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Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource....

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Autores principales: Xu, Yuanyuan, Xing, Miaomiao, Song, Lixiao, Yan, Jiyong, Lu, Wenjiang, Zeng, Aisong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695497/
https://www.ncbi.nlm.nih.gov/pubmed/34956251
http://dx.doi.org/10.3389/fpls.2021.726084
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author Xu, Yuanyuan
Xing, Miaomiao
Song, Lixiao
Yan, Jiyong
Lu, Wenjiang
Zeng, Aisong
author_facet Xu, Yuanyuan
Xing, Miaomiao
Song, Lixiao
Yan, Jiyong
Lu, Wenjiang
Zeng, Aisong
author_sort Xu, Yuanyuan
collection PubMed
description Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage ‘TO1000.’ Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14–0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
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spelling pubmed-86954972021-12-24 Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.) Xu, Yuanyuan Xing, Miaomiao Song, Lixiao Yan, Jiyong Lu, Wenjiang Zeng, Aisong Front Plant Sci Plant Science Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage ‘TO1000.’ Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14–0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis. Frontiers Media S.A. 2021-12-09 /pmc/articles/PMC8695497/ /pubmed/34956251 http://dx.doi.org/10.3389/fpls.2021.726084 Text en Copyright © 2021 Xu, Xing, Song, Yan, Lu and Zeng. 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
Xu, Yuanyuan
Xing, Miaomiao
Song, Lixiao
Yan, Jiyong
Lu, Wenjiang
Zeng, Aisong
Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title_full Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title_fullStr Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title_full_unstemmed Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title_short Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)
title_sort genome-wide analysis of simple sequence repeats in cabbage (brassica oleracea l.)
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695497/
https://www.ncbi.nlm.nih.gov/pubmed/34956251
http://dx.doi.org/10.3389/fpls.2021.726084
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