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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 inbred-specific 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. Electronic supplementary material The online version of this article (10.1186/s12864-018-4490-7) contains supplementary material, which is available to authorized users.

Recent advances in high-throughput sequencing technologies have triggered a shift toward single-nucleotide polymorphism (SNP) markers. A systematic bias can be introduced if SNPs are ascertained in a small panel of genotypes and then used for characterizing a larger population (ascertainment bias). With the objective of evaluating a potential ascertainment bias of the Illumina MaizeSNP50 array with respect to elite European maize dent and flint inbred lines, we compared the genetic diversity among these materials based on 731 amplified fragment length polymorphisms (AFLPs), 186 simple sequence repeats (SSRs), 41,434 SNPs of the MaizeSNP50 array (SNP-A), and two subsets of it, i.e., 30,068 Panzea (SNP-P) and 11,366 Syngenta markers (SNP-S). We evaluated the bias effects on major allele frequency, allele number, gene diversity, modified Roger's distance (MRD), and on molecular variance (AMOVA). We revealed ascertainment bias in SNP-A, compared to AFLPs and SSRs. It affected especially European flint lines analyzed with markers (SNP-S) specifically developed to maximize differences among North American dent germplasm. The bias affected all genetic parameters, but did not substantially alter the relative distances between inbred lines within groups. For these reasons, we conclude that the SNP markers of the MaizeSNP50 array can be employed for breeding purposes in the investigated material. However, attention should be paid in case of comparisons between genotypes belonging to different heterotic groups. In this case, it is advisable to prefer a marker subset with potentially low ascertainment bias, like in our case the SNP-P marker set.

Early vigor, earliness and cold tolerance are the main potential contributions of European maize (Zea mays L.) for breeding programs for adaptation to areas with short growing seasons and cold springs. The objective of this research was to determine the potential contributions of populations from different European regions to breeding for adaptation. Six Spanish and six French maize populations differing on variability for earliness, vigor and cold tolerance were crossed in a complete diallel without reciprocals. The populations and their crosses were evaluated in the field and in a cold chamber. Minimum temperatures were the main environmental trait affecting genotype × environment interaction, probably due to the cold sensitivity of the genotypes with the best performance in the field. The best population cross, based on specific heterosis for adaptation-related traits in the field, was Viana × Rastrojero, but this cross was cold sensitive. Tuy × Lazcano should be the best choice for a breeding program for adaptation, based on performance in the field and cold tolerance. As conclusions, there was variability for earliness, vigor and cold tolerance among the populations and crosses involved in this study, being tolerant to cold conditions the populations with medium growing cycle originated in areas with short growing seasons. The highest yielding crosses were cold sensitive., Research supported by the Ministry of Science and Technology (Ref. HF1999-0138), the Ministère de l’Education Nationale et de la Recherche, the Committee for Science and Technology of Spain (Project AGL2004-06776), the Autonomous government of Galicia (PGIDIT04RAG403006PR), the Excma. Diputación Provincial de Pontevedra, and the European Union (RESGEN 88 CT96).