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AcceptedCC BY V4.0, Open Access
AcceptedCC BY V4.0, Open
Journal article
Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa
Plant Biotechnology Journal (Online), Vol.20(7), pp.1298-1310
07/2022
PMID: 35278263
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Source: InCites
Abstract
Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.
Details
- Title
- Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa
- Creators
- Xu Cai - Chinese Academy of Agricultural SciencesRunmao Lin - Chinese Academy of Agricultural SciencesJianli Liang - Chinese Academy of Agricultural SciencesGraham J King - Southern Cross UniversityJian Wu - Chinese Academy of Agricultural SciencesXiaowu Wang - Chinese Academy of Agricultural Sciences
- Publication Details
- Plant Biotechnology Journal (Online), Vol.20(7), pp.1298-1310
- Publisher
- Wiley-Blackwell Publishing Ltd.
- Grant note
- This work was funded by the National Key Research and Development Program of China (2021YFF1000101), the National Natural Science Foundation of China (grant no. 32072593), the National Natural Science Foundation of China (grant no. 32072594), the Central Public-Interest Scientific Institution Basal Research Fund (Y2020PT21) and the Agricultural Science and Technology Innovation Program (ASTIP). The research was conducted in the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China and the Sino-Dutch Joint Lab of Horticultural Genomics Technology.
- Identifiers
- 991013002493202368
- Copyright
- This article is protected by copyright. All rights reserved. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited (https://creativecommons.org/licenses/by/4.0/).
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article