Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (8): 1823-1832.doi: 10.16420/j.issn.0513-353x.2023-0468
• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles
QIN Zilu, XU Zhengkang, DAI Xiaogang, CHEN Yingnan*()
Received:
2024-01-15
Revised:
2024-04-22
Online:
2024-08-25
Published:
2024-08-21
Contact:
CHEN Yingnan
QIN Zilu, XU Zhengkang, DAI Xiaogang, CHEN Yingnan. Genetic Diversity Analysis and Core Collection Construction of Magnolia biondii Germplasm[J]. Acta Horticulturae Sinica, 2024, 51(8): 1823-1832.
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URL: https://www.ahs.ac.cn/EN/10.16420/j.issn.0513-353x.2023-0468
引物名称 Primer name | 引物序列(5′-3′) Primer sequence | 重复基序 Repeat motif | 预期产物大小/bp Expected product length |
---|---|---|---|
Chr02-1 | F:ATTGGAGCTTGGCTTGTTTG;R:GGGCCACGTTAGATTTTTCA | (TCGAG)3 | 119 |
Chr06-10 | F:CAAGCTGGCCTCTTTTGTCT;R:TGCATTCATCATATTCAGCCTC | (AAT)11 | 128 |
Chr08-5 | F:AGATTGGCGTCCTCAATAGG;R:AGTCCTGCAACAGCTCCACT | (AGAAA)3 | 125 |
Chr09-2 | F:GGATCGTCCAATTAGCAGACA;R:TCTGAGTTGACCAGCTGACG | (CAATC)3 | 138 |
Chr10-7 | F:TGGAGTCTATTAAGACTATGGCA;R:CGAAAGCCTATCTCGGATCA | (ATTATA)4 | 134 |
Chr13-5 | F:TTCCCTTTTTGCAGTTCGAG;R:GCCCTCTATAGATACGGCCTG | (GAGGC)3 | 127 |
Chr16-5 | F:CCCTTTCCTCTTCCGACTTT;R:CACATTTGCTCACGAACACC | (AAGGG)3 | 105 |
Chr17-22 | F:GTTCAAGTCGGGTCGAGGTA;R:TGGGTTTAGTCGTTCTTGGG | (ACCCA)5 | 143 |
Chr18-17 | F:TCCATGGACGACCACAGTTA;R:GCCGGGACTGCTTTTACTTA | (AAAAT)6 | 118 |
Chr19-6 | F:CAGGAACGTCCAGCTTCTCT;R:AAATTTCAATGGTCTCGGCA | (AAT)10 | 125 |
Table 1 Sequence of SSR primers
引物名称 Primer name | 引物序列(5′-3′) Primer sequence | 重复基序 Repeat motif | 预期产物大小/bp Expected product length |
---|---|---|---|
Chr02-1 | F:ATTGGAGCTTGGCTTGTTTG;R:GGGCCACGTTAGATTTTTCA | (TCGAG)3 | 119 |
Chr06-10 | F:CAAGCTGGCCTCTTTTGTCT;R:TGCATTCATCATATTCAGCCTC | (AAT)11 | 128 |
Chr08-5 | F:AGATTGGCGTCCTCAATAGG;R:AGTCCTGCAACAGCTCCACT | (AGAAA)3 | 125 |
Chr09-2 | F:GGATCGTCCAATTAGCAGACA;R:TCTGAGTTGACCAGCTGACG | (CAATC)3 | 138 |
Chr10-7 | F:TGGAGTCTATTAAGACTATGGCA;R:CGAAAGCCTATCTCGGATCA | (ATTATA)4 | 134 |
Chr13-5 | F:TTCCCTTTTTGCAGTTCGAG;R:GCCCTCTATAGATACGGCCTG | (GAGGC)3 | 127 |
Chr16-5 | F:CCCTTTCCTCTTCCGACTTT;R:CACATTTGCTCACGAACACC | (AAGGG)3 | 105 |
Chr17-22 | F:GTTCAAGTCGGGTCGAGGTA;R:TGGGTTTAGTCGTTCTTGGG | (ACCCA)5 | 143 |
Chr18-17 | F:TCCATGGACGACCACAGTTA;R:GCCGGGACTGCTTTTACTTA | (AAAAT)6 | 118 |
Chr19-6 | F:CAGGAACGTCCAGCTTCTCT;R:AAATTTCAATGGTCTCGGCA | (AAT)10 | 125 |
引物 Primer | Na 等位基因数 Number of alleles | Ne 有效等位基因数 Number of effective alleles | Ng 基因型数 Number of genotypes | I Shannon’s指数 Shannon’s index | Ho 观测杂合度 Observing heterozygosity | He 期望杂合度 Expected heterozygosity | PIC 多态性指数 Polymorphism index |
---|---|---|---|---|---|---|---|
Chr02-1 | 6 | 2.627 | 20 | 1.275 | 0.470 | 0.619 | 0.585 |
Chr06-10 | 6 | 2.632 | 13 | 1.210 | 0.437 | 0.620 | 0.577 |
Chr08-5 | 2 | 1.616 | 3 | 0.569 | 0.174 | 0.381 | 0.309 |
Chr09-2 | 4 | 3.038 | 7 | 1.202 | 0.592 | 0.671 | 0.608 |
Chr10-7 | 6 | 3.725 | 11 | 1.429 | 0.487 | 0.732 | 0.687 |
Chr13-5 | 4 | 1.530 | 7 | 0.667 | 0.213 | 0.346 | 0.421 |
Chr16-5 | 5 | 2.414 | 9 | 1.012 | 0.349 | 0.586 | 0.498 |
Chr17-22 | 8 | 4.045 | 20 | 1.535 | 0.670 | 0.753 | 0.712 |
Chr18-17 | 6 | 1.904 | 15 | 0.974 | 0.304 | 0.475 | 0.447 |
Chr19-6 | 10 | 3.144 | 16 | 1.364 | 0.522 | 0.682 | 0.628 |
平均Mean | 5.7 | 2.668 | 12.1 | 1.124 | 0.422 | 0.586 | 0.547 |
Table 2 The genetic diversity information of Magnolia biondii germplasms
引物 Primer | Na 等位基因数 Number of alleles | Ne 有效等位基因数 Number of effective alleles | Ng 基因型数 Number of genotypes | I Shannon’s指数 Shannon’s index | Ho 观测杂合度 Observing heterozygosity | He 期望杂合度 Expected heterozygosity | PIC 多态性指数 Polymorphism index |
---|---|---|---|---|---|---|---|
Chr02-1 | 6 | 2.627 | 20 | 1.275 | 0.470 | 0.619 | 0.585 |
Chr06-10 | 6 | 2.632 | 13 | 1.210 | 0.437 | 0.620 | 0.577 |
Chr08-5 | 2 | 1.616 | 3 | 0.569 | 0.174 | 0.381 | 0.309 |
Chr09-2 | 4 | 3.038 | 7 | 1.202 | 0.592 | 0.671 | 0.608 |
Chr10-7 | 6 | 3.725 | 11 | 1.429 | 0.487 | 0.732 | 0.687 |
Chr13-5 | 4 | 1.530 | 7 | 0.667 | 0.213 | 0.346 | 0.421 |
Chr16-5 | 5 | 2.414 | 9 | 1.012 | 0.349 | 0.586 | 0.498 |
Chr17-22 | 8 | 4.045 | 20 | 1.535 | 0.670 | 0.753 | 0.712 |
Chr18-17 | 6 | 1.904 | 15 | 0.974 | 0.304 | 0.475 | 0.447 |
Chr19-6 | 10 | 3.144 | 16 | 1.364 | 0.522 | 0.682 | 0.628 |
平均Mean | 5.7 | 2.668 | 12.1 | 1.124 | 0.422 | 0.586 | 0.547 |
亚群 Subgroup | 各亚群种质总数 Total number of germplasms in each subgroup | 种质数量(比例/%) Number of germplasms | |||
---|---|---|---|---|---|
Q < 0.6 | 0.6 ≤ Q < 0.8 | 0.8 ≤ Q < 0.9 | Q ≥ 0.9 | ||
Ⅰ | 271 | 74(27.3) | 85(31.4) | 67(24.7) | 45(16.6) |
Ⅱ | 163 | 44(27.0) | 40(24.5) | 38(23.3) | 41(25.2) |
Ⅲ | 243 | 52(21.4) | 63(25.9) | 58(23.9) | 70(28.8) |
Ⅳ | 240 | 60(25.0) | 56(23.3) | 66(27.5) | 58(24.2) |
合计Total | 917 | 230(25.1) | 244(26.6) | 229(25.0) | 214(23.3) |
Table 3 Distribution of maximum Q-value of each subgroup of 917 Magnolia biondii germplasms
亚群 Subgroup | 各亚群种质总数 Total number of germplasms in each subgroup | 种质数量(比例/%) Number of germplasms | |||
---|---|---|---|---|---|
Q < 0.6 | 0.6 ≤ Q < 0.8 | 0.8 ≤ Q < 0.9 | Q ≥ 0.9 | ||
Ⅰ | 271 | 74(27.3) | 85(31.4) | 67(24.7) | 45(16.6) |
Ⅱ | 163 | 44(27.0) | 40(24.5) | 38(23.3) | 41(25.2) |
Ⅲ | 243 | 52(21.4) | 63(25.9) | 58(23.9) | 70(28.8) |
Ⅳ | 240 | 60(25.0) | 56(23.3) | 66(27.5) | 58(24.2) |
合计Total | 917 | 230(25.1) | 244(26.6) | 229(25.0) | 214(23.3) |
构建方法 Construction method | 取样比例/% Sampling ration | 种质数 Number of germplasms | Na(%) | Ne(%) | I(%) | Ho(%) | He(%) |
---|---|---|---|---|---|---|---|
原始种质 Initial collection | — | 917 | 5.700 | 2.667 | 1.124 | 0.422 | 0.586 |
SANA | 10 | 92 | 5.200(91.23) | 2.650(99.36) | 1.108(98.58) | 0.404(95.73) | 0.576(98.29) |
20 | 183 | 5.400(94.74) | 2.650(99.36) | 1.121(99.73) | 0.418(99.05) | 0.586(100.00) | |
30 | 275 | 5.700(100.00) | 2.657(99.63) | 1.127(100.27) | 0.422(100.00) | 0.586(100.00) | |
40 | 367 | 5.700(100.00) | 2.664(99.89) | 1.124(100.00) | 0.428(101.42) | 0.587(100.17) | |
SAGD | 10 | 92 | 5.200(91.23) | 2.893(108.47) | 1.178(104.80) | 0.438(103.79) | 0.624(106.48) |
20 | 183 | 5.400(94.74) | 2.811(105.40) | 1.162(103.38) | 0.440(104.27) | 0.613(104.61) | |
30 | 275 | 5.700(100.00) | 2.743(102.85) | 1.152(102.49) | 0.423(100.24) | 0.606(103.41) | |
40 | 367 | 5.700(100.00) | 2.694(101.01) | 1.137(101.16) | 0.416(98.58) | 0.597(101.88) |
Table 4 Comparisons of genetic diversity index of core collection of Magnolia biondii
构建方法 Construction method | 取样比例/% Sampling ration | 种质数 Number of germplasms | Na(%) | Ne(%) | I(%) | Ho(%) | He(%) |
---|---|---|---|---|---|---|---|
原始种质 Initial collection | — | 917 | 5.700 | 2.667 | 1.124 | 0.422 | 0.586 |
SANA | 10 | 92 | 5.200(91.23) | 2.650(99.36) | 1.108(98.58) | 0.404(95.73) | 0.576(98.29) |
20 | 183 | 5.400(94.74) | 2.650(99.36) | 1.121(99.73) | 0.418(99.05) | 0.586(100.00) | |
30 | 275 | 5.700(100.00) | 2.657(99.63) | 1.127(100.27) | 0.422(100.00) | 0.586(100.00) | |
40 | 367 | 5.700(100.00) | 2.664(99.89) | 1.124(100.00) | 0.428(101.42) | 0.587(100.17) | |
SAGD | 10 | 92 | 5.200(91.23) | 2.893(108.47) | 1.178(104.80) | 0.438(103.79) | 0.624(106.48) |
20 | 183 | 5.400(94.74) | 2.811(105.40) | 1.162(103.38) | 0.440(104.27) | 0.613(104.61) | |
30 | 275 | 5.700(100.00) | 2.743(102.85) | 1.152(102.49) | 0.423(100.24) | 0.606(103.41) | |
40 | 367 | 5.700(100.00) | 2.694(101.01) | 1.137(101.16) | 0.416(98.58) | 0.597(101.88) |
种质 Germplasm | 种质数 Collection number | Na | Ne | I | Ho | He |
---|---|---|---|---|---|---|
原始种质Initial collection | 917 | 5.700 | 2.667 | 1.124 | 0.422 | 0.586 |
核心种质Core collection | 183 | 5.400 | 2.811 | 1.162 | 0.440 | 0.613 |
保留种质Reserve collection | 734 | 5.700 | 2.625 | 1.106 | 0.417 | 0.577 |
t1 | 0.317 | -0.383 | -0.275 | -0.238 | -0.447 | |
t2 | -0.317 | 0.495 | 0.399 | 0.297 | 0.583 |
Table 5 Comparisons of the genetic diversity among core collection,reserved collection and initial collection of Magnolia biondii
种质 Germplasm | 种质数 Collection number | Na | Ne | I | Ho | He |
---|---|---|---|---|---|---|
原始种质Initial collection | 917 | 5.700 | 2.667 | 1.124 | 0.422 | 0.586 |
核心种质Core collection | 183 | 5.400 | 2.811 | 1.162 | 0.440 | 0.613 |
保留种质Reserve collection | 734 | 5.700 | 2.625 | 1.106 | 0.417 | 0.577 |
t1 | 0.317 | -0.383 | -0.275 | -0.238 | -0.447 | |
t2 | -0.317 | 0.495 | 0.399 | 0.297 | 0.583 |
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