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A common resequencing-based genetic marker data set for global maize diversity.

Marcin W Grzybowski1,2,3, Ravi V Mural1,2, Gen Xu1,2

  • 1Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.

The Plant Journal : for Cell and Molecular Biology
|January 27, 2023
PubMed
Summary
This summary is machine-generated.

This study unifies maize genetic data, creating a comprehensive variant set for enhanced analysis. This resource improves the identification of key genes and tracks allele frequency changes in global maize populations.

Keywords:
GWASdiversity panelgenetic markersmaizenatural genetic variatonwhole-genome resequencing

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Area of Science:

  • Genetics
  • Genomics
  • Plant Science

Background:

  • Maize (Zea mays ssp. mays) exhibits extensive genetic and phenotypic diversity.
  • Whole-genome resequencing projects identify millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels).
  • Inconsistent analytical pipelines and reference genomes hinder data reuse across maize genetic diversity studies.

Purpose of the Study:

  • To generate a unified marker set from diverse maize resequencing data.
  • To enhance the ability to analyze genetic variation within and between maize populations.
  • To facilitate new biological questions and data integration in maize genetics.

Main Methods:

  • Combined resequencing data from 1276 published and 239 new maize samples.
  • Generated a unified marker set of approximately 366 million segregating variants.
  • Scored high-confidence variants across crop wild relatives, landraces, and diverse breeding lines.

Main Results:

  • Developed a unified variant set of ~366 million segregating and ~46 million high-confidence variants.
  • Demonstrated increased power to identify known causal flowering-time genes.
  • Showcased the potential to track allele frequency changes across global maize distribution.

Conclusions:

  • The unified marker set overcomes limitations of disparate datasets for maize genetic diversity research.
  • This resource improves the power of genetic analyses and facilitates evolutionary studies.
  • Enables tracking of functional allele frequency shifts in modern maize populations globally.