Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Dec 1;16(12):e0260709.
doi: 10.1371/journal.pone.0260709. eCollection 2021.

Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

Shaimaa Mahmoud Ahmed  1   2 , Alsamman Mahmoud Alsamman  3   4 , Abdulqader Jighly  5 , Mohamed Hassan Mubarak  6 , Khaled Al-Shamaa  7 , Tawffiq Istanbuli  2 , Osama Ahmed Momtaz  1 , Achraf El Allali  4 , Aladdin Hamwieh  2
Affiliations

Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

Shaimaa Mahmoud Ahmed et al. PLoS One. .

Abstract

Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars.

PubMed Disclaimer

Conflict of interest statement

NO authors have competing interests.

Figures

Fig 1
Fig 1. The salinity tolerance in the studied chickpea.
The distribution for salinity tolerance phenotypic scaling among different chickpea genotypes.
Fig 2
Fig 2. The correlation analysis of the genetic markers.
Correlation analysis of genetic data obtained through SNP and DArT technologies.
Fig 3
Fig 3. The linkage disequilibrium decay analysis.
The linkage disequilibrium decay analysis showing the r2 values of the 1854 SNP and DArT markers used in this study.
Fig 4
Fig 4. The PCA analysis generated by genetic markers.
The PCA analysis of the studied chickpea population shows the contribution of chickpea genotypes based on cos2 value (A) and their grouping versus country of origin (B).
Fig 5
Fig 5. The analysis of molecular variance generated by genetic markers.
AMOVA analysis of genetic variation among and within chickpea according to population, country of origin, as well as Monte-Carlo test results.
Fig 6
Fig 6. Chickpea population structure.
Ancestry inference and genetic structure analysis of the chickpea populations based on the 1854 DArTs and SNPs markers conducted using ADMIXTURE software.
Fig 7
Fig 7. Phylogenetic trees conducted using genetic markers.
The phylogenetic tree of chickpea genotypes based on SNP (A), and DArT (B) markers. The country origin (C) and the mean of phenotypic scale for salinity tolerance rate was assigned.
Fig 8
Fig 8. GWAS analysis results.
Manhattan plots of highly associated haplotypes for salinity response trait under field and greenhouse conditions generated by mtGWAS analysis. A) Salinity-associated whole-genome markers identified on chromosome Ca4 at 10618070 bp (rs = 5825813) correlated with salinity tolerance in hydroponic and field systems, with a significant threshold for association at 3 x 10–3 located within the gene of EMB8-like. B) Salinity-associated identified on chromosome Ca2 at 30537619 bp (rs = 5825939) be correlated with salinity tolerance in hydroponic system located within the RPLP0 gene.
Fig 9
Fig 9. Salinity-tolerance associated genes.
The location of the salinity-associated markers of 5825813 (A) and 5825939 (B) within chickpea genes.
See this image and copyright information in PMC

References

    1. Rosegrant MW, Cai X, Cline SA. World water and food to 2025: dealing with scarcity. Intl Food Policy Res Inst; 2002.
    1. FAO-Food, of the United Nations AO. FAOSTAT statistical database; 2017.
    1. Shaheenuzzamn M. Screening of chickpea genotypes against salinity stress. Bangladesh Journal of Agricultural Research. 2014;39(4):605–619. doi: 10.3329/bjar.v39i4.22539 - DOI
    1. Parihar P, Singh S, Singh R, Singh VP, Prasad SM. Effect of salinity stress on plants and its tolerance strategies: a review. Environmental Science and Pollution Research. 2015;22(6):4056–4075. doi: 10.1007/s11356-014-3739-1 - DOI - PubMed
    1. Kaashyap M, Ford R, Kudapa H, Jain M, Edwards D, Varshney R, et al. Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea. Scientific reports. 2018;8(1):1–19. doi: 10.1038/s41598-018-23116-9 - DOI - PMC - PubMed

Publication types