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

Changsheng Li, Xiaoli Xiang, Yongcai Huang, Yong Zhou, Dong An, Jiaqiang Dong, Chenxi Zhao, Hongjun Liu, Yubin Li, Qiong Wang, Chunguang Du, Joachim Messing, Brian A. Larkins, Yongrui Wu () and Wenqin Wang ()
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Changsheng Li: Shanghai Jiao Tong University
Xiaoli Xiang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Yongcai Huang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Yong Zhou: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Dong An: Shanghai Jiao Tong University
Jiaqiang Dong: Rutgers University
Chenxi Zhao: University of Chinese Academy of Sciences
Hongjun Liu: Shandong Agricultural University
Yubin Li: Qingdao Agricultural University
Qiong Wang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Chunguang Du: Montclair State University
Joachim Messing: Rutgers University
Brian A. Larkins: University of Arizona
Yongrui Wu: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Wenqin Wang: Shanghai Jiao Tong University

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract 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 F2 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.

Date: 2020
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DOI: 10.1038/s41467-019-14023-2

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