||
序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype | 序号 No. | 品种 Variety | 代号 Code | 生态类型 Ecotype |
32 | 琼十 Qiongshi | QS | CVd | 68 | 赢纹形 Yingwenxing | YWX | JV2 |
33 | 四海 Sihai | SH | CVd | 69 | J115 | J115 | JV2 |
34 | 兰十 Lanshi | LanS | CVd | 70 | 830 | 830 | JV2 |
35 | 罗萨 Luosa | LuoS | EV1 | 71 | 春四 Chunsi | CS | JV2 |
36 | 阿利可斯 Alikesi | ALKS | EV1 | 72 | T8 | T8 | JV2 |
图2 Bmamy2基因扩增区序列结构(黑框代表外显子, 斜线框代表内含子)
Fig. 2 Schematic illustration of Bmamy2 gene in amplified region. The black frame indicates exons, and bias frame indicates introns.
序列长度 Sequence length (bp) | 碱基插入/缺失位点数 Insert/delete (%) | 变异位点数 Variable site (%) | 单个突变位点 Singleton variable site (%) | 简约信息位点 Parsimony variable site (%) | |
---|---|---|---|---|---|
外显子 Exon | 493 | 2(0.4)* | 10(2.0) | 2(0.4) | 8(1.6) |
内含子 Intron | 670 | 139(20.7) | 55(8.2) | 7(1.0) | 48(7.2) |
全序列 Entire | 1,163 | 141(12.1) | 65(5.6) | 9(0.8) | 56(4.8) |
表2 72个家蚕地方品种Bmamy2基因扩增片段碱基变化统计
Table 2 Statistics of the varieties bases of 72 local silkworm varieties in the Bmamy2 gene amplified region
序列长度 Sequence length (bp) | 碱基插入/缺失位点数 Insert/delete (%) | 变异位点数 Variable site (%) | 单个突变位点 Singleton variable site (%) | 简约信息位点 Parsimony variable site (%) | |
---|---|---|---|---|---|
外显子 Exon | 493 | 2(0.4)* | 10(2.0) | 2(0.4) | 8(1.6) |
内含子 Intron | 670 | 139(20.7) | 55(8.2) | 7(1.0) | 48(7.2) |
全序列 Entire | 1,163 | 141(12.1) | 65(5.6) | 9(0.8) | 56(4.8) |
CV2 | EV1 | T | CV1M3 | JV2 | CV1M4 | JV1 | CVd | |
---|---|---|---|---|---|---|---|---|
CV2 | ||||||||
EV1 | 0.025 | |||||||
T | 0.027 | 0.024 | ||||||
CV1M3 | 0.026 | 0.015 | 0.023 | |||||
JV2 | 0.026 | 0.012 | 0.024 | 0.016 | ||||
CV1M4 | 0.026 | 0.013 | 0.024 | 0.017 | 0.014 | |||
JV1 | 0.027 | 0.025 | 0.024 | 0.025 | 0.026 | 0.025 | ||
CVd | 0.025 | 0.025 | 0.024 | 0.025 | 0.026 | 0.025 | 0.024 | |
EV2 | 0.025 | 0.044 | 0.029 | 0.039 | 0.044 | 0.042 | 0.026 | 0.026 |
表3 不同生态类型家蚕品种间的遗传距离
Table 3 Genetic distance among different ecotypic varieties of local silkworm
CV2 | EV1 | T | CV1M3 | JV2 | CV1M4 | JV1 | CVd | |
---|---|---|---|---|---|---|---|---|
CV2 | ||||||||
EV1 | 0.025 | |||||||
T | 0.027 | 0.024 | ||||||
CV1M3 | 0.026 | 0.015 | 0.023 | |||||
JV2 | 0.026 | 0.012 | 0.024 | 0.016 | ||||
CV1M4 | 0.026 | 0.013 | 0.024 | 0.017 | 0.014 | |||
JV1 | 0.027 | 0.025 | 0.024 | 0.025 | 0.026 | 0.025 | ||
CVd | 0.025 | 0.025 | 0.024 | 0.025 | 0.026 | 0.025 | 0.024 | |
EV2 | 0.025 | 0.044 | 0.029 | 0.039 | 0.044 | 0.042 | 0.026 | 0.026 |
图3 家蚕地方品种单倍型网络图(H代表单倍型, mv代表可能存在的单倍型, 生态类型代号见表1)
Fig. 3 Network based on the haplotypes of Bombyx mori. H, Haplotype; mv, Probably existing haplotype. Codes for cological types see Table 1.
图4 基于Bmamy2基因核苷酸序列的家蚕NJ树(MEGA4.0建树, 模型选择: P-距离, 成对删除gaps, 1,000次重复, 节点处仅显示>40%的bootstrap值)。品种代号见表1。
Fig. 4 Phylogenetic (NJ) tree based on nucleotide sequence of Bmamy2 gene of Bombyx mori. Nucleotide P-distance model and pairwise deletion of gaps were selected for the tree reconstruction in the program MEGA 4.0, and bootstrap values (1,000 replicate) of >40% are shown. Variety codes see Table 1.
聚类支 Clade | 地理生态类型 Ecotype | 品种数(个) No. of varieties | 占各支百分比 % |
---|---|---|---|
A | 中系一化 CV1 | 15 | 36.59 |
中系二化 CV2 | 4 | 9.76 | |
中系多化 CVd | 3 | 7.32 | |
日系一化 JV1 | 3 | 7.32 | |
日系二化 JV2 | 5 | 12.20 | |
欧系一化 EV1 | 6 | 14.63 | |
热带系统 T | 5 | 12.20 | |
小计 Sum | 41 | ||
B | 中系一化 CV1 | 6 | 33.33 |
中系多化 CVd | 2 | 11.11 | |
日系一化 JV1 | 2 | 11.11 | |
日系二化 JV2 | 1 | 5.56 | |
欧系一化 EV1 | 1 | 5.46 | |
热带系统 T | 6 | 33.33 | |
小计 Sum | 18 | ||
C | 中系二化 CV2 | 4 | 30.77 |
中系多化 CVd | 2 | 15.38 | |
日系一化 JV1 | 2 | 14.38 | |
欧系二化 EV2 | 4 | 30.77 | |
热带系统 T | 1 | 7.69 | |
小计 Sum | 13 | ||
合计 | Total | 72 |
表4 各聚类支家蚕品种构成
Table 4 Silkworm varieties belonging to different clades
聚类支 Clade | 地理生态类型 Ecotype | 品种数(个) No. of varieties | 占各支百分比 % |
---|---|---|---|
A | 中系一化 CV1 | 15 | 36.59 |
中系二化 CV2 | 4 | 9.76 | |
中系多化 CVd | 3 | 7.32 | |
日系一化 JV1 | 3 | 7.32 | |
日系二化 JV2 | 5 | 12.20 | |
欧系一化 EV1 | 6 | 14.63 | |
热带系统 T | 5 | 12.20 | |
小计 Sum | 41 | ||
B | 中系一化 CV1 | 6 | 33.33 |
中系多化 CVd | 2 | 11.11 | |
日系一化 JV1 | 2 | 11.11 | |
日系二化 JV2 | 1 | 5.56 | |
欧系一化 EV1 | 1 | 5.46 | |
热带系统 T | 6 | 33.33 | |
小计 Sum | 18 | ||
C | 中系二化 CV2 | 4 | 30.77 |
中系多化 CVd | 2 | 15.38 | |
日系一化 JV1 | 2 | 14.38 | |
欧系二化 EV2 | 4 | 30.77 | |
热带系统 T | 1 | 7.69 | |
小计 Sum | 13 | ||
合计 | Total | 72 |
变异来源 Source of variance | 自由度 df | 方差分量 Variance component | 变异百分比 (%) | P-value |
---|---|---|---|---|
地理生态类型组群间 Among geo-voltings | 7 | 6.93028 | 19.86 | > 0.05 |
地理生态类型组群内 Among population within geo-voltings | 1 | 1.23267 | 3.53 | > 0.05 |
种群内 Within populations | 63 | 26.73978 | 76.61 | < 0.01 |
表5 家蚕72个品种Bmamy2基因的分子变异(按地理生态类型分类)
Table 5 AMOVA of Bmamy2 gene for 72 silkworm varieties of Bombyx mori based on geo-ecotype
变异来源 Source of variance | 自由度 df | 方差分量 Variance component | 变异百分比 (%) | P-value |
---|---|---|---|---|
地理生态类型组群间 Among geo-voltings | 7 | 6.93028 | 19.86 | > 0.05 |
地理生态类型组群内 Among population within geo-voltings | 1 | 1.23267 | 3.53 | > 0.05 |
种群内 Within populations | 63 | 26.73978 | 76.61 | < 0.01 |
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