Assessing Root System Architecture of Wheat Seedlings Using A High-Throughput Root Phenotyping System

Adeleke, Ekundayo; Millas, Reneth; McNeal, Waymon; Faris, Justin D.; Taheri, Ali

doi:10.1101/677955

Cited by 7 publications

(6 citation statements)

References 31 publications

(45 reference statements)

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“…Based on a previous 2D phenotyping pipeline implemented by Atkinson et al (2015), our platform increases the throughput from 360 to 1,800 seedlings while maintaining a similar phenotyping rate (∼4.5 min per plant). A similar high-throughput phenotyping platform was also recently adapted by (Adeleke et al 2019) with a maximum phenotyping capacity of 672 plants. It is also worth noting that our high-throughput platform is relatively inexpensive and easy to implement using widely-available low-cost materials: storage boxes, germination paper, plastic sheets and paper binder clips.…”

Section: Discussionmentioning

confidence: 99%

“…The recent development of an in-silico platform for the rapid identification of mutations in 1,200 ethyl methanesulfonate (EMS) mutagenized lines in the UK hexaploid wheat cultivar ‘Cadenza’ now makes large-scale reverse and forward genetic investigation of traits more feasible in wheat (Krasileva et al 2017). Progress has also been made on the root phenomics front, with the development of fast, low-cost, and flexible two-dimensional (2D) root phenotyping pipelines with sufficient throughput for phenotyping large populations (Selvara et al 2013; Atkinson et al 2019; Adeleke et al 2019).…”

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confidence: 99%

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Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform

Shorinola

Kaye

Golan

et al. 2019

G3 Genes|Genomes|Genetics

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Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F 2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform

Shorinola

Kaye

Golan

et al. 2019

G3 Genes|Genomes|Genetics

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“…These approaches known as non-destructive techniques are generally relied on rhizoboxes, transparent enclosures allowing the study of root system development in two-dimensional (2D) using different substrates such as soil or vermiculite (Trachsel et al, 2011). In contrast, soil-free techniques such as hydroponics (Hargreaves et al, 2009;Ayalew et al, 2018;Beyer et al, 2019), aeroponics (Osvald et al, 2001;Lakhiar et al, 2018;Selvaraj et al, 2019), gel plates (Wojciechowski et al, 2009), and growth pouches (Hund et al, 2009;Adu et al, 2014;Adeleke et al, 2019) are used for a better contrast between roots and substrate. Plant RSA is a three-dimensional (3D) structure and phenotyping systems in 2D are limited to quantify all RSA component features.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020

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Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

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“…Images obtained can be analyzed and screened through publicly available user-friendly software programs. Adeleke et al made germination pouches at an even lower cost than those purchased for this study and were able to successfully germinate seedlings and obtain photographs at the end of the study in less than five minutes per plant, producing fast and effective results [21]. This phenotyping strategy can increase non-invasive screenings by saving time and space in the seedling stage of development, leading to exploring traits in the accessions screened [21].…”

Section: Introductionmentioning

confidence: 91%

“…Adeleke et al made germination pouches at an even lower cost than those purchased for this study and were able to successfully germinate seedlings and obtain photographs at the end of the study in less than five minutes per plant, producing fast and effective results [21]. This phenotyping strategy can increase non-invasive screenings by saving time and space in the seedling stage of development, leading to exploring traits in the accessions screened [21]. This study aimed to characterize root morphological traits of allelopathic and non-allelopathic weedy rice and identify root traits related to allelopathy.…”

Section: Introductionmentioning

confidence: 95%

Phenotyping of Weedy Rice to Assess Root Characteristics Associated with Allelopathy

Schumaker¹,

Stallworth²,

Tucker³

et al. 2021

AJPS

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Weedy rice is a species of Oryza, and is a wild relative of cultivated rice. The weed possesses unique hardiness that allows them to thrive in dynamic and stressful environments. These characteristics suggest that weedy rice is a stored source of novel genes for competitive traits. One such trait is allelopathy, where a species releases secondary metabolites that suppress the growth and development of neighboring species. Weed competition is a limiting factor in rice production systems; therefore, it is critical to identify specific allelopathic weedy rice accessions to determine the genetic pathways and mechanisms associated with allelopathy to be used in breeding programs. Due to the complex nature of allelochemical production and the lack of knowledge of allelopathy mechanisms in weedy rice, phenotypic traits, particularly root traits, can be used to overcome this limitation and serve as target characteristics for breeding weed suppressive rice varieties. Five weedy rice accessions were chosen from preliminary screenings of larger sample sizes with the ability to suppress barnyardgrass weed seedling growth. Another five weedy rice with low barnyardgrass suppression was selected for the current root phenotypic study. Five cultivated rice lines were used as a comparison. All plants were propagated in a transparent germination pouch for four weeks. Roots were scanned and analyzed for root length and area covered. No differences were found in the seedling root area among weedy rice and rice accessions; however, allelopathic weedy rice plants exhibited a 14% increase in root length than non-allelopathic weedy rice plants. The allelopathic weedy rice accession B2 possessed the most extended root system (22.4 cm root length). The highly allelopathic weedy rice accessions (including B2) screened and phenotyped in this study are ideal candidates for identifying the genetic controls of early root length, a possible trait contributing to underground allelopathic production and competitive advantage.

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Assessing Root System Architecture of Wheat Seedlings Using A High-Throughput Root Phenotyping System

Abstract: 7Background and aims 8

Cited by 7 publications

References 31 publications

Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform

Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform

Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

Phenotyping of Weedy Rice to Assess Root Characteristics Associated with Allelopathy

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