Low cost high throughput image based root phenotyping pipeline for evaluation of sugarcane root system architecture under drought stress
462 / 267
Authors
-
Valarmathi Ramanathan
ICAR-SUGARCANE BREEDING INSTITUTE
https://orcid.org/0000-0001-8824-9780
-
H.K MahadevaSwamy
-
V Ulaganathan
-
C Appunu
-
G Hemaprabha
-
R Sathishraj
Kansas State University, Manhattan KS 66506.USA.
Keywords:
Sugarcane, Root phenotyping, droughtAbstract
Root System Architecture (RSA) plays an important role in the agronomic performance of a crop. Incorporation of these root traits in breeding program is hampered by the complexity in accessing the roots and its phenotyping. Lack of high throughput root phenotyping platforms for sugarcane is one of the major constraints in sugarcane root studies. In the present study an attempt was made to develop high throughput sugarcane root phenotyping pipeline comprising of a low cost plant cultivation platform and customized root image acquisition platform and image analyses using already available automated software. PVC tube system of specified dimension were used for plant growth and customized optical correction tank were used for imaging RSA. The acquired root images were fed into automated software GIAroots and about twenty quantitative root phenotype data were extracted and analysed. The working of the whole pipeline from plant growth to image analyses is demonstrated through comparative root phenotyping under drought using five genotypes of sugarcane wild relative Erianthus arundinaceus and three commercial sugarcane varieties.The relationships between the different root variables and genotypes in PCA biplots indicated high correlation among the different root traits. The study shows the low cost high throughput image based root phenotyping pipeline can be used to extract quantifiable root traits and analysed within a short span of time.
References
Ana Paez-Garcia, Christy M Motes, Wolf-Rüdiger Scheible, Rujin Chen, Elison B Blancaflor Maria J Monteros 2015). Roottraits and phenotyping strategies for plant improvement. Plants 4:334-355.
Anjum SA, Xie XY, Wang LC, Saleem MF,Man C, Lei W 2011. Morphological, physiological and biochemical responses of Figure. 4 Contribution of different Variable to principal components under drought and control conditions plants to drought stress. African Journal of Agricultural Research 6: 2026-2032.
Burton AL, Williams M, Lynch JP, Brown KM 2012. Root Scan: Software for highthroughput analysis of root anatomical traits. Plant Soil 357:189–203
Clark Randy T, Adam NFamoso, Keyan Zhao, Jon EShaff, Eric JCraft, Carlos D Bustamante, Susan RMcCouch, Daniel JAneshansley, Leon VKochian 2013. High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell and Environment 36: 454-466.
Clark RT, Mac Curdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV 2011. Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiology 156:455-465.
Galkovskyi T,Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles A Price, Christopher N Topp, Anjali S Iyer- Pascuzzi, Paul R Zurek, Suqin Fang, John Harer, Philip N Benfey, Joshua S Weitz 2012. GiA Roots: software for the high throughput analysis of plant root system architecture. BMC plant biology 12:116.
Garcia FHS, Ane M das Chagas Mendonca, Marcelo Rodrigues, Filipe I Matias, Mario P da Silva Filho, Hugo RBS, Julian Taffner, Joao PRADB 2020. Water deficit tolerance in sugarcane is dependent on the accumulation of sugar in the leaf. Annals of Applied Biology 176:65-74.
Grossman JD, Rice KJ 2012. Evolution of root plasticity responses to variation in soil nutrient distribution and concentration. Evolutionary Application 5:850–857.
Hargreaves CE, Gregory PJ, Bengough AG 2009.Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and X-ray microtomography. Plant and Soil 316:285–297.
Hemaprabha G, Nagarajan R, Alarmelu S, Natarajan US. 2006. Parental potential of sugarcane clones for drought resistance breeding. Sugar Tech 8:59-62.
Hemaprabha G, Simon Swapna, Leena Lavanya D, Sajitha B, Venkataramana S. 2013. Evaluation of drought tolerance potential of elite genotypes and progenies of sugarcane (Saccharum sp. hybrids). Sugar Tech 15(1):9-16.
Kanbar A, Chandrashekara M, Manjunatha K, Vinod MS, Hittalmani S, Janamatti M, Shashidhar HE 2004. Molecular markers for root morphological traits under lowmoisture stress using transgressant backcross of rice (Oryza sativa L.). Indian Journal of Genetics and Plant Breeding 4(3):185-188.
Kanbar A, Shashidhar HE, Hittalmani S. 2002. Mapping of QTL associated with root and related traits in DH mapping population of rice (Oryza sativa L.). Indian Journal of Genetics 62:287- 290.
Kano M, Inukai Y, Kitano H, Yamauchi A 2011. Root plasticity as the key root trait for adaptation to various intensities of drought stress in rice. Plant and Soil 342:189–196
Le Marie C, Norbert Kirchgessner, Daniela Marschall, Achim Walter, Andreas Hund 2014. Rhizoslides: paper-based growth system for non-destructive, high throughput phenotyping of root development by means of image analysis. Plant Methods 10:13.
Lynch J. 1995. Root architecture and plant productivity. Plant Physiology 109: 7-13. Lynch JP. 2011. Root phenes for enhanced soil exploration and phosphorus acquisition: tools for future crops. Plant Physiology 156 (3):1041-1049.
Lynch JP. 2014. Root phenes that reduce the metabolic costs of soil exploration: Opportunities for 21st century agriculture. Plant Cell Environment 38 (9):1775-1784.
Lynch JP, Wojciechowski T. 2015. Opportunities and challenges in the subsoil: Pathways to deeper rooted crops. Journal of Experimental Botany 66:2199-2210.
Meister R, Rajani M, Ruzicka D, Schachtman DP. 2014. Challenges of modifying root traits in crops for agriculture. Trends in Plant Science 19: 779-788.
Misra Varucha, Solomon S, Mall AK, Prajapati CP, Abeer Hashem, Elsayed Fathi AbdAllah, Mohammad Israil Ansari 2020. Morphological assessment of water stressed sugarcane: A comparison of waterlogged and drought affected crop. Saudi Journal of Biological Sciencies 27: 1228-1236.
Nair NV. 2011. Sugarcane Varietal development programmes in India: An overview. Sugar Tech 13(4): 275-280.
Narayanan S, Mohan A, Gill KS, Prasad PV. 2014. Variability of root traits in spring wheat germplasm. PLoS ONE 9:10.
Pierre JS, Jai M. Perroux, Anne LR. 2019. Screening for sugarcane root phenes reveals that reducing tillering does not lead to an increased root mass fraction. Frontiers in Plant Science 10: 1-12.
Prince SJ, Mackensie Murphy, Raymond N Mutava, Lorellin A Durnell, Babu Valliyodan, Grover J Shannon, Henry T Nguyen 2017. Root xylem plasticity to improve water use and yield in water-stressed soybean. Journal of Experimental Botany 68(8): 2027-2036.
René CP Kuijken, Fred A van Eeuwijk, Leo FM Marcelis, Harro J Bouwmeester. 2015. Root phenotyping: from component trait in the lab to breeding. Journal of Experimental Botany 66 (18):5389-5401.
Richards RA. 2008. Genetic opportunities to improve cereal root systems for dryland agriculture. Plant Production Science 11:12-16.
Sato EM, Hijazi H, Bennett MJ, Vissenberg K, Swarup R. 2014. New insights into root gravitropic signalling. Journal of Experimental Botany 66(8):2155-2165.
Schonfeld MA, Johnson RE, Carver BE, Mornhinweg DW. 1988. Water relations in winter wheat as drought resistance indicators. Crop Science 28: 526-531.
Shashidhar HE, Vimarsh Gowda HS, Raveendra GM, Pavan J Kundur, Naveen Kumar G, Suprabha N, Preethi Upadhya, Rakhi Sonam. 2012. PVC tubes to characterize roots and shoots to complement field plant productivity studies, In: Methodologies for root drought studies in rice, H.E. Shashidhar, Amelia Henry, and Bill Hardy Eds. 15-21.
Siddique M, Hamid A, Islam M. 2000. Drought stress effects on water relations of wheat. Botanical Bulletin of Academia Sinica.41.
Smith S, De Smet I. 2012. Root system architecture: insights from Arabidopsis and cereal crops. Philosophical Transactions of the Royal Society B-Biological Sciences 367:1595.
Valarmathi R, Mahadeva Swamy HK, Preethi K, Ashwin Narayan, Appunu C, Hifzur Rahman. 2020. Characterization and in silico analyses of RTCS gene from sugarcane encoding LOB protein family of transcription factors: a key regulator of shoot-borne root initiation. Journal of Sugarcane Research 10:12-23.
Valarmathi R, Mahadevaswamy HK, Appunu C. 2018a. Sugarcane root phenotyping for drought tolerance using customized PVC platforms, SBI News 38(2):1-3.
Valarmathi R, Hifzur Rahman, Saravanan S, Jagadeesh selvam N, Ashok kumar K, Sudha M, Chandrababu R Raveendran M. 2018b. OsARD4 encoding an acireductone dioxygenase improves root architecture in rice by promoting development of secondary root. Scientific Reports 8:15713.
Venuprasad R, Shashidhar HE, Hittalmani S, Hemamalini GS. 2002. Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica 128:293-300.
Downloads
Submitted
Published
Issue
Section
License
Copyright (c) 2021 https://creativecommons.org/licenses/by-nc-sa/4.0/
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
It is mandatory on the part of the corresponding author to furnish the article declaration form at the time of submission of the manuscript or after acceptance.
Authors who publish with JSR agree to the following terms:
- Authors retain copyright and grant JSR right of first publication with the work simultaneously licensed under Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
Society for Sugarcane Research and Development
How to Cite
