Genome-wide diversity in lowland and highland maize landraces from southern South America: Population genetics insights to assist conservation

Maize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome-wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the Highland Northwestern maize (HNWA) and the Floury Northeastern maize (FNEA). Subsequently, we..., This dataset includes four VCF files generated from ddRADseq data analysed in Dominguez et al. The study sequenced 87 maize (Zea mays ssp. mays L.) individuals representing various genetic and morphological landrace groups from the Northeast and Northwest regions of Argentina. The raw sequencing data are accessible at the Sequence Read Archive (SRA) under the project ID PRJNA1073562.
SNP calling was conducted using Stacks v1.42 (Catchen et al., 2013), resulting in Complementary Table A. Reads from each sample were aligned to the maize B73 reference genome (version V4) available at MaizeGDB (https://www.maizegdb.org/genome/assembly/Zm-B73-REFERENCE-GRAMENE-4.0) using Bowtie 2 (Langmead et al., 2012). The initial VCF file was filtered with VCFTools (Danecek et al., 2011), producing Complementary File B.
The filtered VCF file was subsequently imputed with Beagle (Browning et al., 2018), generating Complementary File C, and annotated with SnpEff (Cingolani et al., 2012), resulting in Comple..., , # Data from: Genome-wide diversity in lowland and highland maize landraces from southern South America: population genetics insights to assist conservation

[https://doi.org/10.5061/dryad.5dv41nsg7](https://doi.org/10.5061/dryad.5dv41nsg7)

## Description of the data and file structure

This dataset comprises four VCF files derived from ddRADseq data generated and analysed in Dominguez et al. Metadata of samples are included in Supplementary table 1 of Dominguez et al. (also available here). Raw data for this study are available at the Sequence Read Archive (SRA), PRJNA1073562.

### Files and variables

#### File: Complementary\_tables\_VCF\_files\_Dominguez\_et\_al.zip

**Description:** 

**Complementary table A.** Unfiltered VCF file obtained with Stacks v1.42 (Catchen et al., 2013). The parameters used were: -m 3 (minimum depth of coverage), -M 2 (distance allowed between stacks), -n 3 (distance allowed between catalog loci).

**Complementary table B.** Filtered VCF file. Filtering ...