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Published (Version of record)CC BY-NC V4.0, Open Access
Published (Version of record)CC BY-NC V4.0, Open
Journal article
Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate
DNA Research, Vol.28(5), pp.1-11
03/09/2021
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Abstract
Abstract Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.
Details
- Title
- Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate
- Creators
- Haijiang Liu - Huazhong Agricultural UniversityXiaojuan Li - Huazhong Agricultural UniversityQianwen Zhang - Shanghai Jiao Tong UniversityPan Yuan - Huazhong Agricultural UniversityLei Liu - Southern Cross UniversityGraham J King - Southern Cross Plant Science, Southern Cross UniversityGuangda Ding - Huazhong Agricultural UniversitySheliang Wang - Huazhong Agricultural UniversityHongmei Cai - Huazhong Agricultural UniversityChuang Wang - Huazhong Agricultural UniversityFangsen Xu - Huazhong Agricultural UniversityLei Shi - Huazhong Agricultural University
- Publication Details
- DNA Research, Vol.28(5), pp.1-11
- Publisher
- Oxford University Press
- Grant note
- This work was supported by the National Key R&D Program of China (Grant No. 2017YFD0200200) and the National Nature Science Foundation of China (Grant No. 32172662). We also acknowledge the Applied Basic Research Fronts Program of Wuhan city (Grant No. 2018020401011302) and the Natural and Fundamental Research Funds for the Central Universities of China (Grant No. 2662019PY013).
- Identifiers
- 991012968350002368
- Copyright
- © The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
- Academic Unit
- Faculty of Science and Engineering; School of Environment, Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article