A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria

Molecular Plant
Noah FahlgrenIvan Baxter

Abstract

Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available.

Associated Software

References

Aug 14, 1998·Plant Physiology·F SchöfflA Reindl
Aug 12, 2000·Journal of Experimental Botany·K Maxwell, G N Johnson
Sep 17, 2002·Briefings in Bioinformatics·Harry Mangalam
Jul 1, 1997·The Plant Cell·T. Nelson, N. Dengler
Nov 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ajay K GargRay J Wu
Sep 24, 2004·Briefings in Bioinformatics·Don Gilbert
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Dec 5, 2006·Current Opinion in Plant Biology·Andrew N Doust
Feb 7, 2008·BMC Bioinformatics·Mathieu Fourment, Michael R Gillings
Apr 26, 2008·Science·Philip N Benfey, Thomas Mitchell-Olds
May 1, 2008·Annual Review of Plant Biology·Rana Munns, Mark Tester
Jan 8, 2009·Plant Physiology·Andrew N DoustJeffrey L Bennetzen
Dec 25, 2009·Bioinformatics·Kristian KvilekvalB S Manjunath
Dec 31, 2009·PLoS Computational Biology·Joel T Dudley, Atul J Butte
Feb 23, 2010·Biochemical and Biophysical Research Communications·Charu LataManoj Prasad
Jun 18, 2010·The Plant Journal : for Cell and Molecular Biology·Olivia WilkinsMalcolm M Campbell
Jul 28, 2010·Journal of Experimental Botany·Bettina BergerMark Tester
Aug 10, 2010·The Plant Cell·Thomas P BrutnellJoyce Van Eck
Feb 3, 2011·Plant Methods·Mahmood R GolzarianDesmond S Lun
Apr 5, 2011·Journal of Experimental Botany·Pinghua Li, Thomas P Brutnell
May 17, 2011·BMC Bioinformatics·Anja HartmannFalk Schreiber
Jun 10, 2011·Journal of Experimental Botany·Rowan F Sage, Xin-Guang Zhu
Nov 15, 2011·Trends in Plant Science·Robert T Furbank, Mark Tester
May 5, 2012·BMC Plant Biology·Anthony PaprokiJurgen Fripp
May 15, 2012·Nature Biotechnology·Jeffrey L BennetzenKatrien M Devos
Jan 1, 2011·Frontiers in Plant Science·Stephen A GoffDan Stanzione
Jul 5, 2013·Nature·Susan McCouchDaniel Zamir
Jul 11, 2013·PloS One·Deepak K RayJonathan A Foley
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Oct 11, 2013·Plant Methods·Guillaume LobetClaire Périlleux
Feb 4, 2014·Journal of Plant Physiology·Nieves Fernández-GarcíaJosé Salvador Rubio-Asensio
May 6, 2014·Proceedings of the National Academy of Sciences of the United States of America·Hans-Henning KunzJulian I Schroeder
May 29, 2014·Journal of Experimental Botany·Sankalpi N Warnasooriya, Thomas P Brutnell
Oct 11, 2014·Science·Patrick GerlandJohn Wilmoth
Nov 12, 2014·BMC Genetics·Shyamal Krishna TalukderAllan Fritz

❮ Previous
Next ❯

Citations

May 5, 2016·Journal of Experimental Botany·Avi C KnechtHarkamal Walia
Dec 15, 2016·Frontiers in Plant Science·Pu HuangThomas P Brutnell
Jan 19, 2018·GigaScience·Dijun ChenChristian Klukas
Jan 23, 2020·The Plant Journal : for Cell and Molecular Biology·Patrick Z EllsworthAsaph B Cousins
May 21, 2020·G3 : Genes - Genomes - Genetics·Fan LinSeung Y Rhee
Dec 27, 2016·Frontiers in Plant Science·Shankar R PantKranthi K Mandadi
Aug 31, 2019·Applications in Plant Sciences·Brandin GrindstaffJ Chris Pires
Feb 1, 2016·Functional Plant Biology : FPB·Lucia M Acosta-GamboaArgelia Lorence
Oct 2, 2020·Applications in Plant Sciences·Sunil K Kenchanmane RajuJames C Schnable
Nov 30, 2016·PeerJ·Tjelvar S G Olsson, Matthew Hartley
Aug 5, 2017·Plant Methods·Carlos Antônio Ferreira de SousaManoel Teixeira Souza
Jul 25, 2017·Frontiers in Plant Science·Jordan R Ubbens, Ian Stavness
Jun 1, 2018·BioMed Research International·Rita ArmonienéAakash Chawade
Jun 14, 2018·Frontiers in Plant Science·Hao HuAndrew N Doust
Aug 9, 2018·Plant Methods·Sarah Taghavi NaminJustin O Borevitz
Oct 3, 2018·Communications Biology·Dijun ChenKerstin Kaufmann
Jun 20, 2019·Frontiers in Plant Science·Chunjiang ZhaoJiangchuan Fan
Jun 28, 2019·Plant Direct·Tara A EndersCory D Hirsch
Mar 1, 2017·Current Protocols in Plant Biology·Erica AgnewChristopher N Topp
Aug 1, 2020·Frontiers in Plant Science·Marouane BaslamÁlvaro Sanz-Sáez
May 8, 2018·Applications in Plant Sciences·Jose C TovarMalia A Gehan
Jul 25, 2020·Briefings in Bioinformatics·Xiaoxia MaTian Xie
Jun 11, 2020·Nature Communications·Chong TengVirginia Walbot
Aug 22, 2017·Frontiers in Plant Science·Piyush PandeyJames C Schnable
Oct 13, 2017·Frontiers in Plant Science·Riccardo LudovisiAntoine Harfouche
Feb 2, 2021·Frontiers in Bioengineering and Biotechnology·Daoliang LiAkhter Muhammad
Nov 21, 2020·Scientific Reports·Shilpi GuptaRajeev J Ram
Feb 26, 2020·Current Biology : CB·Marjorie R Lundgren, David L Des Marais
Apr 18, 2020·Plant Physiology and Biochemistry : PPB·Lucia M Acosta-GamboaLorence Argelia
Apr 24, 2021·Chemical Research in Toxicology·Justin B RenaudMark W Sumarah

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Landau-Kleffner Syndrome

Landau Kleffner syndrome (LKS), also called infantile acquired aphasia, acquired epileptic aphasia, or aphasia with convulsive disorder, is a rare childhood neurological syndrome characterized by the sudden or gradual development of aphasia (the inability to understand or express language) and an abnormal electroencephalogram. Discover the latest research on LKS here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.