Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)

Hakla, Haroon Rashid; Sharma, Shubham; Urfan, Mohammad; Mandlik, Rushil; Kumawat, Surbhi; Rajput, Prakriti; Khajuria, Bhubneshwari; Chowdhary, Rehana; Deshmukh, Rupesh; Roychowdhury, Rajib; Pal, Sikander

doi:10.3390/plants13030457

Cited by 4 publications

(1 citation statement)

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“…Genetic diversity within the wild progenitors of our cultivated crop species has been largely recognized as an important resource for increasing climate resilience of modern-day agriculture [12,37]. In tomato, GWAS has been used for detecting genetic variations underlying complex agronomic and morphological traits [38][39][40][41][42][43]. Although various components of salinity tolerance have been identified in S. pimpinellifolium [12,28,29], this is the first study that explores root system architecture-derived mechanisms of salt tolerance.…”

Section: Discussionmentioning

confidence: 99%

Dissecting the genetic regulation of lateral root development in tomato under salt stress

Rahmati Ishka,

Sussman,

Zhao

et al. 2024

Preprint

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Tomatoes are crucial for global food security and agricultural economies. With over 50% of arable land projected to become saline by 2050, understanding tomato responses to saline environments is essential. Soil salinization, prevalent in arid regions, leads to salt stress. Roots are primary salinity sensors and integrate stress responses like nutrient deficiency. Understanding the molecular processes maintaining root growth is vital for crop resilience. While salt stress impacts on tomato seed germination, shoot growth, and fruit yield are documented, root development remains underexplored. Most studies have focused on a limited number of cultivars and their physiological responses, not the genetic basis of salt resilience. Wild tomato relatives, such asSolanum pimpinellifolium, offer traits that are beneficial for breeding resilient crops. However, few studies have examined the genetics of salinity tolerance inS. pimpinellifolium. This study characterizes salt stress-induced changes in root system architecture (RSA) using a natural diversity panel of 220 wild tomato accessions. We identified natural variation in lateral root development and several candidate loci through Genome-Wide Association Study (GWAS). Bulk segregant analysis (BSA) revealed 22 candidate genes overlapping with GWAS findings. Exploring root transcriptome reprogramming in two accessions with differing lateral root responses highlighted genotype-specific changes. Integrating GWAS, BSA, and RNA sequencing data identified four key genes underlying differential lateral root development under salt stress. These findings offer novel genetic targets for improving salt resilience in tomatoes, providing opportunities for future research and breeding programs to enhance crop sustainability and productivity.

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