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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-9606697 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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