Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize

BMC Genomics

Research Article

Gengyun Zhang¹  James C. Schnable²  Yunbi Xu³  Jie Xu⁴  Yanli Lu⁴  Chuan Li⁴  Erliang Hu⁴  Xianjun Lai⁴  Tingzhao Rong⁴  Zhengqiao Liao⁴ 

[1] Bejing Genomics Institute (BGI)-Shenzhen, 518083, Shenzhen, China;Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583, Lincoln, NE, USA;Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian, 100081, Beijing, China;International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56130, Texcoco, CP, México;Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China;

关键词: Adaptation;    Genetic recombination;    GWAS;    Maize;    Transposable elements;    Non-redundant TEs (NRTE);   

DOI  :  10.1186/s12864-017-4103-x

 received in 2016-06-02, accepted in 2017-08-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMaize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines.ResultsIn total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent.ConclusionsThis study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments.

【 授权许可】

CC BY   
© The Author(s). 2017