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Genetic Associations Underpinning the Metabolite-Mediated Salt Stress Tolerance in Barley

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Abstract

Salinity stress is one of the abiotic factors that greatly affect agriculture by limiting plant growth and yield worldwide. A set of 138 barley accessions from different geographical regions was characterized with the aim to identify metabolite, biochemical, and morphological phenotypes under salinity stress. Salt stress resulted in significant increases in the phytochemicals, including the contents of total phenolic (TPC), total flavonoid (TFC), proline (ProC), and total antioxidant capacity (TAC) except soluble protein (SP). Positive relationships between proline content and the secondary metabolites or antioxidants, including total phenolics and flavonoids, were detected among barley accessions, indicating a critical adaptive strategy against free radicals under salt stress. Genome-wide association study (GWAS) revealed 122 significant quantitative trait nucleotides (QTNs) associated with the measured traits which resulted in the identification of 203 potential candidate genes. Interestingly, the QTN G:A was located inside the candidate gene HORVU.MOREX.r3.3HG0291720 at position 501,703,401 on chromosome 3H. This gene encodes Ca-binding protein and contributes to the signalling pathway that in turn triggers the expression of salt-stress responsive genes. The identified QTNs/ candidate genes provide information useful for the genetic improvement of barley genotypes under salt stress.

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All data supporting the findings of this study are available within the paper and within its supplementary materials published online.

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Acknowledgements

The author (M.D.A) would like to acknowledge Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2023R355), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.

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The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

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Authors and Affiliations

  1. Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt

    Samar G. Thabet

  2. Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O.Box. 84428, 11671, Riyadh, Saudi Arabia

    Mashael Daghash Alqahtani

  3. Department of Biology, Faculty of Applied Science, Umm Al-Qura University, 21955, Makkah, Saudi Arabia

    Alae A. Jabbour

  4. Biological Science Program, Department of Biological and Environmental Sciences, Collage of Art and Science, Qatar University, Doha, Qatar

    Ahmad M. Alqudah

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  1. Samar G. Thabet
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  2. Mashael Daghash Alqahtani
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  3. Alae A. Jabbour
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  4. Ahmad M. Alqudah
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Contributions

SGT and AMA designed the experiment and analyzed the data. SGT, M.D.A, A.A.J, and AMA wrote and edited the manuscript. SGT conceived the idea and participated in the interpretation of the results.

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Correspondence to Samar G. Thabet or Ahmad M. Alqudah.

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Highlights 

• This study focuses on characterizing a metabolite-based genome-wide association study (mGWAS) that is involved in salt adaptation in barley.

• The identified QTN/candidate genes provide information useful for the genetic improvement of barley genotypes under salt stress.

• However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive.

Supplementary Information

Below is the link to the electronic supplementary material.

11105_2023_1408_MOESM1_ESM.pptx

Fig. S1: The number of SNPs within 1 MB window size for barley; Fig. S2: Distribution of accessions for antioxidants under control and salt stress in barley. Proline content (ProC), Soluble protein (SP), Total antioxidant capacity (TAC), Total phenolic content (TPC), and Total flavonoid content (TFC); Fig. S3: Phenotypic distribution of accessions for all agronomic traits under control and salt stress in barley. Spike Length (SL), spikelet per spike (SS), grains per spike (GS), Weight of grains per spike (WGS), and Thousand kernel weight (TKW); Fig. S4: Phenotypic distribution of accessions for all of the studied traits underlie salt-tolerant indices (STI) in barley; Fig. S5: Comparison association analysis for FarmCPU, GLM, MLM models indicates Manhattan plot for; ProC—Proline content, SP—Soluble protein, TAC—Total antioxidant capacity, TFC— Total Flavonoid content, and TPC— Total phenolic content, SL— Spike Length, SS—Spikelets per Spike, GS — Grains per Spike, WGS—Weight Grains per Spike, and TKW—Thousand Kernel Weight in barley. The x-axis shows the chromosomes and the SNP order. The y-axis shows the − Log10 (P-value) for each SNP marker. The x-axis shows the chromosomes and the SNP order. The y-axis shows the − Log10 (P-value) for each SNP marker; Fig. S6: Quantile–quantile scale representing expected versus observed -log10 (p-value) underlying FarmCPU, GLM, MLM models for traits, including ProC—Proline content, SP—Soluble protein, TAC—Total antioxidant capacity, TFC— Total Flavonoid content, and TPC— Total phenolic content, SL— Spike Length, SS—Spikelets per Spike, GS — Grains per Spike, WGS—Weight Grains per Spike, and TKW—Thousand Kernel Weight in barley (PPTX 17788 KB)

11105_2023_1408_MOESM2_ESM.xlsx

Table S1: The detailed information of barley accessions; Table S2: Heritability and analysis of variance for all biochemical traits; Table S3: Heritability and analysis of variance for all morphological traits; Table S4: Marker trait association with the studied traits. Physical position of markers which are passing -log10(4) and R2 10%; Table S5: Marker trait association with the multi traits. Physical position of markers which are passing -log10(4) and R2 10%; Table S6: The list of candidate genes based on the linkage disequilibrium of multi-traits associated marker. (XLSX 54 KB)

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Thabet, S.G., Alqahtani, M.D., Jabbour, A.A. et al. Genetic Associations Underpinning the Metabolite-Mediated Salt Stress Tolerance in Barley. Plant Mol Biol Rep (2023). https://doi.org/10.1007/s11105-023-01408-3

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