Deciphering salt stress responses in Solanum pimpinellifolium through high-throughput phenotyping

Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor unde..., Illumina whole genome sequencing of 265 Solanum pimpinellifolium accessions using paired-end PE 150 insert llibraries sequenced on Novaseq was newly performed in this study. SNP variant calling was then performed within these 265 newly seqeunced accessions together with 226 additional accessions of wild and cultivated tomatoes previously resequenced and available under the SRA project PRJNA454805. 
SNP variant calling was performed following the method described in (Abrouk et al., 2020) and available on GitHub (https://github.com/IBEXCluster/Wheat-SNPCaller) with a few modifications. Raw sequence reads were filtered with Trimmomatic-v0.38 (Bolger et al., 2014) using the following criteria: SLIDINGWINDOW:5:20; MINLEN:50. The filtered paired-end reads were then aligned for each sample individually against the LA2093_genome_v1.4 reference assembly (Wang et al., 2020a) using BWA-MEM (v-0.7.17) (Li and Durbin, 2010), only reads mapping with a quality Q>20 were retained, followed by sortin..., GATK or vcftools