Using system mapping to analyze genetic regulation mechanism of neighboring plant interaction in <i>Populus szechuanica</i> var. <i>tibetica</i>

Ding Mengdong; Wei Xueda; Wang Yu; Zhu Xuli

doi:10.12171/j.1000-1522.20220519

Journal of Beijing Forestry University > 2024 > 46(10): 63-73. > DOI: 10.12171/j.1000-1522.20220519

Ding Mengdong, Wei Xueda, Wang Yu, Zhu Xuli. Using system mapping to analyze genetic regulation mechanism of neighboring plant interaction in Populus szechuanica var. tibetica[J]. Journal of Beijing Forestry University, 2024, 46(10): 63-73. DOI: 10.12171/j.1000-1522.20220519

Citation:

PDF (4849 KB)

Using system mapping to analyze genetic regulation mechanism of neighboring plant interaction in Populus szechuanica var. tibetica

Ding Mengdong^1,,
Wei Xueda¹,
Wang Yu¹,
Zhu Xuli^{1, 2, ,}

1.
Center for Computational Biology, School of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
2.
National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China

More Information

Received Date: December 25, 2022
Revised Date: May 07, 2023
Accepted Date: October 07, 2024
Available Online: October 17, 2024

Graphical Abstract

Abstract

Abstract

Objective
The interactions between plants are of great significance to the formation of ecosystems. This study investigated the genetic regulatory mechanisms of plant interactions at the level of neighboring plant interactions, the smallest unit of intraspecific interactions.
Method
Using the natural population of Populus szechuanica var. tibetica as research material, different series numbers were randomly paired and cuttings were planted in pots to investigate the growth dynamic phenotypes of plant height throughout the growing season. Combining SNP marker data from the population, system mapping was performed to locate significant QTLs. GO enrichment analysis and construction of ordinary differential interaction networks were used to analyze the functions of candidate genes.
Result
(1) A total of 92 significant loci were mapped, annotating 31 candidate genes. (2) In GO enrichment analysis, biological processes included auxin signaling pathways and abscisic acid signaling pathways, molecular functions included endopeptidase activity and protease activity, and cellular components included respiratory chains and cytochromes. (3) Among the 31 candidate genes, genes 5, 8, 10, 12 and 21 were hub genes in the direct effect network, genes 5, 8, 10 and 13 were hub genes in the indirect effect network, and genes 5, 8 and 13 were hub genes in the epistatic interaction network, with genes 5, 10 and 13 involved in plant immune response and environmental stress response.
Conclusion
For neighboring interactions among P. szechuanica var. tibetica, system mapping can screen for interaction-related genetic loci, construct genetic regulatory networks, and mine hub genes, providing a new perspective for analyzing the genetic mechanisms of woody plant interactions.
- system mapping,
- neighboring plant interaction,
- regulatory network,
- QTL,
- Populus szechuanica var. tibetica

FullText(HTML)

References (40)

References

[1]	Gundel P E, Pierik R, Mommer L, et al. Competing neighbors: light perception and root function[J]. Oecologia, 2014, 176(1): 1−10. doi: 10.1007/s00442-014-2983-x
[2]	Bascompte J. Structure and dynamics of ecological networks[J]. Science, 2010, 329: 765−766. doi: 10.1126/science.1194255
[3]	Goldberg D E, Barton A M. Patterns and consequences of interspecific competition in natural communities: a review of field experiments with plants[J]. The American Naturalist, 1991, 139: 771−801.
[4]	Subrahmaniam H J, Libourel C, Journet E, et al. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions[J]. The Plant Journal, 2018, 93(4): 747−770. doi: 10.1111/tpj.13799
[5]	Keddy P A, Cahill J. Competition in plant communities[J]. Ecology, 2012.110−115.
[6]	Chaney L, Baucom R S. The costs and benefits of tolerance to competition in Ipomoea purpurea, the common morning glory[J]. Evolution, 2014, 68(6): 1698−1709. doi: 10.1111/evo.12383
[7]	Wendling M, Büchi L, Amossé C, et al. Specific interactions leading to transgressive overyielding in cover crop mixtures[J]. Agriculture, Ecosystems & Environment, 2017, 241: 88−99.
[8]	杨文亭, 王晓维, 王建武. 豆科–禾本科间作系统中作物和土壤氮素相关研究进展[J]. 生态学杂志, 2013, 32(9): 2480−2484. Yang W T, Wang X W, Wang J W. Crop and soil nitrogen in legume-Gramineae intercropping system: research progress[J]. Chinese Journal of Ecology, 2013, 32(9): 2480−2484.
[9]	Bailey J K. From genes to ecosystems: a genetic basis to ecosystem services[J]. Population Ecology, 2011, 53(1): 47−52. doi: 10.1007/s10144-010-0251-4
[10]	Ehlers B K, Damgaard C F, Laroche F. Intraspecific genetic variation and species coexistence in plant communities[J]. Biology Letters, 2016, 12(1): 20150853. doi: 10.1098/rsbl.2015.0853
[11]	Brooker R W. Plant-plant interactions and environmental change[J]. New Phytologist, 2006, 171(2): 271−284. doi: 10.1111/j.1469-8137.2006.01752.x
[12]	Hughes A R, Inouye B D, Johnson M T J, et al. Ecological consequences of genetic diversity[J]. Ecology Letters, 2008, 11(6): 609−623. doi: 10.1111/j.1461-0248.2008.01179.x
[13]	Becker C, Berthome R, Delavault P, et al. The ecologically relevant genetics of plant-plant interactions[J]. Trends in Plant Sciences, 2023, 28(1): 31−42. doi: 10.1016/j.tplants.2022.08.014
[14]	Wade M J. The co-evolutionary genetics of ecological communities[J]. Nature Reviews Genetics, 2007, 8(3): 185−195. doi: 10.1038/nrg2031
[15]	Sun L, Wu R. Mapping complex traits as a dynamic system[J]. Physics of Life Reviews, 2015, 13: 155−185. doi: 10.1016/j.plrev.2015.02.007
[16]	Fu L, Sun L, Hao H, et al. How trees allocate carbon for optimal growth: insight from a game-theoretic model[J]. Briefings in Bioinformatics, 2018, 19(4): 593−602. doi: 10.1093/bib/bbx003
[17]	Cao X, Dong A, Kang G, et al. Modeling spatial interaction networks of the gut microbiota[J/OL]. Gut Microbes, 2022, 14(1): 2106103.
[18]	Ye M, Zhu X, Gao P, et al. Identification of quantitative trait loci for altitude adaptation of tree leaf shape with Populus szechuanica in the Qinghai-Tibetan Plateau[J]. Frontiers in Plant Science, 2020, 11: 632. doi: 10.3389/fpls.2020.00632
[19]	沈登锋, 薄文浩, 徐放, 等. 色季拉山不同海拔高度的藏川杨种群遗传多样性研究[J]. 植物遗传资源学报, 2014, 15(4): 692−698. Shen D F, Bo W H, Xu F, et al. Study on genetic diversity among populations in Populus szechuanica var. tibetica at different altitudes in Sejila Mountain[J]. Journal of Plant Genetic Resources, 2014, 15(4): 692−698.
[20]	郑晨飞. 藏川杨异形叶全基因组关联分析[D]. 北京: 北京林业大学, 2020. Zheng C F. Genome-wide association analysis of heterophylly for the tibet poplar, Populus szechuanica var. tibetica[D]. Beijing: Beijing Forestry University, 2020.
[21]	Arditi R, Ginzburg L R. Coupling in predator-prey dynamics: ratio-dependence[J]. Journal of Theoretical Biology, 1989, 139(3): 311−326. doi: 10.1016/S0022-5193(89)80211-5
[22]	Fu G, Wang Z, Li J, et al. A mathematical framework for functional mapping of complex phenotypes using delay differential equations[J]. Journal of Theoretical Biology, 2011, 289: 206−216. doi: 10.1016/j.jtbi.2011.08.002
[23]	Zhao W, Chen Y Q, Casella G, et al. A non-stationary model for functional mapping of complex traits[J]. Bioinformatics, 2005, 21(10): 2469−2477. doi: 10.1093/bioinformatics/bti382
[24]	Hart S P, Schreiber S J, Levine J M. How variation between individuals affects species coexistence[J]. Ecology Letters, 2016, 19(8): 825−838. doi: 10.1111/ele.12618
[25]	Chen C, Jiang L, Fu G, et al. An omnidirectional visualization model of personalized gene regulatory networks[J]. NPJ Systems Biology and Applications, 2019, 5(1): 1−11.
[26]	Humphrey L D, Pyke D A. Demographic and growth responses of a guerrilla and a phalanx perennial grass in competitive mixtures[J]. Journal of Ecology, 1998, 86(5): 854−865. doi: 10.1046/j.1365-2745.1998.8650854.x
[27]	解婷婷, 单立山, 苏培玺. 不同施氮量下干旱胁迫对棉花生长及种内关系的影响[J]. 中国生态农业学报, 2020, 28(5): 643−651. Xie T T, Shan L S, Su P X. Effects of drought stress on cotton growth and intraspecific relationship under different nitrogen application rates[J]. Chinese Journal of Eco-Agriculture, 2020, 28(5): 643−651.
[28]	杨雪芳. 化感水稻对邻近植物的生物化学响应及其化感物质衍生物的抑草机制[D]. 北京: 中国农业大学, 2017. Yang X F. Biological and chemical responses of allelopathic rice toneighboring plants and the weed-suppressive mechanisms of riceallelochemical derivatives[D]. Beijing: China Agricultural University, 2017.
[29]	Rasmann S. As above so below: recent and future advances in plant-mediated above-and belowground interactions[J]. American Journal of Botany, 2022, 109(5): 672−675. doi: 10.1002/ajb2.1845
[30]	Wu R, Cao J, Huang Z, et al. Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems[J]. BMC Systems Biology, 2011, 5(1): 1−11. doi: 10.1186/1752-0509-5-1
[31]	Emenecker R J, Strader L C. Auxin-abscisic acid interactions in plant growth and development[J]. Biomolecules, 2020, 10(2): 281. doi: 10.3390/biom10020281
[32]	Popko J, Hansch R, Mendel R R, et al. The role of abscisic acid and auxin in the response of poplar to abiotic stress[J]. Plant Biology, 2010, 12(2): 242−258. doi: 10.1111/j.1438-8677.2009.00305.x
[33]	Delory B M, Delaplace P, Fauconnier M, et al. Root-emitted volatile organic compounds: can they mediate belowground plant-plant interactions?[J]. Plant and Soil, 2016, 402(1−2): 1−26. doi: 10.1007/s11104-016-2823-3
[34]	王艳萍, 范宇浍, 马华燕, 等. 外源脱落酸对水稻苗期根系形态建成及其诱导化感作用的影响[J]. 应用与环境生物学报, 2024, 30(1): 126−132. Wang Y P, Fan Y H, Ma H Y, et al. Effects of exogenous abscisic acid on root morphogenesis and induced allelopathy of rice at seedling stage[J]. Chinese Journal of Applied and Environmental Biology, 2024, 30(1): 126−132.
[35]	Yao X, Xiong W, Ye T, et al. Overexpression of the aspartic protease ASPG1 gene confers drought avoidance in Arabidopsis[J]. Journal of Experimental Botany, 2012, 63(7): 2579−2593. doi: 10.1093/jxb/err433
[36]	Li G, Liu K, Baldwin S A, et al. Equilibrative nucleoside transporters of Arabidopsis thaliana: cDNA cloning, expression pattern, and analysis of transport activities[J]. Journal of Biological Chemistry, 2003, 278(37): 35732−35742. doi: 10.1074/jbc.M304768200
[37]	Kim M, Lim J, Ahn C S, et al. Mitochondria-associated hexokinases play a role in the control of programmed cell death in Nicotiana benthamiana[J]. The Plant Cell, 2006, 18(9): 2341−2355. doi: 10.1105/tpc.106.041509
[38]	Wang F, Jing Y, Wang Z, et al. Arabidopsis profilin isoforms, PRF1 and PRF2 show distinctive binding activities and subcellular distributions[J]. Journal of Integrative Plant Biology, 2009, 51(2): 113−121. doi: 10.1111/j.1744-7909.2008.00781.x
[39]	Choi K, Khan R, Lee S. Dissection of plant microbiota and plant-microbiome interactions[J]. Journal of Microbiology, 2021, 59(3): 281−291. doi: 10.1007/s12275-021-0619-5
[40]	Mine A. Multifaceted involvement of abscisic acid in plant interactions with pathogenic and mutualistic microbes[J]. Advances in Botanical Research, 2019, 92: 219−253.

[1]	Qi Wanxin, Chen Tingting, Song Jiali, An Xinmin. Creating a new germplasm of aneuploid Populus tomentosa with insect-resistance based on hybridization of transgenic 741 poplar and P. alba var. pyramidalis[J]. Journal of Beijing Forestry University, 2024, 46(12): 92-102. DOI: 10.12171/j.1000-1522.20240021
[2]	Xu Xinghua, Huang Qilun, Li Shanwen, Meng Xianwei, Li Zongtai, Qiao Yanhui, Dong Yufeng, Zhang Zhiyi. Creation and comprehensive evaluation of Populus deltoides germplasm resources[J]. Journal of Beijing Forestry University, 2024, 46(8): 79-86. DOI: 10.12171/j.1000-1522.20220101
[3]	Wei Xueda, Wang Yu, Ding Mengdong, Wu Shuang, Liang Dan, Ye Meixia, Wu Rongling. Using allometric model and game theory to analyze the genetic regulation mechanism of dynamic growth of Populus tibetica trunk[J]. Journal of Beijing Forestry University, 2024, 46(6): 154-164. DOI: 10.12171/j.1000-1522.20220414
[4]	Xu Jiahong, Zeng Qing, Ye Fuyu, Hu Yangyang, Shi Huanyu, Zhang Xuan, Chen Jinhui. Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes[J]. Journal of Beijing Forestry University, 2021, 43(10): 28-37. DOI: 10.12171/j.1000-1522.20200286
[5]	Wang Ping, Wang Dongyang, Wang Jing, Jiang Libo, Wu Rongling. QTL epistasis effect analysis of seedling growth-related traits in Populus euphratica[J]. Journal of Beijing Forestry University, 2018, 40(12): 49-59. DOI: 10.13332/j.1000-1522.20180332
[6]	WANG Cong-peng, JIA Fu-li, LIU Sha, LIU Chao, XIA Xin-li, YIN Wei-lun. Drought induces alterations in stomatal development in Populus deltoides×P. nigra[J]. Journal of Beijing Forestry University, 2016, 38(6): 28-34. DOI: 10.13332/j.1000-1522.20160050
[7]	ZHAO Hui, WANG Sui, JIANG Jing, LIU Gui-feng. Screening of Populus simonii×Populus nigra WRKY70-interactive proteins by the yeast two-hybrid system[J]. Journal of Beijing Forestry University, 2016, 38(2): 44-51. DOI: 10.13332/j.1000-1522.20150162
[8]	GUO Peng, XING Xin, ZHANG Wan-jun, JIANG Jian. Cloning and characterization of PdDHN2b gene from Populus deltoides×Populus nigra.[J]. Journal of Beijing Forestry University, 2015, 37(1): 22-36. DOI: 10.13332/j.cnki.jbfu.2015.01.017
[9]	WEI Zun-zheng, GUO Li-qin, ZHANG Jin-feng, LI Bai-lian, ZHANG De-qiang, GUO Hua. Phylogenetic relationship of Populus by trnL-F sequence analysis[J]. Journal of Beijing Forestry University, 2010, 32(2): 27-33.
[10]	LI Jun, YANG Qiu-zhen, HUANG Jing-feng, WANG Yan, GE Jian-ming, FENG Chun. Impact of Clostera anachoreta and Micromelalopha troglodyta insect-induced damage on the hyperspectral features of Populus×canadesis cv.‘I-214’[J]. Journal of Beijing Forestry University, 2007, 29(6): 148-155. DOI: 10.13332/j.1000-1522.2007.06.021

Cited By

Cited by

Periodical cited type(15)

1.	隆吉辉，田银芳，汪超群. 湘西杉木人工林树高-胸径混合效应模型构建. 湖南林业科技. 2024(02): 25-32 .
2.	王帆，贾炜玮，唐依人，李丹丹. 基于TLS的红松树冠半径提取及其外轮廓模型构建. 南京林业大学学报(自然科学版). 2023(01): 13-22 .
3.	单华平，冯骏，翟丕斌，侯义梅，陈东升，朱红军. 鄂西山区日本落叶松树高曲线的研究. 湖北林业科技. 2023(04): 1-4+10 .
4.	孙天旭，张勇，郑燕凤，高莉，李庆，陈雪，林倩倩，张宜雪，王成德. 鲁中山区主要针叶树种树干削度方程研究——以侧柏、赤松、黑松为例. 山东农业大学学报(自然科学版). 2023(04): 613-619 .
5.	聂璐毅，董利虎，李凤日，苗铮，谢龙飞. 基于两水平非线性混合效应模型的长白落叶松削度方程构建. 南京林业大学学报(自然科学版). 2022(03): 194-202 .
6.	刘家腾，赵雪晗，刘伟韬，李建荣，蒋丽娟，周宇航，高慧淋，顾巍. 基于边际回归的沈阳市绿化树种人工油松冠形模拟. 应用生态学报. 2022(11): 2915-2922 .
7.	刘金义. 辽东山区人工红松树高曲线研究. 辽宁林业科技. 2021(04): 9-11+31 .
8.	吴丹子，王成德，李倞，刘敏. 福建杉木树冠外轮廓和树冠体积相容性模型. 浙江农林大学学报. 2020(01): 114-121 .
9.	高慧淋，董利虎，李凤日. 基于修正Kozak方程的人工樟子松树冠轮廓预估模型. 林业科学. 2019(08): 84-94 .
10.	全迎，李明泽，甄贞，郝元朔. 运用无人机激光雷达数据提取落叶松树冠特征因子及树冠轮廓模拟. 东北林业大学学报. 2019(11): 52-58 .
11.	耿林，李明泽，范文义，王斌. 基于机载LiDAR的单木结构参数及林分有效冠的提取. 林业科学. 2018(07): 62-72 .
12.	马载阳，张怀清，李永亮，杨廷栋，陈中良，李思佳. 基于空间结构的杉木树冠生长可视化模拟. 林业科学研究. 2018(04): 150-157 .
13.	高慧淋，董利虎，李凤日. 黑龙江省红松和长白落叶松人工林树冠外部轮廓模拟. 南京林业大学学报(自然科学版). 2018(03): 10-18 .
14.	马载阳，张怀清，李永亮，杨廷栋，彭文娥，李思佳. 林木多样性模型及生长模拟. 地球信息科学学报. 2018(10): 1422-1431 .
15.	高慧淋，董利虎，李凤日. 基于混合效应的人工落叶松树冠轮廓模型. 林业科学. 2017(03): 84-93 .

Other cited types(11)

Get Citation

PDF

XML

Article views (149) PDF downloads (20) Cited by(26)

Turn off MathJax

Article Contents

Abstract

References

Using system mapping to analyze genetic regulation mechanism of neighboring plant interaction in Populus szechuanica var. tibetica