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Hakla HR, Sharma S, Urfan M, Mandlik R, Kumawat S, Rajput P, Khajuria B, Chowdhary R, Deshmukh R, Roychowdhury R, Pal S. Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato ( Solanum lycopersicum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:457. [PMID: 38337989 PMCID: PMC10857258 DOI: 10.3390/plants13030457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
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.
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Affiliation(s)
- Haroon Rashid Hakla
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
- Central Integrated Pest Management Centre (CIPMC), Srinagar 190008, India
| | - Shubham Sharma
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
| | - Mohammad Urfan
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
| | - Rushil Mandlik
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.M.); (S.K.); (R.D.)
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Surbhi Kumawat
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.M.); (S.K.); (R.D.)
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Prakriti Rajput
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
| | - Bhubneshwari Khajuria
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
| | - Rehana Chowdhary
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
| | - Rupesh Deshmukh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India; (R.M.); (S.K.); (R.D.)
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—Volcani Center, Rishon LeZion 7505101, Israel
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India; (H.R.H.); (S.S.); (M.U.); (P.R.); (B.K.); (R.C.)
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