Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.)
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) h...
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MDPI AG
2024-02-01
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| author | Haroon Rashid Hakla Shubham Sharma Mohammad Urfan Rushil Mandlik Surbhi Kumawat Prakriti Rajput Bhubneshwari Khajuria Rehana Chowdhary Rupesh Deshmukh Rajib Roychowdhury Sikander Pal |
| author_facet | Haroon Rashid Hakla Shubham Sharma Mohammad Urfan Rushil Mandlik Surbhi Kumawat Prakriti Rajput Bhubneshwari Khajuria Rehana Chowdhary Rupesh Deshmukh Rajib Roychowdhury Sikander Pal |
| author_sort | Haroon Rashid Hakla |
| collection | DOAJ |
| description | 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 (<i>Solanum lycopersicum</i> 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. <i>Solyc10g050370</i> for PB under control, <i>Solyc08g062490</i>, and <i>Solyc08g062500</i> for SiP and <i>Solyc09g010450</i>, <i>Solyc09g010460</i>, <i>Solyc09g010690</i>, and <i>Solyc09g010710</i> 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. |
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| spelling | doaj.art-1694f4eb844b499b96c1d0f3dd911d622024-02-09T15:20:35ZengMDPI AGPlants2223-77472024-02-0113345710.3390/plants13030457Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.)Haroon Rashid Hakla0Shubham Sharma1Mohammad Urfan2Rushil Mandlik3Surbhi Kumawat4Prakriti Rajput5Bhubneshwari Khajuria6Rehana Chowdhary7Rupesh Deshmukh8Rajib Roychowdhury9Sikander Pal10Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, IndiaICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, IndiaPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, IndiaDepartment of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—Volcani Center, Rishon LeZion 7505101, IsraelPlant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, IndiaPhosphate (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 (<i>Solanum lycopersicum</i> 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. <i>Solyc10g050370</i> for PB under control, <i>Solyc08g062490</i>, and <i>Solyc08g062500</i> for SiP and <i>Solyc09g010450</i>, <i>Solyc09g010460</i>, <i>Solyc09g010690</i>, and <i>Solyc09g010710</i> 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.https://www.mdpi.com/2223-7747/13/3/457tomatogenotype-by-sequencinggeneGWASSNPphosphate uptake |
| spellingShingle | Haroon Rashid Hakla Shubham Sharma Mohammad Urfan Rushil Mandlik Surbhi Kumawat Prakriti Rajput Bhubneshwari Khajuria Rehana Chowdhary Rupesh Deshmukh Rajib Roychowdhury Sikander Pal Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) Plants tomato genotype-by-sequencing gene GWAS SNP phosphate uptake |
| title | Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) |
| title_full | Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) |
| title_fullStr | Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) |
| title_full_unstemmed | Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) |
| title_short | Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (<i>Solanum lycopersicum</i> L.) |
| title_sort | genome wide association study gwas for identifying snps and genes related to phosphate induced phenotypic traits in tomato i solanum lycopersicum i l |
| topic | tomato genotype-by-sequencing gene GWAS SNP phosphate uptake |
| url | https://www.mdpi.com/2223-7747/13/3/457 |
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