Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

Seed oil content (SOC) is a highly important and complex trait in oil crops. Here, we decipher the genetic basis of natural variation in SOC of Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) that control...

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Main Authors: Tang, Shan, Zhao, Hu, Lu, Shaoping, Yu, Liangqian, Zhang, Guofang, Zhang, Yuting, Yang, Qing-Yong, Zhou, Yongming, Wang, Xuemin, Ma, Wei, Xie, Weibo, Guo, Liang
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2021
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Online Access:https://hdl.handle.net/10356/146610
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-1466102023-02-28T17:08:44Z Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus Tang, Shan Zhao, Hu Lu, Shaoping Yu, Liangqian Zhang, Guofang Zhang, Yuting Yang, Qing-Yong Zhou, Yongming Wang, Xuemin Ma, Wei Xie, Weibo Guo, Liang School of Biological Sciences Science::Biological sciences Brassica Napus Seed Oil Content Seed oil content (SOC) is a highly important and complex trait in oil crops. Here, we decipher the genetic basis of natural variation in SOC of Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) that control SOC in eight environments, evaluated the effect of each QTL on SOC, and analyzed selection in QTL regions during breeding. Six-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds. A gene prioritization framework, POCKET (prioritizing the candidate genes by incorporating information on knowledge-based gene sets, effects of variants, genome-wide association studies, and transcriptome-wide association studies), was implemented to determine the causal genes in the QTL regions based on multi-omic datasets. A pair of homologous genes, BnPMT6s, in two QTLs were identified and experimentally demonstrated to negatively regulate SOC. This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of B. napus and other oil crops. Accepted version 2021-03-03T02:27:22Z 2021-03-03T02:27:22Z 2021 Journal Article Tang, S., Zhao, H., Lu, S., Yu, L., Zhang, G., Zhang, Y., ... Guo, L. (2021). Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Molecular Plant, 14(3), 470-487. doi:10.1016/j.molp.2020.12.003 1674-2052 0000-0001-7191-5062 https://hdl.handle.net/10356/146610 10.1016/j.molp.2020.12.003 33309900 2-s2.0-85099239596 3 14 470 487 en Molecular Plant © 2020 The Author(s) (Published by the Molecular Plant Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and IPPE, SIBS, CAS). All rights reserved. This paper was published in Molecular Plant and is made available with permission of The Author(s) (Published by the Molecular Plant Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and IPPE, SIBS, CAS). application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Science::Biological sciences
Brassica Napus
Seed Oil Content
spellingShingle Science::Biological sciences
Brassica Napus
Seed Oil Content
Tang, Shan
Zhao, Hu
Lu, Shaoping
Yu, Liangqian
Zhang, Guofang
Zhang, Yuting
Yang, Qing-Yong
Zhou, Yongming
Wang, Xuemin
Ma, Wei
Xie, Weibo
Guo, Liang
Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
description Seed oil content (SOC) is a highly important and complex trait in oil crops. Here, we decipher the genetic basis of natural variation in SOC of Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) that control SOC in eight environments, evaluated the effect of each QTL on SOC, and analyzed selection in QTL regions during breeding. Six-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds. A gene prioritization framework, POCKET (prioritizing the candidate genes by incorporating information on knowledge-based gene sets, effects of variants, genome-wide association studies, and transcriptome-wide association studies), was implemented to determine the causal genes in the QTL regions based on multi-omic datasets. A pair of homologous genes, BnPMT6s, in two QTLs were identified and experimentally demonstrated to negatively regulate SOC. This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of B. napus and other oil crops.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Tang, Shan
Zhao, Hu
Lu, Shaoping
Yu, Liangqian
Zhang, Guofang
Zhang, Yuting
Yang, Qing-Yong
Zhou, Yongming
Wang, Xuemin
Ma, Wei
Xie, Weibo
Guo, Liang
format Article
author Tang, Shan
Zhao, Hu
Lu, Shaoping
Yu, Liangqian
Zhang, Guofang
Zhang, Yuting
Yang, Qing-Yong
Zhou, Yongming
Wang, Xuemin
Ma, Wei
Xie, Weibo
Guo, Liang
author_sort Tang, Shan
title Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
title_short Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
title_full Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
title_fullStr Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
title_full_unstemmed Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus
title_sort genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in brassica napus
publishDate 2021
url https://hdl.handle.net/10356/146610
_version_ 1759854347911430144