Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Sites and Collection of Seeds
2.2. Provenance Trials
2.3. Molecular Procedures
2.4. Analysis of Data from the Provenance Trials
2.5. Analysis of SSR Markers
3. Results
3.1. Population Genetic Differentiation
3.2. Genetic Diversity according to GST and IBD
3.3. Genetic Structure and Genetic Relationships among Populations
3.4. Population Differentiation in Phenotypic Traits and QST Distance Matrices
3.5. Correlations between QST Distance Matrices and The Geographic Distance Matrix
3.6. Analysis of Ecological Adaptation
3.6.1. QST Matrices of Traits Correlated with Climate Factors
3.6.2. Seedling Survival
3.7. QST–FST Comparison
4. Discussion
4.1. Detection of Local Adaptation
4.2. FST–QST Comparison in a Common Garden Experiment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Provenance Code a | Experiments b | Family Number c | Sample Number | Province/Location | Latitude | Longitude | Altitude |
---|---|---|---|---|---|---|---|
412 | I,II | 16 | 15 | Guangdong Renhua | 25°19′ | 113°55′ | 99 |
415 | I,II | 20 | 15 | Guangdong Kaiping | 22°25′ | 112°43′ | 7 |
524 | I,II | 22 | 15 | Hainan Tunchang | 19°24′ | 110°07′ | 160 |
525 | I,II | 16 | 14 | Hainan Wuzhishan | 18°47′ | 109°29′ | 280 |
628 | I,II | 10 | 15 | Guangxi Guilin | 25°16′ | 110°17′ | 166 |
739 * | I,II | 7 | 15 | Yunnan Mengla | 21°48′ | 101°15′ | 1010 |
741 | I,II | 11 | 15 | Yunnan Malipo | 23°06′ | 104°40′ | 1180 |
842 * | I,II | 9 | 15 | Guizhou Xingyi | 25°03′ | 104°37′ | 1407 |
843 * | I,II | 26 | 15 | Guizhou Ceheng | 24°57′ | 105°41′ | 1117 |
844 | I,II | 4 | 15 | Guizhou Liping | 26°13′ | 109°08′ | 618 |
102 | I | - | 15 | Fujian Yong’an | 25°49′ | 117°06′ | 255 |
205 | I | - | 15 | Jiangxi Yudu | 25°59′ | 115°25′ | 132 |
248 | I | - | 15 | Jiangxi Ruichang | 29°40′ | 115°40′ | 18 |
307 | I | - | 15 | Hunan Dong’an | 26°22′ | 111°14′ | 205 |
308 | I | - | 15 | Hunan Liuyang | 28°9′ | 113°38′ | 124 |
310 | I | - | 15 | Hunan Yanling | 26°27′ | 113°40′ | 200 |
631 | I | - | 15 | Guangxi Qinzhou | 21°58′ | 108°39′ | 17 |
652 | I | - | 15 | Guangxi Du’an | 23°55′ | 108° 6′ | 373 |
754 * | I | - | 14 | Yunnan Chuxiong | 25°2′ | 101°31′ | 2173 |
858 * | I | - | 15 | Guizhou Zunyi | 27°43′ | 106°55′ | 1168 |
959 | I | - | 15 | Zhejiang Lin’an | 30°13′ | 119°43′ | 47 |
1060 * | I | - | 15 | Sichuan Chengdu | 30°34′ | 104° 3′ | 495 |
1061 * | I | - | 15 | Sichuan Dazhou | 31°12′ | 107°28′ | 593 |
1162 | I | - | 15 | Anhui Chuzhou | 32°18′ | 118°19′ | 15 |
1363 | I | - | 15 | Hubei Jingmen | 31°2′ | 112°11′ | 98 |
1464 | I | - | 15 | Shanxi Weinan | 34°29′ | 109°30′ | 351 |
1565 * | I | - | 14 | Gansu Longnan | 33°24′ | 104°55′ | 1106 |
1666 | I | - | 15 | Hebei Baoding | 38°52′ | 115°27′ | 22 |
1767 | I | - | 15 | Shandong Jinan | 36°39′ | 117°7′ | 122 |
1768 | I | - | 15 | Shandong Tai’an | 36°13′ | 117°6′ | 641 |
1869 | I | - | 14 | Henan Xuchang | 34°2′ | 113°51′ | 71 |
103 | II | 1 | - | Fujian Zhangping | 25°16′ | 117°26′ | 219 |
413 | II | 9 | - | Guangdong Yunan | 22°48′ | 111°21′ | 22 |
416 | II | 7 | - | Guangdong Qingyuan | 23°51′ | 113°31′ | 73 |
417 | II | 4 | - | Guangdong En’ping | 23°18′ | 112°25′ | 17 |
418 | II | 3 | - | Guangdong Raoping | 23°39′ | 117°00′ | 20 |
523 | II | 8 | - | Hainan Haikou | 19°49′ | 110°15′ | 129 |
526 | II | 9 | - | Hainan Lingshui | 18°39′ | 109°52′ | 79 |
629 | II | 18 | - | Guangxi Rong’an | 25°13′ | 109°23′ | 226 |
630 | II | 19 | - | Guangxi Sanjiang | 25°50′ | 109°34′ | 240 |
651 | II | 10 | - | Guangxi Qinzhou | 21°58′ | 108°39′ | 250 |
740 | II | 3 | - | Yunnan Luoping | 24°58′ | 104°26′ | 1415 |
753 | II | 4 | - | Yunnan Xichou | 23°26′ | 104°40′ | 1217 |
Population | Na (±Sd) | Range | Ne (±Sd) | Range | He (±Sd) | H (±Sd) | I_Shannon’s | PIC |
---|---|---|---|---|---|---|---|---|
412 | 8.07 ± 2.71 | (4, 12) | 5.24 ± 1.64 | (2.99, 8.03) | 0.82 ± 0.07 | 0.79 ± 0.07 | 1.78 ± 0.34 | 0.761 |
741 | 7.53 ± 2.56 | (4, 12) | 5.33 ± 1.84 | (2.96, 8.33) | 0.82 ± 0.07 | 0.79 ± 0.07 | 1.75 ± 0.36 | 0.759 |
631 | 6.40 ± 2.41 | (4, 10) | 4.61 ± 1.90 | (2.26, 7.04) | 0.77 ± 0.12 | 0.74 ± 0.11 | 1.57 ± 0.44 | 0.698 |
739 | 8.00 ± 2.62 | (4, 11) | 5.70 ± 2.29 | (2.47, 9.78) | 0.82 ± 0.09 | 0.79 ± 0.09 | 1.80 ± 0.41 | 0.763 |
205 | 7.20 ± 2.51 | (4, 13) | 5.06 ± 1.77 | (3.02, 8.65) | 0.81 ± 0.07 | 0.78 ± 0.07 | 1.71 ± 0.33 | 0.749 |
524 | 6.60 ± 2.56 | (3, 11) | 4.56 ± 1.73 | (2.49, 7.75) | 0.78 ± 0.10 | 0.75 ± 0.09 | 1.58 ± 0.40 | 0.709 |
525 | 6.00 ± 2.93 | (3, 11) | 4.09 ± 1.86 | (2.27, 8.45) | 0.74 ± 0.11 | 0.72 ± 0.10 | 1.46 ± 0.43 | 0.666 |
628 | 7.60 ± 2.72 | (4, 12) | 5.29 ± 1.99 | (2.79, 8.82) | 0.81 ± 0.08 | 0.78 ± 0.08 | 1.74 ± 0.38 | 0.752 |
415 | 6.87 ± 2.36 | (4, 11) | 4.58 ± 1.56 | (2.43, 7.89) | 0.78 ± 0.09 | 0.76 ± 0.09 | 1.62 ± 0.37 | 0.718 |
307 | 7.20 ± 2.39 | (4, 12) | 5.30 ± 2.05 | (2.28, 9.18) | 0.81 ± 0.10 | 0.78 ± 0.10 | 1.72 ± 0.41 | 0.746 |
842 | 6.53 ± 2.83 | (2, 12) | 4.56 ± 2.09 | (2.00, 8.82) | 0.77 ± 0.11 | 0.74 ± 0.10 | 1.56 ± 0.45 | 0.696 |
308 | 7.87 ± 2.47 | (5, 14) | 5.36 ± 1.33 | (3.24, 7.26) | 0.83 ± 0.06 | 0.80 ± 0.06 | 1.80 ± 0.29 | 0.773 |
310 | 7.80 ± 2.14 | (5, 12) | 5.33 ± 1.81 | (2.92, 9.00) | 0.82 ± 0.07 | 0.79 ± 0.06 | 1.78 ± 0.31 | 0.764 |
843 | 8.60 ± 3.44 | (4, 14) | 5.78 ± 2.62 | (2.84, 10.22) | 0.82 ± 0.09 | 0.79 ± 0.09 | 1.81 ± 0.46 | 0.760 |
102 | 6.93 ± 2.21 | (3, 11) | 4.83 ± 1.42 | (2.38, 6.61) | 0.80 ± 0.08 | 0.77 ± 0.08 | 1.67 ± 0.33 | 0.738 |
844 | 7.87 ± 2.64 | (5, 12) | 5.55 ± 2.18 | (2.82, 9.18) | 0.82 ± 0.08 | 0.79 ± 0.08 | 1.79 ± 0.38 | 0.764 |
1061 | 8.07 ± 2.79 | (3, 14) | 5.51 ± 2.28 | (2.26, 10.47) | 0.81 ± 0.10 | 0.78 ± 0.10 | 1.78 ± 0.44 | 0.751 |
1767 | 6.87 ± 2.17 | (4, 10) | 5.05 ± 1.71 | (2.74, 8.18) | 0.81 ± 0.08 | 0.78 ± 0.08 | 1.69 ± 0.35 | 0.746 |
754 | 6.73 ± 2.99 | (3, 13) | 4.76 ± 2.38 | (2.11, 10.56) | 0.77 ± 0.11 | 0.75 ± 0.10 | 1.59 ± 0.46 | 0.704 |
959 | 6.60 ± 2.29 | (4, 12) | 4.78 ± 1.95 | (2.59, 9.78) | 0.79 ± 0.09 | 0.76 ± 0.09 | 1.62 ± 0.36 | 0.723 |
1565 | 7.20 ± 1.70 | (4, 10) | 4.94 ± 1.40 | (2.99, 7.68) | 0.81 ± 0.06 | 0.78 ± 0.06 | 1.71 ± 0.27 | 0.750 |
1666 | 7.60 ± 2.41 | (3, 13) | 5.18 ± 1.61 | (2.38, 7.76) | 0.81 ± 0.08 | 0.79 ± 0.08 | 1.75 ± 0.34 | 0.754 |
1768 | 7.60 ± 2.10 | (4, 11) | 5.29 ± 1.76 | (2.60, 9.33) | 0.82 ± 0.08 | 0.79 ± 0.07 | 1.76 ± 0.33 | 0.759 |
1464 | 7.40 ± 2.61 | (4, 13) | 5.10 ± 1.83 | (3.49, 8.49) | 0.81 ± 0.06 | 0.78 ± 0.06 | 1.72 ± 0.33 | 0.752 |
1363 | 7.33 ± 2.49 | (3, 11) | 5.14 ± 1.86 | (2.51, 8.05) | 0.81 ± 0.10 | 0.78 ± 0.09 | 1.71 ± 0.40 | 0.742 |
652 | 7.60 ± 1.76 | (5, 11) | 5.32 ± 1.87 | (3.23, 9.56) | 0.82 ± 0.06 | 0.79 ± 0.06 | 1.76 ± 0.29 | 0.763 |
1869 | 7.13 ± 2.50 | (4, 12) | 4.71 ± 1.70 | (2.60, 8.34) | 0.79 ± 0.08 | 0.76 ± 0.08 | 1.64 ± 0.36 | 0.725 |
1060 | 7.27 ± 2.66 | (4, 12) | 4.99 ± 2.25 | (2.67, 10.00) | 0.79 ± 0.10 | 0.76 ± 0.10 | 1.67 ± 0.43 | 0.724 |
1162 | 7.60 ± 2.06 | (5, 11) | 5.19 ± 1.58 | (3.21, 8.90) | 0.82 ± 0.05 | 0.79 ± 0.05 | 1.76 ± 0.27 | 0.764 |
858 | 6.73 ± 2.87 | (3, 14) | 4.71 ± 2.16 | (2.13, 10.00) | 0.77 ± 0.11 | 0.74 ± 0.11 | 1.59 ± 0.45 | 0.703 |
248 | 6.67 ± 1.50 | (4, 9) | 4.58 ± 1.07 | (2.76, 6.42) | 0.80 ± 0.06 | 0.77 ± 0.06 | 1.63 ± 0.24 | 0.734 |
Mean | 7.27 ± 2.46 | □ | 5.05 ± 1.85 | □ | 0.80 ± 0.08 | 0.77 ± 0.08 | 1.69 ± 0.39 | 0.739 |
Locus | Gst | a | b | p-Value | r |
---|---|---|---|---|---|
SSR02 | 0.0731 | 0.0721 | −0.0023 | 0.300 | 0.0400 |
SSR29 | 0.0915 | 0.0580 | −0.0003 | 0.520 | 0.0032 |
SSR54 | 0.1010 | −0.2353 | 0.0221 | 0.010 | 0.2625 |
SSR59 | 0.0687 | 0.0856 | −0.0035 | 0.240 | 0.0640 |
SSR74 | 0.1230 | −0.1200 | 0.0145 | 0.030 | 0.1552 |
SSR111 | 0.0623 | −0.1486 | 0.0138 | 0.010 | 0.2311 |
SSR113 | 0.1017 | 0.0060 | 0.0042 | 0.260 | 0.0374 |
SSR114 | 0.1064 | 0.0920 | −0.0021 | 0.330 | 0.0224 |
SSR116 | 0.1097 | −0.0553 | 0.0091 | 0.060 | 0.1100 |
SSR117 | 0.1281 | −0.1173 | 0.0147 | 0.050 | 0.1265 |
SSR118 | 0.0762 | 0.0537 | −0.0008 | 0.460 | 0.0141 |
SSR119 | 0.0448 | 0.0125 | 0.0009 | 0.350 | 0.0283 |
SSR120 | 0.0327 | 0.0065 | 0.0008 | 0.280 | 0.0332 |
SSR122 | 0.0866 | −0.0019 | 0.0039 | 0.190 | 0.0608 |
SSR123 | 0.0984 | −0.2884 | 0.0260 | 0.010 | 0.3056 |
Multilocus | 0.0860 | −0.0353 | 0.0063 | 0.010 | 0.2449 |
Qst_HEIT | Qst_GBH/DBH | Qst_NOB/CBH | Qst_SMT | Qst_CRB | Qst_SR | |
---|---|---|---|---|---|---|
1st Year | −0.3219 *** | −0.0190 ns | −0.1024 ns | −0.2176 *** | −0.1937 *** | −0.1832 ** |
2nd Year | −0.2675 *** | −0.1524 * | 0.0105 ns | −0.0493 ns | −0.0896 ns | 0.0746 ns |
3rd Year | −0.3327 *** | −0.1454 * | −0.0447 ns | −0.1558 * | −0.1567 * | 0.0210 ** |
4th Year | −0.2367 *** | −0.1111 ns | −0.0760 ns | −0.1161 ns | −0.3726 *** | −0.1704 ** |
5th Year | −0.3384 *** | −0.1736 ** | −0.1795 ** | −0.0952 ns | −0.1793 ** | −0.1193 ns |
Trait Code | Qst–Fst | Lower Bound Crit. Value. 2.5% | Upper Bound Crit. Value. 97.5% |
---|---|---|---|
HEIT1 | −0.0615 * | −0.0529 | 0.0720 |
HEIT2 | −0.0648 * | −0.0565 | 0.0833 |
HEIT3 | −0.0711 ** | −0.0565 | 0.0815 |
HEIT4 | −0.0484 ns | −0.0578 | 0.0885 |
HEIT5 | −0.0330 ns | −0.0597 | 0.0917 |
GBH1 | 0.0306 ns | −0.0540 | 0.0713 |
DBH2 | −0.0127 ns | −0.0567 | 0.0813 |
DBH3 | −0.0120 ns | −0.0558 | 0.0773 |
DBH4 | −0.0072 ns | −0.0566 | 0.0803 |
DBH5 | −0.0285 ns | −0.0557 | 0.0792 |
NOB1 | −0.0112 ns | −0.0533 | 0.0699 |
NOB2 | −0.0112 ns | −0.0533 | 0.0699 |
CBH3 | −0.0120 ns | −0.0558 | 0.0773 |
CBH4 | 0.0329 ns | −0.0817 | 0.3663 |
CBH5 | 0.0789 ns | −0.0859 | 0.4238 |
SMT1 | −0.0156 ns | −0.0593 | 0.0984 |
SMT2 | −0.0591 ns | −0.0609 | 0.0999 |
SMT3 | −0.0725 ** | −0.0584 | 0.0937 |
SMT4 | −0.0639 ns | −0.0647 | 0.1297 |
SMT5 | −0.0477 ns | −0.0613 | 0.1001 |
CRB1 | −0.0179 ns | −0.0540 | 0.0753 |
CRB2 | 0.0041 ns | −0.0586 | 0.0929 |
CRB3 | −0.0081 ns | −0.0574 | 0.0925 |
CRB4 | −0.0099 ns | −0.0571 | 0.0873 |
CRB5 | −0.0245 ns | −0.0573 | 0.0866 |
SR1 | 0.0350 ns | −0.0569 | 0.0825 |
SR2 | 0.1047 * | −0.0557 | 0.0790 |
SR3 | 0.1016 * | −0.0551 | 0.0763 |
SR4 | 0.1254 ** | −0.0558 | 0.0756 |
SR5 | 0.1235 ** | −0.0536 | 0.0746 |
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Liao, B.; Que, Q.; Xu, X.; Zhou, W.; Ouyang, K.; Li, P.; Li, H.; Lai, C.; Chen, X. Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes 2022, 13, 1924. https://doi.org/10.3390/genes13111924
Liao B, Que Q, Xu X, Zhou W, Ouyang K, Li P, Li H, Lai C, Chen X. Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes. 2022; 13(11):1924. https://doi.org/10.3390/genes13111924
Chicago/Turabian StyleLiao, Boyong, Qingmin Que, Xingming Xu, Wei Zhou, Kunxi Ouyang, Pei Li, Huaqiang Li, Can Lai, and Xiaoyang Chen. 2022. "Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment" Genes 13, no. 11: 1924. https://doi.org/10.3390/genes13111924
APA StyleLiao, B., Que, Q., Xu, X., Zhou, W., Ouyang, K., Li, P., Li, H., Lai, C., & Chen, X. (2022). Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes, 13(11), 1924. https://doi.org/10.3390/genes13111924