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 modifier s ( Mo2 s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we r...

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Bibliographic Details
Published in:Nature communications 2020-01, Vol.11 (1), p.17-17, Article 17
Main Authors: 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
Format: Article
Language:English
Subjects:
38/39
45/23
49/91
631/208/212
631/449/1870
631/449/711
631/61/447/8
Annotations
Chromosome Mapping
Chromosomes
Corn
Cultivars
Developing countries
Endosperm
Endosperm - genetics
Gene Expression Regulation, Plant
Genes
Genome, Plant
Genomes
Genomics
Humanities and Social Sciences
Kernels
LDCs
Lysine
multidisciplinary
Mutants
Mutation
Nucleotide sequence
Phenotypes
Plant Proteins - genetics
Proteins
Quantitative Trait Loci
Ribonucleic acid
RNA
Science
Science (multidisciplinary)
Zea mays - genetics
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Summary:Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifier s ( Mo2 s) 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 Mo2 s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F 2 population derived from crossing K0326Y and W64A o2 . 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. The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-019-14023-2