Entire chloroplast genome comparison of maize native landraces from Northern Argentina: lights into genetic diversity and variant distribution

LÓPEZ M.G.; PUEBLA A.; FASS M.; VERA P.; PANIEGO N.; HOPP H.E.; LIA V.V.

Lima

Congreso; IX Encuentro REDBIO 2016-PERÚ; 2016

REDBIO

Native maize landraces are valuable reservoirs of original alleles for crop improvement. They also possess local historical and cultural significance. In Argentina, one of the southernmost areas of native maize cultivation, ca. 70 different landraces are grown and maintained by traditional farmers, descendant from indigenous populations. Nowadays, local landraces are threatened by the mixing with commercial material and the replacement of native varieties by more productive crops knowledge of the levels and distribution patterns of genetic variation in traditional landraces is essential in order to make proper decisions for conservation and to develop successful protection programs.Recent studies have detected significant genetic structuring between maize landraces from North West (NWA) and East (NEA) Argentina using microsatellite markers. However, additional information is still needed to clarify the origin of the Argentinean native germplasm, reconstruct the routes of dispersion to South America and establish the focus of future conservation efforts. Therefore, we obtained whole chloroplast genome sequences to analyze the observed patterns of variation within a phylogeographic framework. Chloroplast genomes from a set of 18 different maize native landraces, from NWA (4) and NEA (14), and two teosintes (Zea mays ssp. parviglumis and Z. mays ssp. mexicana) were amplified with long-PCR protocols. The amplification products were purified and subsequently sequenced with Illumina MiSeq technologies. The B73 inbred line was used as reference chloroplast genome; mapping and variant calling were performed with CLC Genomics Workbench software. Sequences were aligned using MAFFT program. Thirty nine di-allelic SNP, one Multiple Nucleotide Variant, one InDel and more than twenty microsatellite loci were identified. Comparisons among native populations and differences from teosintes are provided. Our results suggest the existence of three distinctive gene pools in South America (NWA, NEA Floury and NEA Popcors). These also support previous hypotheses proposing two separate routes of maize diffusion into South America.