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3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architect...

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Autores principales: Tross, Michael C., Gaillard, Mathieu, Zwiener, Mackenzie, Miao, Chenyong, Grove, Ryleigh J., Li, Bosheng, Benes, Bedrich, Schnable, James C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710048/
https://www.ncbi.nlm.nih.gov/pubmed/35036135
http://dx.doi.org/10.7717/peerj.12628
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author Tross, Michael C.
Gaillard, Mathieu
Zwiener, Mackenzie
Miao, Chenyong
Grove, Ryleigh J.
Li, Bosheng
Benes, Bedrich
Schnable, James C.
author_facet Tross, Michael C.
Gaillard, Mathieu
Zwiener, Mackenzie
Miao, Chenyong
Grove, Ryleigh J.
Li, Bosheng
Benes, Bedrich
Schnable, James C.
author_sort Tross, Michael C.
collection PubMed
description Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.
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spelling pubmed-87100482022-01-14 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves Tross, Michael C. Gaillard, Mathieu Zwiener, Mackenzie Miao, Chenyong Grove, Ryleigh J. Li, Bosheng Benes, Bedrich Schnable, James C. PeerJ Agricultural Science Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops. PeerJ Inc. 2021-12-22 /pmc/articles/PMC8710048/ /pubmed/35036135 http://dx.doi.org/10.7717/peerj.12628 Text en ©2021 Tross et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Tross, Michael C.
Gaillard, Mathieu
Zwiener, Mackenzie
Miao, Chenyong
Grove, Ryleigh J.
Li, Bosheng
Benes, Bedrich
Schnable, James C.
3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title_full 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title_fullStr 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title_full_unstemmed 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title_short 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
title_sort 3d reconstruction identifies loci linked to variation in angle of individual sorghum leaves
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710048/
https://www.ncbi.nlm.nih.gov/pubmed/35036135
http://dx.doi.org/10.7717/peerj.12628
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