Please wait a minute...
Journal of Integrative Agriculture  2023, Vol. 22 Issue (12): 3804-3809    DOI: 10.1016/j.jia.2023.05.017
Short Communication Advanced Online Publication | Current Issue | Archive | Adv Search |
Analyzing architectural diversity in maize plants using the skeletonimage- based method
LIU Min-guo1, 2, 3, Thomas CAMPBELL4, LI Wei1, 2, 3, WANG Xi-qing1, 2, 3#
1 College of Biological Sciences, China Agricultural University, Beijing 100193, P.R.China
2 Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen 518000, P.R.China
3 Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P.R.China
4 Department of Biology, Northeastern Illinois University, Chicago 60625, USA
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

由于玉米植株的结构特征对其冠层的资源利用和对风雨等因素造成倒伏的忍耐能力以及产量的稳定性具有重要影响,因此受到广泛关注。量化自交系之间的形态多样性对于杂交育种至关重要,尤其在描述大量的种质资源时。然而,传统的几何描述方法过于简化植株结构并忽略了植株整体结构特征,因此难以反映和展示植株结构的多样性。本文介绍了一种新的描述玉米植株结构并量化其多样性的方法,该方法结合了计算机视觉算法和数学的持续同调理论。结果表明,持续同调方法可以捕捉玉米植株结构的关键特征和其他通常被传统几何分析方法所忽略的细节。基于这种方法,可以挖掘(量化)植株结构的形态多样性,并分析玉米植株结构的主要类型。



Abstract  Shoot architecture in maize is critical since it determines resource use, impacts wind and rain damage tolerance, and affects yield stability. Quantifying the diversity among inbred lines in heterosis breeding is essential, especially when describing germplasm resources. However, traditional geometric description methods oversimplify shoot architecture and ignore the plant’s overall architecture, making it difficult to reflect and illustrate diversity. This study presents a new method to describe maize shoot architecture and quantifies its diversity by combining computer vision algorithms and persistent homology. Our results reveal that persistent homology can capture key characteristics of shoot architecture in maize and other details often overlooked by traditional geometric analysis. Based on this method, the morphological diversity of shoot architecture can be mined (quantified), and the main shoot architecture types can be obtained. Consequently, this method can easily describe the diversity of shoot architecture in many maize materials.
Keywords:  maize        shoot architecture        persistent homology        phenotyping technology        morphological diversity  
Received: 22 December 2022   Accepted: 06 April 2023
Fund: The study work was supported by the National KeY Research and Development Program of China (2022ZD0401801) and the Chinese Universities Scientific Funds (2023TC107).
About author:  LIU Min-guo, E-mail: liumg@cau.edu.cn; #Correspondence WANG Xi-qing, Tel/Fax: +86-10-62733599, E-mail: wangxq21@ cau.edu.cn

Cite this article: 

LIU Min-guo, Thomas CAMPBELL, LI Wei, WANG Xi-qing. 2023. Analyzing architectural diversity in maize plants using the skeletonimage- based method. Journal of Integrative Agriculture, 22(12): 3804-3809.

Andrieu B, Moulia B, Maddonni G, Birch C, Sonohat G, Fournier C, Allirand J, Chartier M, Hillier J, Drouet J, Bonhomme R. 2004. Plasticity of plant architecture in response to density: Using maize as a model. In 4th International Workshop on Functional-Structural Plant Models, Montpellier, France.

Bouchet S, Bertin P, Presterl T, Jamin P, Coubriche D, Gouesnard B, Laborde J, Charcosset A. 2017. Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits. Heredity, 118, 249–259.

Buckler E S, Gaut B S, McMullen M D. 2006. Molecular and functional diversity of maize. Current Opinion in Plant Biology, 9, 172–176.

Ci X, Li M, Liang X, Xie Z, Zhang D, Li X, Lu Z, Ru G, Bai L, Xie C, Hao Z, Zhang S. 2011. Genetic contribution to advanced yield for maize hybrids released from 1970 to 2000 in China. Crop Science, 51, 13–20.

Csardi G, Nepusz T. 2006. The igraph software package for complex network research. InterJournal Complex Systems, 1695, 1-9.

Delory B M, Li M, Topp C N, Lobet G. 2018. ArchiDART v3. 0: A new data analysis pipeline allowing the topological analysis of plant root systems. F1000Research, 7, 22.

Dhakal K, Zhu Q, Zhang B, Li M, Li S. 2021. Analysis of shoot architecture traits in edamame reveals potential strategies to improve harvest efficiency. Frontiers in Plant Science, 12, 249.

Duncan W. 1971. Leaf angles, leaf area, and canopy photosynthesis. Crop Science, 11, 482–485.

Fasoula V A, Fasoula D A. 2010. Honeycomb breeding: Principles and applications. Plant Breeding Reviews, 18, 177.

Fasy B T, Kim J, Lecci F, Maria C, Millman D L, Rouvreau V. 2021. TDA: Statistical tools for topological data analysis. [April 3, 2022]. https://CRAN.R-project.org/package=TDA

Fei J, Lu J, Jiang Q, Liu Z, Yao D, Qu J, Liu S, Guan S, Ma Y. 2022. Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations. BMC Plant Biology, 22, 110.

Gage J L, Miller N D, Spalding E P, Kaeppler S M, de Leon N. 2017. TIPS: A system for automated image-based phenotyping of maize tassels. Plant Methods, 13, 21.

Gao X, Li Y, Yang M, Li C, Song Y, Wang T, Li Y, Shi Y. 2023. Changes in grain-filling characteristics of single-cross maize hybrids released in China from 1964 to 2014. Journal of Integrative Agriculture, 22(3), 691-700.

Gehan M A, Fahlgren N, Abbasi A, Berry J C, Callen S T, Chavez L, Doust A N, Feldman M J, Gibert K B, Hodge J G, Hoyer J S, Lin A, Liu S, Lizárraga C, Lorence A, Miller M, Platon E, Tessman M, Sax T. 2017. PlantCV v2: Image analysis software for high-throughput plant phenotyping. PeerJ, 5, e4088.

Han D, Yang G, Yang H, Qiu C, Chen M, Wen W, Niu Q, Yang W. 2018. Three dimensional information extraction from maize tassel based on stereoscopic vision. Transactions of the Chinese Society of Agricultural Engineering, 34, 166–173.

Kassambara A. 2019. Ggcorrplot: Visualization of a correlation matrix using “ggplot2.” [February 12, 2022]. https://CRAN.R-project.org/package=ggcorrplot

Lambert R, Johnson R. 1978. Leaf angle, tassel morphology, and the performance of maize hybrids. Crop Science, 18, 499–502.

Li M, Duncan K, Topp C N, Chitwood D H. 2017. Persistent homology and the branching topologies of plants. American Journal of Botany, 104, 349-353.

Li M, Klein L L, Duncan K E, Jiang N, Chitwood D H, Londo J P, Miller A J, Topp C N. 2019. Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: Implications for understanding cluster density. Journal of Experimental Botany, 70, 6261–6276.

Li P, Wei J, Wang H, Fang Y, Yin S, Xu Y, Liu J, Yang Z, Xu C. 2019. Natural variation and domestication selection of zmpgp1 affects plant architecture and yield-related traits in maize. Genes, 10, 664.

Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. 2021. Cluster: Cluster analysis basics and extensions. [May 12, 2022]. https://CRAN.R-project.org/package=cluster

Park H S, Jun C H. 2009. A simple and fast algorithm for K-medoids clustering. Expert Systems with Applications, 36, 3336–3341.

R Core Team. 2021. R: A language and environment for statistical computing. Vienna, Austria: R foundation for statistical computing. [August 16, 2021]. https://www.R-project.org/

Shrestha J. 2016. Cluster analysis of maize inbred lines. Journal of Nepal Agricultural Research Council, 2, 33–36.

Smith J C, Smith O. 1989. The description and assessment of distances between inbred lines of maize. II: The utility of morphological biochemical, and genetic descriptors and a scheme for the testing of distinctiveness between inbred lines. Maydica, 34, 151–161.

Stewart D, Costa C, Dwyer L, Smith D, Hamilton R, Ma B. 2003. Canopy structure, light interception, and photosynthesis in maize. Agronomy Journal, 95, 1465–1474.

Strable J, Wallace J G, Unger-Wallace E, Briggs S, Bradbury P J, Buckler E S, Vollbrecht E. 2017. Maize YABBY genes drooping leaf1 and drooping leaf2 regulate plant architecture. The Plant Cell, 29, 1622–1641.

Tausz A, Vejdemo-Johansson M, Adams H. 2014. JavaPlex: A research software package for persistent (co) homology. In: Hong H, Yap C, eds., Proceedings of ICMS (International Congress on Mathematical Software) 2014. Lecture Notes in Computer Science, vol. 8592, Springer, Berlin, Heidelberg, pp. 129–136.

Tian J, Wang C, Xia J, Wu L, Xu G, Wu W, Dan L, Qin W, Han X, Chen Q, Jin W, Tian F. 2019. Teosinte ligule allele narrows plant architecture and enhances high-density maize yields. Science, 365, 658–664.

Tibshirani R, Walther G, Hastie T. 2001. Estimating the number of clusters in a data set via the gap statistic. Journal of the Royal Statistical Society (Series B: Statistical Methodology), 63, 411–423.

Tokatlidis I, Koutroubas S. 2004. A review of maize hybrids’ dependence on high plant populations and its implications for crop yield stability. Field Crops Research, 88, 103–114.

Vazin F, Hassanzadeh M, Madani A, Nassiri-Mahallati M, Nasri M. 2010. Modeling light interception and distribution in mixed canopy of common cocklebur (Xanthium stramarium) in competition with corn. Planta Daninha, 28, 455–462.

Wang Y, Li J. 2006. Genes controlling plant architecture. Current Opinion in Biotechnology, 17, 123–129.

Xue J, Xie R, Zhang W, Wang K, Hou P, Bo M, Gou L, Li S. 2017. Research progress on reduced lodging of high-yield and-density maize. Journal of Integrative Agriculture, 16, 2717–2725.

Yang X, Gao S, Xu S, Zhang Z, Prasanna B M, Li L, Li J, Yan J. 2011. Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Molecular Breeding, 28, 511–526.

Yang X, Yan J, Shah T, Warburton M L, Li Q, Li L, Gao Y, Chai Y, Fu Z, Zhou Y, Xu S, Bai G, Meng Y, Zheng Y, Li J. 2010. Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theoretical and Applied Genetics, 121, 417–431.

Zhang X, Huang C, Wu D, Qiao F, Li W, Duan L, Wang K, Xiao Y, Chen G, Liu Q, Xiong L, Yang W, Yan J. 2017. High-throughput phenotyping and QTL mapping reveals the genetic architecture of maize plant growth. Plant Physiology, 173, 1554–1564.

Zhang B, Hu H, Guo Z, Gong S, Sheng S, Liao S, Wang X, Zhou S, Zhang Z. 2023. Plastic-film-side seeding, as an alternative to traditional film mulching, improves yield stability and income in maize production in semi-arid regions. Journal of Integrative Agriculture, 22(4), 1021-1034.

Zheng Z, Liu X. 2013. Genetic analysis of agronomic traits associated with plant architecture by QTL mapping in maize. Genetics Molecular Research, 12, 1243–1253. 

[1] WANG Peng, WANG Cheng-dong, WANG Xiao-lin, WU Yuan-hua, ZHANG Yan, SUN Yan-guo, SHI Yi, MI Guo-hua. Increasing nitrogen absorption and assimilation ability under mixed NO3 and NH4+ supply is a driver to promote growth of maize seedlings[J]. >Journal of Integrative Agriculture, 2023, 22(6): 1896-1908.
[2] XU Meng-ze, WANG Yu-hong, NIE Cai-e, SONG Gui-pei, XIN Su-ning, LU Yan-li, BAI You-lu, ZHANG Yin-jie, WANG Lei. Identifying the critical phosphorus balance for optimizing phosphorus input and regulating soil phosphorus effectiveness in a typical winter wheat-summer maize rotation system in North China[J]. >Journal of Integrative Agriculture, 2023, 22(12): 3769-3782.
[3] SHA Xiao-qian, GUAN Hong-hui, ZHOU Yu-qian, SU Er-hu, GUO Jian, LI Yong-xiang, ZHANG Deng-feng, LIU Xu-yang, HE Guan-hua, LI Yu, WANG Tian-yu, ZOU Hua-wen, LI Chun-hui. Genetic dissection of crown root traits and their relationships with aboveground agronomic traits in maize[J]. >Journal of Integrative Agriculture, 2023, 22(11): 3394-3407.
[4] XIE Si-di, TIAN Ran, ZHANG Jun-jie, LIU Han-mei, LI Yang-ping, HU Yu-feng, YU Guo-wu, HUANG Yu-bi, LIU Ying-hong. Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize[J]. >Journal of Integrative Agriculture, 2023, 22(10): 2961-2980.
[5] LI Peng-cheng, YANG Xiao-yi, WANG Hou-miao, PAN Ting, YANG Ji-yuan, WANG Yun-yun, XU Yang, YANG Ze-feng, XU Chen-wu. Metabolic responses to combined water deficit and salt stress in maize primary roots[J]. >Journal of Integrative Agriculture, 2021, 20(1): 109-119.
[6] Sooyeon Lim, Gibum Yi. Investigating seed mineral composition in Korean landrace maize (Zea mays L.) and its kernel texture specificity[J]. >Journal of Integrative Agriculture, 2019, 18(9): 1996-2005.
[7] LI Xiang-ling, GUO Li-guo, ZHOU Bao-yuan, TANG Xiang-ming, CHEN Cong-cong, ZHANG Lei, ZHANG Shao-yun, LI Chong-feng, XIAO Kai, DONG Wei-xin, YIN Bao-zhong, ZHANG Yue-chen . Characterization of low-N responses in maize (Zea mays L.) cultivars with contrasting nitrogen use efficiency in the North China Plain[J]. >Journal of Integrative Agriculture, 2019, 18(9): 2141-2152.
[8] GU Ri-liang, HUANG Ran, JIA Guang-yao, YUAN Zhi-peng, REN Li-sha, LI Li, WANG Jian-hua. Effect of mechanical threshing on damage and vigor of maize seed threshed at different moisture contents[J]. >Journal of Integrative Agriculture, 2019, 18(7): 1571-1578.
[9] HE An-le, LIU Jia, WANG Xin-hua, ZHANG Quan-guo, SONG Wei, CHEN Jie. Soil application of Trichoderma asperellum GDFS1009 granules promotes growth and resistance to Fusarium graminearum in maize[J]. >Journal of Integrative Agriculture, 2019, 18(3): 599-607.
[10] WANG Li-jun, ZHANG Ping, WANG Ruo-nan, WANG Pu, HUANG Shou-bing. Effects of variety and chemical regulators on cold tolerance during maize germination[J]. >Journal of Integrative Agriculture, 2018, 17(12): 2662-2669.
No Suggested Reading articles found!