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Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize

Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we repo...

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Autores principales: Li, Changsheng, Xiang, Xiaoli, Huang, Yongcai, Zhou, Yong, An, Dong, Dong, Jiaqiang, Zhao, Chenxi, Liu, Hongjun, Li, Yubin, Wang, Qiong, Du, Chunguang, Messing, Joachim, Larkins, Brian A., Wu, Yongrui, Wang, Wenqin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6946643/
https://www.ncbi.nlm.nih.gov/pubmed/31911615
http://dx.doi.org/10.1038/s41467-019-14023-2
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author Li, Changsheng
Xiang, Xiaoli
Huang, Yongcai
Zhou, Yong
An, Dong
Dong, Jiaqiang
Zhao, Chenxi
Liu, Hongjun
Li, Yubin
Wang, Qiong
Du, Chunguang
Messing, Joachim
Larkins, Brian A.
Wu, Yongrui
Wang, Wenqin
author_facet Li, Changsheng
Xiang, Xiaoli
Huang, Yongcai
Zhou, Yong
An, Dong
Dong, Jiaqiang
Zhao, Chenxi
Liu, Hongjun
Li, Yubin
Wang, Qiong
Du, Chunguang
Messing, Joachim
Larkins, Brian A.
Wu, Yongrui
Wang, Wenqin
author_sort Li, Changsheng
collection PubMed
description Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is assembled from single-molecule, real-time shotgun sequencing reads collinear with an optical map. We achieve a N50 contig length of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73 and 1.48 Mb for Mo17. To characterize Mo2s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F(2) population derived from crossing K0326Y and W64Ao2. RNA-seq analysis of QPM and o2 endosperms reveals a group of differentially expressed genes that coincide with Mo2 QTLs, suggesting a potential role in vitreous endosperm formation.
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spelling pubmed-69466432020-01-09 Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize Li, Changsheng Xiang, Xiaoli Huang, Yongcai Zhou, Yong An, Dong Dong, Jiaqiang Zhao, Chenxi Liu, Hongjun Li, Yubin Wang, Qiong Du, Chunguang Messing, Joachim Larkins, Brian A. Wu, Yongrui Wang, Wenqin Nat Commun Article Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is assembled from single-molecule, real-time shotgun sequencing reads collinear with an optical map. We achieve a N50 contig length of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73 and 1.48 Mb for Mo17. To characterize Mo2s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F(2) population derived from crossing K0326Y and W64Ao2. RNA-seq analysis of QPM and o2 endosperms reveals a group of differentially expressed genes that coincide with Mo2 QTLs, suggesting a potential role in vitreous endosperm formation. Nature Publishing Group UK 2020-01-07 /pmc/articles/PMC6946643/ /pubmed/31911615 http://dx.doi.org/10.1038/s41467-019-14023-2 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Li, Changsheng
Xiang, Xiaoli
Huang, Yongcai
Zhou, Yong
An, Dong
Dong, Jiaqiang
Zhao, Chenxi
Liu, Hongjun
Li, Yubin
Wang, Qiong
Du, Chunguang
Messing, Joachim
Larkins, Brian A.
Wu, Yongrui
Wang, Wenqin
Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title_full Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title_fullStr Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title_full_unstemmed Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title_short Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
title_sort long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6946643/
https://www.ncbi.nlm.nih.gov/pubmed/31911615
http://dx.doi.org/10.1038/s41467-019-14023-2
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