Biodiv Sci ›› 2013, Vol. 21 ›› Issue (5): 601-609. DOI: 10.3724/SP.J.1003.2013.09098
• Orginal Article • Previous Articles Next Articles
Deyun Wang1, Jie Peng1, Yajing Chen1, Guosheng Lü1, Xiaoping Zhang1,2, Jianwen Shao1,3,*()
Received:
2013-04-18
Accepted:
2013-07-01
Online:
2013-09-20
Published:
2013-10-08
Contact:
Shao Jianwen
Deyun Wang,Jie Peng,Yajing Chen,Guosheng Lü,Xiaoping Zhang,Jianwen Shao. Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides[J]. Biodiv Sci, 2013, 21(5): 601-609.
种群 Population | 地点 Locality | 生境 Habitat | 地理位置 Geographical location | 海拔 Altitude (m) | 面积 Area (m2) | 花朵类型 Flower type | 种群大小 Population size |
---|---|---|---|---|---|---|---|
杨家坪A YJPA | 江西省修水县杨家坪 Yangjiaping, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside under forests | 28°47'45"N, 114°43'56"E | 300-375 | 720 | 两型花 Distyle | ~2,000 |
杨家坪B YJPB | 江西省修水县杨家坪 Yangjiaping, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside, under forest | 28°47'04"N, 114°44'13"E | 350-360 | 1,060 | 两型花 Distyle | ~6,000 |
毛竹山 MZS | 江西省修水县毛竹山 Maozhushan, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside, under forest | 28°50'31"N, 114°52'00"E | 390-410 | 1,650 | 两型花 Distyle | ~1,500 |
三界A SJA | 湖北省通山县三界 Sanjie, Tongshan County, Hubei | 林下溪边或路边 Brook-side or roadside, under forest | 29°24'16"N, 114°27'15"E | 255-285 | 545 | 两型花 Distyle | ~1,000 |
三界B SJB | 湖北省通山县三界 Sanjie, Tongshan County, Hubei | 林下溪边或路边 Brook-side or roadside, under forest | 29°22'57"N, 114°27'08"E | 265-280 | 385 | 两型花 Distyle | ~700 |
七姊妹山 JPT | 湖北省宣恩县七姊妹山 Qizimei Mount, Xuanen County, Hubei | 林下溪边 Brook-side, under forest | 30°02'09"N, 109°43'57"E | 1,310-1,365 | 1,200 | 同型花 Monostyle | ~600 |
银炉 YL | 江西省武宁县银炉 Yinlu, Wuning County, Jiangxi | 溪边石壁 Rock near brook-side | 28°59'31''N, 114°49'39''E | 420 | 50 | 两型花 Distyle | ~200 |
Table 1 Locality and information of studied populations of Primula ranunculoides
种群 Population | 地点 Locality | 生境 Habitat | 地理位置 Geographical location | 海拔 Altitude (m) | 面积 Area (m2) | 花朵类型 Flower type | 种群大小 Population size |
---|---|---|---|---|---|---|---|
杨家坪A YJPA | 江西省修水县杨家坪 Yangjiaping, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside under forests | 28°47'45"N, 114°43'56"E | 300-375 | 720 | 两型花 Distyle | ~2,000 |
杨家坪B YJPB | 江西省修水县杨家坪 Yangjiaping, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside, under forest | 28°47'04"N, 114°44'13"E | 350-360 | 1,060 | 两型花 Distyle | ~6,000 |
毛竹山 MZS | 江西省修水县毛竹山 Maozhushan, Xiushui County, Jiangxi | 林下溪边或路边 Brook-side or roadside, under forest | 28°50'31"N, 114°52'00"E | 390-410 | 1,650 | 两型花 Distyle | ~1,500 |
三界A SJA | 湖北省通山县三界 Sanjie, Tongshan County, Hubei | 林下溪边或路边 Brook-side or roadside, under forest | 29°24'16"N, 114°27'15"E | 255-285 | 545 | 两型花 Distyle | ~1,000 |
三界B SJB | 湖北省通山县三界 Sanjie, Tongshan County, Hubei | 林下溪边或路边 Brook-side or roadside, under forest | 29°22'57"N, 114°27'08"E | 265-280 | 385 | 两型花 Distyle | ~700 |
七姊妹山 JPT | 湖北省宣恩县七姊妹山 Qizimei Mount, Xuanen County, Hubei | 林下溪边 Brook-side, under forest | 30°02'09"N, 109°43'57"E | 1,310-1,365 | 1,200 | 同型花 Monostyle | ~600 |
银炉 YL | 江西省武宁县银炉 Yinlu, Wuning County, Jiangxi | 溪边石壁 Rock near brook-side | 28°59'31''N, 114°49'39''E | 420 | 50 | 两型花 Distyle | ~200 |
位点 Locus | 序列 Repeat motif | 引物 Primer (5'-3') | 退火温度(℃) Annealing temperature | 荧光标记 Fluorescent label | 等位基因数 No. of alleles |
---|---|---|---|---|---|
Pm1 | (TC)10(CT)3 | F:ATCTTTGAGGTCCTTTTA | 50 | FAM | 7 |
R: ATCGCCCAATGGAGTGAA | |||||
Pm2 | (AG)14 | F: CGCCTACAGTGTTTGGGA | 55 | FAM | 2 |
R: CTATCTCACCTGCGTTCT | |||||
Pm7 | (AG)3GG(AG)8 | F: TTGTTCACCGACGCATAC | 54 | HEX | 18 |
R: TTACACGCACCAAATCAT | |||||
Pm9 | (TTTC)2(TC)6 | F: AGACTCACGAGGAATACG | 50 | HEX | 6 |
R: AGAAAAGGAGGAGACAAA | |||||
Pm12 | (TC)10(CT)3 | F: TAAAACTCCTGGAGGGGTAC | 51 | TAMRA | 10 |
R: ATCGCCCAATGGAGTGAA | |||||
Pm13 | (GATAGG)2GAT(AG)7 | F: GAGGACAGGCACCACAGA | 54 | TAMRA | 6 |
R: TCCCCAACTTCATGCTCTT | |||||
Pm14 | (AG)3(GA)12 | F: TCGCCCAATGGAGTGAAC | 50 | TAMRA | 9 |
R: TCTTTGAGGTCCTTTTAT | |||||
Pm16 | (GAGGGA)3(GA)3 | F: AACCACTCGTCGTCCTAA | 51 | FAM | 5 |
R: CGATAGATTGCCTTACCC | |||||
Pm17 | (GA)9 | F: TAAATCAAGGTAGCAACT | 51 | HEX | 9 |
R: TACCTACCATTACTCCC |
Table 2 The sequences of microsatellite loci and primers in this study
位点 Locus | 序列 Repeat motif | 引物 Primer (5'-3') | 退火温度(℃) Annealing temperature | 荧光标记 Fluorescent label | 等位基因数 No. of alleles |
---|---|---|---|---|---|
Pm1 | (TC)10(CT)3 | F:ATCTTTGAGGTCCTTTTA | 50 | FAM | 7 |
R: ATCGCCCAATGGAGTGAA | |||||
Pm2 | (AG)14 | F: CGCCTACAGTGTTTGGGA | 55 | FAM | 2 |
R: CTATCTCACCTGCGTTCT | |||||
Pm7 | (AG)3GG(AG)8 | F: TTGTTCACCGACGCATAC | 54 | HEX | 18 |
R: TTACACGCACCAAATCAT | |||||
Pm9 | (TTTC)2(TC)6 | F: AGACTCACGAGGAATACG | 50 | HEX | 6 |
R: AGAAAAGGAGGAGACAAA | |||||
Pm12 | (TC)10(CT)3 | F: TAAAACTCCTGGAGGGGTAC | 51 | TAMRA | 10 |
R: ATCGCCCAATGGAGTGAA | |||||
Pm13 | (GATAGG)2GAT(AG)7 | F: GAGGACAGGCACCACAGA | 54 | TAMRA | 6 |
R: TCCCCAACTTCATGCTCTT | |||||
Pm14 | (AG)3(GA)12 | F: TCGCCCAATGGAGTGAAC | 50 | TAMRA | 9 |
R: TCTTTGAGGTCCTTTTAT | |||||
Pm16 | (GAGGGA)3(GA)3 | F: AACCACTCGTCGTCCTAA | 51 | FAM | 5 |
R: CGATAGATTGCCTTACCC | |||||
Pm17 | (GA)9 | F: TAAATCAAGGTAGCAACT | 51 | HEX | 9 |
R: TACCTACCATTACTCCC |
种群 Population | 取样数 Sample size | 有效种群大小 Effective population size | 期望杂合度(He) Expected heterozygosity | 观察杂合度(Ho) Observed heterozygosity | 稀有等位基因 Rare alleles | 近交系数(Fis) Inbreeding coefficient |
---|---|---|---|---|---|---|
YJPA | 32 | 166 | 0.430 | 0.424 | 2 | 0.014 ns |
YJPB | 31 | 231 | 0.412 | 0.399 | 4 | 0.032** |
MZS | 30 | 105 | 0.297 | 0.155 | 2 | 0.484*** |
SJA | 33 | 169 | 0.348 | 0.330 | 4 | 0.055*** |
SJB | 31 | 149 | 0.281 | 0.230 | 1 | 0.184*** |
JPT | 33 | 127 | 0.203 | 0.132 | 2 | 0.350*** |
YL | 32 | 153 | 0.340 | 0.328 | 2 | 0.037** |
平均 Mean | 31.7 | 157.1 | 0.330 | 0.286 | 2.4 |
Table 3 Genetic characteristics of Primula ranunculoides populations
种群 Population | 取样数 Sample size | 有效种群大小 Effective population size | 期望杂合度(He) Expected heterozygosity | 观察杂合度(Ho) Observed heterozygosity | 稀有等位基因 Rare alleles | 近交系数(Fis) Inbreeding coefficient |
---|---|---|---|---|---|---|
YJPA | 32 | 166 | 0.430 | 0.424 | 2 | 0.014 ns |
YJPB | 31 | 231 | 0.412 | 0.399 | 4 | 0.032** |
MZS | 30 | 105 | 0.297 | 0.155 | 2 | 0.484*** |
SJA | 33 | 169 | 0.348 | 0.330 | 4 | 0.055*** |
SJB | 31 | 149 | 0.281 | 0.230 | 1 | 0.184*** |
JPT | 33 | 127 | 0.203 | 0.132 | 2 | 0.350*** |
YL | 32 | 153 | 0.340 | 0.328 | 2 | 0.037** |
平均 Mean | 31.7 | 157.1 | 0.330 | 0.286 | 2.4 |
YJPA | YJPB | MZS | SJA | SJB | JPT | YL | |
---|---|---|---|---|---|---|---|
YJPA | - | 0.091 | 0.208 | 0.420 | 0.528 | 0.875 | 0.702 |
YJPB | 0.096 | - | 0.167 | 0.311 | 0.363 | 0.793 | 0.588 |
MZS | 0.256 | 0.222 | - | 0.336 | 0.378 | 0.827 | 0.742 |
SJA | 0.301 | 0.262 | 0.399 | - | 0.030 | 0.921 | 0.473 |
SJB | 0.385 | 0.332 | 0.476 | 0.047 | - | 0.929 | 0.467 |
JPT | 0.510 | 0.526 | 0.645 | 0.569 | 0.599 | - | 0.318 |
YL | 0.445 | 0.424 | 0.536 | 0.392 | 0.428 | 0.367 | - |
Table 4 Pairwise population differentiation (below diagonal) and genetic distances (above diagonal) among Primula ranunculoides populations
YJPA | YJPB | MZS | SJA | SJB | JPT | YL | |
---|---|---|---|---|---|---|---|
YJPA | - | 0.091 | 0.208 | 0.420 | 0.528 | 0.875 | 0.702 |
YJPB | 0.096 | - | 0.167 | 0.311 | 0.363 | 0.793 | 0.588 |
MZS | 0.256 | 0.222 | - | 0.336 | 0.378 | 0.827 | 0.742 |
SJA | 0.301 | 0.262 | 0.399 | - | 0.030 | 0.921 | 0.473 |
SJB | 0.385 | 0.332 | 0.476 | 0.047 | - | 0.929 | 0.467 |
JPT | 0.510 | 0.526 | 0.645 | 0.569 | 0.599 | - | 0.318 |
YL | 0.445 | 0.424 | 0.536 | 0.392 | 0.428 | 0.367 | - |
变异来源 Source | 自由度 d.f. | 方差和 Sum of squares | 变异组分 Variance components | 占总变异比例% Percentage of variation | 显著性检验 Significance tests |
---|---|---|---|---|---|
种群间 Among populations | 6 | 225.635 | 0.6596 | 48.08 | P<0.001 |
种群内 Within populations | 215 | 310.851 | 0.7124 | 51.92 | P<0.001 |
总和 Total | 222 | 536.486 | 1.3720 | 100% |
Table 5 Analysis of molecular variance (AMOVA) within/among Primula ranunculoides populations
变异来源 Source | 自由度 d.f. | 方差和 Sum of squares | 变异组分 Variance components | 占总变异比例% Percentage of variation | 显著性检验 Significance tests |
---|---|---|---|---|---|
种群间 Among populations | 6 | 225.635 | 0.6596 | 48.08 | P<0.001 |
种群内 Within populations | 215 | 310.851 | 0.7124 | 51.92 | P<0.001 |
总和 Total | 222 | 536.486 | 1.3720 | 100% |
Fig. 2 The result of Principal coordinates (PCO) analysis of Primula ranunculoides populations. The first and second axis extracted 40.0% and 26.9% of the total genetic variance, respectively. Population codes see Table 1.
Fig. 3 The results of genetic structure analyses by STRUCTURE soft. (a) Plot of mean posterior probability lnP(D) values of each K; (b) The corresponding △K statistics calculated according to Evanno et al. (2005); (c) Histogram of the structure analysis for the model with K = 2-4. Population codes see Table 1.
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