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QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp

Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds a...

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Autores principales: Seki, Kousuke, Toda, Yosuke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9606697/
https://www.ncbi.nlm.nih.gov/pubmed/36311127
http://dx.doi.org/10.3389/fpls.2022.949470
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author Seki, Kousuke
Toda, Yosuke
author_facet Seki, Kousuke
Toda, Yosuke
author_sort Seki, Kousuke
collection PubMed
description Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds are small, a manual phenotypic determination required for a genetic dissection of such traits is challenging. In this study, we built and applied an instance segmentation-based seed morphology quantification pipeline to measure traits in seeds generated from a cross between the domesticated oilseed type cultivar ‘Oilseed’ and the wild species ‘UenoyamaMaruba’ in an automated manner. Quantitative trait locus (QTL) mapping following ddRAD-seq revealed 11 QTLs linked to 7 seed traits (area, width, length, length-to-width ratio, eccentricity, perimeter length, and circularity). Remarkably, the three QTLs with the highest LOD scores, qLWR-3.1, qECC-3.1, and qCIR-3.1, for length-to-width ratio, eccentricity, and circularity, respectively, mapped to linkage group 3 (LG3) around 161.5 to 214.6 Mb, a region previously reported to be associated with domestication traits from wild species. These results suggest that the oilseed cultivar harbors genes acquired during domestication to control seed shape in this genomic region. This study also provides genetic evidence that domestication arose, at least in part, by selection for the oilseed type from wild species and demonstrates the effectiveness of image-based phenotyping to accelerate discoveries of the genetic basis for small morphological features such as seed size and shape.
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spelling pubmed-96066972022-10-28 QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp Seki, Kousuke Toda, Yosuke Front Plant Sci Plant Science Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds are small, a manual phenotypic determination required for a genetic dissection of such traits is challenging. In this study, we built and applied an instance segmentation-based seed morphology quantification pipeline to measure traits in seeds generated from a cross between the domesticated oilseed type cultivar ‘Oilseed’ and the wild species ‘UenoyamaMaruba’ in an automated manner. Quantitative trait locus (QTL) mapping following ddRAD-seq revealed 11 QTLs linked to 7 seed traits (area, width, length, length-to-width ratio, eccentricity, perimeter length, and circularity). Remarkably, the three QTLs with the highest LOD scores, qLWR-3.1, qECC-3.1, and qCIR-3.1, for length-to-width ratio, eccentricity, and circularity, respectively, mapped to linkage group 3 (LG3) around 161.5 to 214.6 Mb, a region previously reported to be associated with domestication traits from wild species. These results suggest that the oilseed cultivar harbors genes acquired during domestication to control seed shape in this genomic region. This study also provides genetic evidence that domestication arose, at least in part, by selection for the oilseed type from wild species and demonstrates the effectiveness of image-based phenotyping to accelerate discoveries of the genetic basis for small morphological features such as seed size and shape. Frontiers Media S.A. 2022-10-13 /pmc/articles/PMC9606697/ /pubmed/36311127 http://dx.doi.org/10.3389/fpls.2022.949470 Text en Copyright © 2022 Seki and Toda https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Seki, Kousuke
Toda, Yosuke
QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title_full QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title_fullStr QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title_full_unstemmed QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title_short QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp
title_sort qtl mapping for seed morphology using the instance segmentation neural network in lactuca spp
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9606697/
https://www.ncbi.nlm.nih.gov/pubmed/36311127
http://dx.doi.org/10.3389/fpls.2022.949470
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