Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.)
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Date
2024-02
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Abstract
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
(Solanum lycopersicum 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. Solyc10g050370 for PB under control,
Solyc08g062490, and Solyc08g062500 for SiP and Solyc09g010450, Solyc09g010460, Solyc09g010690,
and Solyc09g010710 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