Abstract
BackgroundMaize 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 inbred-specific regions remain to be elucidated.ResultsDe 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.ConclusionsWe 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.
Highlights
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
Because F2 whole genome assembly (WGA) covers 64.8% of the F2 genome and genes typically represent less than 5% of a maize genome, our F2 WGA clearly extends beyond the gene space
Extraction of PAV sequences allowed us to make a detailed analysis of PAV content and breakpoints, highlighting the possible role of Microhomology mediated end joining (MMEJ)-type Double strand break repair (DSBR) in PAV formation and discovering 395 new genes with transcriptional support
Summary
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. CNVs are considered as major players in driving human evolution, genetic diversity between individuals, and are held responsible for a large number of traits [3] They are implicated in genetic disorders [4], but can have a beneficial phenotypic effect [5]. Presence Absence Variants (PAVs), i.e. sequences that are present in one genome and absent in another, are often considered as extreme forms of CNVs [1]. It is not yet known whether PAVs and CNVs share the same genomic features. PAVs may be original both in their evolutionary dynamics and in their biological impact
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