Article Highlight | 15-Jan-2024

Revolutionizing crop efficiency: Innovations in 2D root phenotyping uncover genetic keys to enhanced agricultural productivity

Plant Phenomics

Root system architecture (RSA) plays a pivotal role in plant yield, shaped by evolution and ecological adaptations for effective nutrient and water uptake and abiotic stress resistance. Current research focuses on utilizing genetic variation in RSA to enhance agricultural productivity, with significant progress in identifying genes like Pstol1 that improve nutrient acquisition and yield in various crops. However, RSA is complex and environmentally responsive, posing challenges to its study and application. Major issues include the limitations of in situ phenotyping techniques and the need to better understand the genetic and environmental influences on RSA. Therefore, the development of advanced phenotyping methods and a more profound exploration of the genetic underpinnings of RSA are important for improving crop efficiency and yield.

In September 2023, Plant Phenomics published a research article entitled by “Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits”.

This study innovated the 2D root growth pouch system, root imaging, and image processing to improve the accuracy of root trait calculations. It employed a revised germination method using vertically stacked, water-soaked paper to maintain root initiation angles and minimize changes in root architecture. By switching from traditional blue to black filter paper, this study significantly increased root-to-background contrast and improved the accuracy of root trait segmentation algorithms. Additionally, to avoid overestimation of root traits caused by water menisci, the study compared air-imaged roots with those imaged underwater and found that underwater imaging provided more accurate trait measurements. This method also addressed the issue of small white particles being miscounted as root tips by implementing an image segmentation and cleaning pipeline that significantly improved the correlation between manual and calculated root tip counts. Broad-sense heritability calculations indicated moderately high to high reproducibility of root trait measurements. The study also modified the pouch design by replacing the solid backing with a perforated sheet and aerating the nutrient solution, which notably increased root growth.

Population structure analysis suggested a correlation between soybean genetic variation and country of origin. Extensive phenotypic variation was observed among soybean genotypes, and GWAS identified numerous loci related to root traits, with several "hotspots" for multiple trait associations. Promising candidate genes were identified near the GWAS peaks, and structural variations in the promoter regions of some of these genes were investigated. The distribution of RSA traits among subpopulations showed patterns aligned with country of origin, indicating genetic and environmental influences on root traits. Phenotypic validation of root COPM in a potting mix affirmed the representativeness of hydroponic pouch system results, highlighting the study's methodological robustness and its implications for understanding and manipulating root architecture for agricultural improvement.

Overall, this research offers a promising avenue for future breeding programs focused on developing more resilient and efficient crops, with the potential for significant agricultural and environmental benefits.




Rahul Chandnani1,2, Tongfei Qin1, Heng Ye3, Haifei Hu4,5, Karim Panjvani1, Mutsutomo Tokizawa1, Javier Mora Macias1, Alma Armenta Medina1, Karine C. Bernardino6, Pierre-Luc Pradier1, Pankaj Banik1, Ashlyn Mooney1, Jurandir V. Magalhaes6, Henry T. Nguyen3*, and Leon V.  Kochian 1*


1Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada.  

2NRGene Canada, 110 Research Dr Suite 101, Saskatoon, SK, Canada.  

3Division of Plant Sciences and Technology, University of Missouri, Columbia, MO  65211, USA.  

4School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia.

5Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong, China.

6Embrapa Maize and Sorghum, Sete Lagoas, Brazil.

About Henry T. Nguyen & Leon V.  Kochian

Henry T. Nguyen: Henry Nguyen has a research program in molecular genetics, genomics, and biotechnology. His research interest is abiotic stress adaptation and tolerance in plants with a current emphasis on soybean. Specific research areas include:

  1. Molecular genetics and integrated functional genomics of plant adaptation to stress environments (drought, flooding, salinity and high temperature).
  2. Application of contemporary genetic and genomic technologies to studying genome variation and inheritance of complex traits in plants (stress adaptation, disease resistance, and value-added seed composition).
  3. Development and application of genomics-assisted breeding strategies for crop improvement.

Leon V.  Kochian: His research program focuses on the molecular physiology and genetics of plant mineral nutrition and root biology with emphasis on plant responses to abiotic stresses in the soil.

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