Plastome Genomics in South American Maize Landraces: Chloroplast Lineages Parallel the Geographical Structuring of Nuclear Gene Pools

This study is linked to the project PR-154-Argentina “Conservación y uso sostenible de los recursos fitogenéticos locales para la alimentación y la agricultura (RFAA) para contribuir a la seguridad alimentaria de los pequeños agricultores de Argentina” funded in the 4^th  project cycle of Benefit-sharing Fund (BSF) of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) of the Food and Agriculture Organization (FAO). 

The aim of this study was to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats.

The research concludes that knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.