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

• Published in: Plants (Basel) Vol. 13; no. 3; p. 457
• Main Authors: Hakla, Haroon Rashid, Sharma, Shubham, Urfan, Mohammad, Mandlik, Rushil, Kumawat, Surbhi, Rajput, Prakriti, Khajuria, Bhubneshwari, Chowdhary, Rehana, Deshmukh, Rupesh, Roychowdhury, Rajib, Pal, Sikander
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 05.02.2024
• Subjects: Bayesian analysis; Biomass; Food security; gene; Genes; Genetic diversity; Genetic factors; Genetic markers; Genome-wide association studies; Genomes; Genomics; genotype-by-sequencing; GWAS; Linkage disequilibrium; Mathematical models; Nucleotides; phosphate uptake; Plant biomass; Plant growth; Plant species; Protein interaction; Proteins; Regression analysis; Salinity; Seeds; Single-nucleotide polymorphism; SNP; Soil conditions; Soils; Solanum lycopersicum; Sustainable agriculture; tomato; Tomatoes; India; genotype-by-sequencing; GWAS; phosphate uptake; tomato; SNP; gene
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants13030457

Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato ( L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. for PB under control, , and for SiP and , , , and for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions' responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security.