Skip to Main content Skip to Navigation
Journal articles

Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

Abstract : Background: Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbredspecific regions remain to be elucidated. Results: De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups. Conclusions: We highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.
Document type :
Journal articles
Complete list of metadata

Cited literature [80 references]  Display  Hide  Download

https://hal.inrae.fr/hal-02625253
Contributor : Migration Prodinra <>
Submitted on : Tuesday, May 26, 2020 - 1:55:35 PM
Last modification on : Friday, May 7, 2021 - 3:36:31 AM

File

2018_Darracq_BMC_Genom_1.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Citation

Aude Darracq, Clémentine Vitte, Stephane Nicolas, Jorge Duarte, Jean-Philippe Pichon, et al.. Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12864-018-4490-7⟩. ⟨hal-02625253⟩

Share

Metrics

Record views

65

Files downloads

93