Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize
Background: Maize 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. Results In 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. Conclusions This 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.
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BioMed Central
2017
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Genetic Recombination, GWAS, Transposable Elements, Non-Redundant Tes (NRTE), ADAPTATION, CROSS-BREEDING, GENOMES, MAIZE, NUCLEOTIDE SEQUENCE, CHROMOSOME MAPPING, |
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dig-cimmyt-10883-193372023-11-28T15:15:27Z Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize Xianjun Lai Schnable, J.C. Zhengqiao Liao Jie Xu Gengyun Zhang Chuan Li Erliang Hu Tingzhao Rong Yunbi Xu Yanli Lu AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING Background: Maize 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. Results In 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. Conclusions This 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. 2018-03-23T22:12:46Z 2018-03-23T22:12:46Z 2017 Article 1471-2164 https://hdl.handle.net/10883/19337 10.1186/s12864-017-4103-x English https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM1_ESM.xlsx https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM2_ESM.tif https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM3_ESM.tif https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM4_ESM.tif https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM5_ESM.tif https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM6_ESM.tif https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-017-4103-x/MediaObjects/12864_2017_4103_MOESM7_ESM.tif CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose. Open Access PDF London BioMed Central 702 18 BMC Genomics |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING Xianjun Lai Schnable, J.C. Zhengqiao Liao Jie Xu Gengyun Zhang Chuan Li Erliang Hu Tingzhao Rong Yunbi Xu Yanli Lu Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
description |
Background: Maize 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. Results In 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. Conclusions This 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. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genetic Recombination GWAS Transposable Elements Non-Redundant Tes (NRTE) ADAPTATION CROSS-BREEDING GENOMES MAIZE NUCLEOTIDE SEQUENCE CHROMOSOME MAPPING |
author |
Xianjun Lai Schnable, J.C. Zhengqiao Liao Jie Xu Gengyun Zhang Chuan Li Erliang Hu Tingzhao Rong Yunbi Xu Yanli Lu |
author_facet |
Xianjun Lai Schnable, J.C. Zhengqiao Liao Jie Xu Gengyun Zhang Chuan Li Erliang Hu Tingzhao Rong Yunbi Xu Yanli Lu |
author_sort |
Xianjun Lai |
title |
Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
title_short |
Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
title_full |
Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
title_fullStr |
Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
title_full_unstemmed |
Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
title_sort |
genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize |
publisher |
BioMed Central |
publishDate |
2017 |
url |
https://hdl.handle.net/10883/19337 |
work_keys_str_mv |
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1787232938850516992 |