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Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum

Citation

Hellwig, Timo; Abbo, Shahal; Sherman, Amir; Ophir, Ron (2021), Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum, Dryad, Dataset, https://doi.org/10.5061/dryad.sxksn0325

Abstract

Plant breeders and conservationists depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 % - 18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1354 markers were significantly correlated with environmental factors, 1233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate change is likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.

Methods

VCF files description
File Description
Pfulvum_raw.vcf.gz raw vcf file from Elshire, where I extracted the fulvum samples, but did not apply any filters
Pfulvum.vcf Filtered Pfulvum.raw.vcf as follow: Biallelic SNPs with minor allele frequency (MAF) ≥ 0.01, minimum depth ≥ 3, minimum mean depth across samples ≥ 5, minimum genotype quality ≥ 25, and genotype calls ≥ 40%.
                     Applied by runnig: vcftools --gzvcf ../data/Pfulvum_raw.vcf.gz --remove-indels --min-alleles 2 --max-alleles 2 --maf 0.01 --max-missing 0.6 --minGQ 25 --min-meanDP 5 --minDP 3 --recode
Pfulvum.imputed.vcf Imputed version of Pfulvum.vcf.   
Applied by running: java -jar ../../software/beagle/beagle.18May20.d20.jar gt=Pfulvum.vcf iterations=30 burnin=10 ap=true gp=true ne=50000 seed=170887 out=Pfulvum.imputed.nohead nthreads=6
Pfulvum.LDpruned.vcf  LD pruned (r^2>0.5) version of Pfulvum.vcf. the outcome of a script
Pfulvum.imputed.LDpruned.vcf  LD pruned (r^2>0.5) version of Pfulvum.imputed.vcf.

 

Funding

Israel Science Foundation, Award: 307/17