Scientia Silvae Sinicae ›› 2022, Vol. 58 ›› Issue (4): 74-81.doi: 10.11707/j.1001-7488.20220408
• Research papers • Previous Articles Next Articles
Wenting Pan,Jianjun Sun,Qinqin Yuan,Lili Zhang,Kangqiao Deng,Yueqiao Li*
Received:
2021-04-16
Online:
2022-04-25
Published:
2022-07-20
Contact:
Yueqiao Li
CLC Number:
Wenting Pan,Jianjun Sun,Qinqin Yuan,Lili Zhang,Kangqiao Deng,Yueqiao Li. Analysis of Genetic Diversity and Structure in Different Provenances of Liriodendron by RAD-seq Technique[J]. Scientia Silvae Sinicae, 2022, 58(4): 74-81.
Table 1
Geographic information and samplenumber of 13 provenances in the experiment"
种源 Provenance | 种源地 Provenance region | 北纬 Latitude | 东经 Longitude | 海拔 Elevation/m | 样品数 Number of samples |
XY | 四川叙永 Sichuang Xuyong | 28.20°N | 105.5°E | 700~900 | 10 |
EX | 湖北鄂西 Hubei Exi | 30.30°N | 109.0°E | 1 100~1 300 | 11 |
MN | 贵州陌南 Guizhou Monan | 26.80°N | 109.5°E | 950~1 150 | 11 |
LY | 湖南浏阳 Hunan Liuyang | 28.05°N | 113.9°E | 1 000~1 200 | 11 |
SZ | 湖南桑植 Hunan Sangzhi | 29.15°N | 110.2°E | 1 100~1 300 | 11 |
LS | 江西庐山 Jiangxi Lushan | 29.53°N | 116.0°E | 1 000~1 200 | 10 |
WYS | 江西武夷山 Jiangxi Wuyishan | 27.92°N | 117.8°E | 900~1 100 | 10 |
MSL | 密苏里州 Missouri | 37.60°N | 91.5°W | 600~800 | 11 |
LYS | 路易斯安纳州 Louisiana | 31.00°N | 93.6°W | 0~100 | 10 |
BK | 北卡罗来纳州 North Carolina | 35.13°N | 80.1°W | 1 000~1 200 | 12 |
NK | 南卡罗来纳州 South Carolina | 34.50°N | 81.8°W | 100~300 | 14 |
YN | 云南勐腊 Yunnan Mengla | 21.40°N | 101.6°E | 600~800 | 11 |
DBS | 大别山舒城 Dabieshan Shucheng | 31.13°N | 118.2°E | 1 350~1 550 | 11 |
Table 2
Statistics of RAD-seq sequencing data of 13 provenances"
种源 Provenance | 总碱基数 Total nucleotides (Gb) | 有效数据 Clean reads (Mb) | RAD标记数 RAD tag | 测序深度 Sequencing depth (x) |
XY | 1.77 | 5.90 | 129 420 | 16.29 |
EX | 2.46 | 8.19 | 140 080 | 20.19 |
MN | 4.20 | 14.01 | 155 030 | 34.20 |
LY | 1.94 | 6.46 | 147 270 | 17.77 |
SZ | 1.41 | 4.70 | 157 950 | 13.70 |
LS | 4.37 | 14.57 | 156 650 | 35.74 |
WYS | 2.71 | 9.02 | 128 700 | 25.34 |
MSL | 3.89 | 12.97 | 136 120 | 39.76 |
LYS | 3.75 | 12.50 | 139 340 | 34.95 |
BK | 1.99 | 6.62 | 140 020 | 19.14 |
NK | 3.14 | 10.48 | 128 720 | 29.78 |
YN | 2.15 | 7.16 | 127 330 | 19.47 |
DBS | 2.16 | 7.20 | 149 230 | 18.97 |
均值Mean | 2.76 | 9.20 | 142 130 | 24.76 |
Table 3
Statistics of genetic structure in different provenances"
种源 Provenance | 等位基因数 Allele number | Ho Observed heterozygosity | He Expected heterozygosity | π Nucleotide diversity | Gst Gene differential coefficient | Nm Gene flow |
XY | 4 334 | 0.035 2 | 0.059 7 | 0.064 0 | 0.211 2 | 0.933 8 |
EX | 5 573 | 0.049 6 | 0.058 1 | 0.061 7 | 0.196 8 | 1.020 3 |
MN | 3 834 | 0.039 5 | 0.047 2 | 0.049 9 | 0.243 0 | 0.778 8 |
LY | 2 934 | 0.036 4 | 0.049 9 | 0.053 0 | 0.237 8 | 0.801 3 |
SZ | 4 212 | 0.036 9 | 0.052 0 | 0.055 5 | 0.213 1 | 0.923 4 |
LS | 855 | 0.044 8 | 0.045 9 | 0.048 9 | 0.235 4 | 0.812 2 |
WYS | 758 | 0.038 9 | 0.044 8 | 0.047 3 | 0.234 9 | 0.814 4 |
MSL | 1 113 | 0.038 6 | 0.038 4 | 0.040 6 | 0.439 8 | 0.318 4 |
LYS | 2 726 | 0.043 8 | 0.055 1 | 0.058 8 | 0.385 5 | 0.398 5 |
BK | 2 017 | 0.044 2 | 0.058 1 | 0.061 6 | 0.367 9 | 0.429 5 |
NK | 3 309 | 0.047 1 | 0.058 8 | 0.061 6 | 0.361 5 | 0.441 6 |
YN | 2 604 | 0.013 2 | 0.029 9 | 0.031 6 | 0.280 2 | 0.642 2 |
DBS | 1 245 | 0.024 4 | 0.022 2 | 0.023 6 | 0.324 8 | 0.519 8 |
均值 Mean | 2 732 | 0.037 9 | 0.047 7 | 0.050 6 | 0.287 1 | 0.679 6 |
Table 4
Subordinative function values of genetic diversity parameters among 13 provenances in Liriodendron"
参数 parameters | XY | EX | MN | LY | SZ | LS | WYS | MSL | LYS | BK | NK | YN | DBS |
Ho得分Ho score | 0.60 | 1.00 | 0.72 | 0.64 | 0.65 | 0.87 | 0.71 | 0.70 | 0.84 | 0.85 | 0.93 | 0.00 | 0.31 |
He得分He score | 1.00 | 0.96 | 0.67 | 0.74 | 0.79 | 0.63 | 0.60 | 0.43 | 0.88 | 0.96 | 0.98 | 0.21 | 0.00 |
π得分π score | 1.00 | 0.94 | 0.65 | 0.73 | 0.79 | 0.63 | 0.59 | 0.42 | 0.87 | 0.94 | 0.94 | 0.20 | 0.00 |
综合得分 Comprehensive score | 2.60 | 2.90 | 2.04 | 2.10 | 2.24 | 2.13 | 1.90 | 1.55 | 2.59 | 2.75 | 2.85 | 0.40 | 0.31 |
Fig.2
Neighbour-joining phylogram illustrating genetic relationships among 143 individuals Each branch represents one piece of germplasm, and the length of the branch represents the evolutionary distance between two species, the number on a branch of the tree represents the percentage of support for that branch."
Fig.3
Bar plot of 2-4 clusters identified with adegenet R package The picture left shows the clustering of 143 samples with cluster values from 2 to 4 (each color represents a subgroup, Each column represents a sample). The figure on the right shows the CV error value corresponding to each K value (When K is 3, the CV error value is minimal)."
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