Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant

Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. 
 
In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites.
 
Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also c..., SNP dataset
According to the manufacturer's instructions, we isolated the genomic DNA from fresh leaves of five seedlings per accession using the FavorPrep Plant Genomic DNA Extraction Mini Kit (FAVORGEN). We then constructed the sequencing library following the approach of Elshire et al. (2011). Genomic DNA was quantified by Qubit and normalized to 100ng in 96-well plates. We digested the DNA samples using the restriction enzyme ApeKI and ligated them with two adapters for sequencing, followed by the polymerase chain reaction to amplify the target DNA fragments to complete the sequencing library preparation. A service provider did sequencing with the Illumina HiseqX platform in a pair-end 150bp run.For the SNP calling, we followed mainly the manual of Stacks software (Catchen et al., 2013). In short, we filtered the raw reads by quality and demultiplexed using the process radtags program. We then mapped the retained reads to the eggplant reference genome (Eggplant_V4.1.fa) (Barchi et a..., , # Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant

## Description of the data and file structure

**File list:**

* Wild African eggplant SNP dataset.vcf
* Wild African eggplant sample details and environmental data.csv

## **Data specific information**

1\. Wild African eggplant SNP dataset\.vcf

The data lines in the .vcf file include

* CHROM - chromosome: An identifier from the reference genome
* POS - position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM
* ID - identifier: Colon-separated list of unique identifiers for the SNPs
* REF - reference base(s)
* ALT - alternate base(s): A list of alternate non-reference alleles.
* QUAL - quality: Phred-scaled quality score for the assertion made in ALT
* FILTER - filter status: PASS if this position has passed all filters, i.e., a call is made at this position
* INFO - additional info...