Huafeng Liu
Joram Kiriga Waititu
Ying Sun
Huan Wang
Junjie Fu
Yanhui Chen
Jun Liu
Lixia Ku
Xiliu Cheng
a Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
b College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China;
c Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Funds: We thank Ms. Lina Zhang from the Core Facility Platform, Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), for managing the high-throughput genomic DNA extraction appliances. This work was supported by grants from the Ministry of Science and Technology of China (2016YFD0101000 and 2016YFD0101001) and the Natural Science Foundation of China (31901595).
Received Date: 2021-04-20
Accepted Date:2021-07-17
Rev Recd Date:2021-07-11
Publish Date:2021-11-20
Abstract
Abstract
In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing (TEAseq). Using TEAseq, we systemically profiled the Dissociation (Ds) insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background. The Ac-containing individuals were excluded for getting rid of the potential somatic insertions. We characterized 35,696 germinal Ds insertions tagging 10,323 genes, representing approximately 23.3% of the total genes in the maize genome. The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci, and insertions occurred preferentially in gene body regions. Furthermore, we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development. We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations. Overall, our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.Keywords: Maize,
Zea mays,
Insertion identification,
Ds transposon,
Mutant library,
Next-generation sequencing,
Functional genomics
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