European maize genomes unveil pan-genomic dynamics of repeats and genes

Haberer, Georg; Bauer, Eva; Kamal, Nadia; Gundlach, Heidrun; Fischer, Iris; Seidel, Michael; Spannagl, Manuel; Marcon, Caroline; Ruban, Alevtina; Urbany, Claude; Nemri, Adnane; Hochholdinger, Frank; Ouzunova, Milena; Houben, Andreas; Schön, Chris‐Carolin; Mayer, Klaus

doi:10.1101/766444

Cited by 7 publications

(8 citation statements)

References 96 publications

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“…Molecular analyses discovered that traditional flint corn (Zea mays var. indurata) populations of Northern Europe have major contributions from North American flints, which were introduced to Europe during the sixteenth century [5,6]. Adaptations to the North and Central European climate included the development of a shorter growing cycle to avoid cold temperatures during the growth period and as another strategy, higher tolerance to cold temperatures [7].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic diversity in seedling roots of European flint maize in response to cold

et al. 2020

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Background: Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resource for genes and alleles conferring cold tolerance which they acquired during their adaptation to the agroecological conditions in Europe. Results: Based on a phenotyping experiment of 276 doubled haploid lines derived from the European flint landrace "Petkuser Ferdinand Rot" diverging for cold tolerance, we selected 21 of these lines for an RNA-seq experiment. The different genotypes showed highly variable transcriptomic responses to cold. We identified 148, 3254 and 563 genes differentially expressed with respect to cold treatment, cold tolerance and growth rate at cold, respectively. Gene ontology (GO) term enrichment demonstrated that the detoxification of reactive oxygen species is associated with cold tolerance, whereas amino acids might play a crucial role as antioxidant precursors and signaling molecules. Conclusion: Doubled haploids representing a European maize flint landrace display genotype-specific transcriptome patterns associated with cold response, cold tolerance and seedling growth rate at cold. Identification of cold regulated genes in European flint germplasm, could be a starting point for introgressing such alleles in modern breeding material for maize improvement.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic diversity in seedling roots of European flint maize in response to cold

et al. 2020

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“…However, additional sites with small arrangements of knobs conserved in flint and dent lines were observed. This study also showed that the knob sequences could affect genes surrounded by them, decreasing their expression level (8).…”

Section: Genome Size Does Not Affect Maize Flowering Time Negative Values Formentioning

confidence: 59%

A heterochromatic knob reducing the flowering time in maize

Mlr

et al. 2021

Preprint

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Maize flowering time is an important agronomic trait, which is associated with variations in the genome size and heterochromatic knobs content. We integrated three steps to show this association. Firstly, we selected inbred lines varying for heterochromatic knob composition at specific sites in the homozygous state. Then, we produced heterozygous hybrids for knobs, which allow us to carry out genetic mapping. Second, we measured the genome size and flowering time for all materials. Knob composition did not affect the genome size. Finally, we developed an association study and identified a knob marker on chromosome 9 showing the strongest association with flowering time. Indeed, modeling allele substitution and dominance effects could offer only one heterochromatic knob locus that could affect flowering time, making it earlier rather than the knob composition.

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“…NGS-based genotyping has become a highly cost-effective and efficient agrigenomics tool in both model and non-model crop species including those with large and complex genomes (Cao et al 2011;Cheng et al 2019;Haberer et al 2019;Lachagari et al 2019). As NGS assembly algorithms and data types have improved, whole-genome sequencing (WGS) has been widely used for de novo assembly (Schatz et al 2014;Zapata et al 2016;Clavijo et al 2017;IWGSC 2018;Haberer et al 2019), as well as for re-sequencing, transcriptome sequencing (RNAseq) and epigenetic sequencing. When combined, these approaches allow experimental annotation of genes, their transcriptional variants and their transcriptional control (ENCODE Consortium 2012).…”

Section: Application Of Genomics To Mppsmentioning

confidence: 99%

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding. Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a

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European maize genomes unveil pan-genomic dynamics of repeats and genes

Abstract: The exceptional diversity of maize (Zea mays)

Cited by 7 publications

References 96 publications

Transcriptomic diversity in seedling roots of European flint maize in response to cold

Transcriptomic diversity in seedling roots of European flint maize in response to cold

A heterochromatic knob reducing the flowering time in maize

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

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