Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize.,Nature Communications

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Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize.
Nature Communications ( IF 14.7 ) Pub Date : 2020-01-07 , DOI: 10.1038/s41467-019-14023-2
Changsheng Li _{1,

2} , Xiaoli Xiang _{2,

3} , Yongcai Huang _{2,

4} , Yong Zhou ₂ , Dong An ₁ , Jiaqiang Dong ₅ , Chenxi Zhao ₆ , Hongjun Liu ₇ , Yubin Li ₈ , Qiong Wang ₂ , Chunguang Du ₉ , Joachim Messing ₅ , Brian A Larkins ₁₀ , Yongrui Wu ₂ , Wenqin Wang ₁

Affiliation

School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, China.
University of the Chinese Academy of Sciences, Beijing, 100049, China.
Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
Department of Biology, Montclair State University, Montclair, NJ, 07043, USA.
School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.

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.

更新日期：2020-01-07

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