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bioRxiv · 10.1101/519744

Dowsing for salinity tolerance related genes in chickpea through genome wide association and in silico PCR analysis

Ahmed, S. M.·Alsamman, A. M.·Mubarak, M. H.·Badawy, M. A.·Kord, M. A.·Momtaz, O. A.·Hamwieh, A.
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Abstract

Soil salinity is a major abiotic stress severely limits agricultural crop production throughout the world, and the stress is increasing particularly in the irrigated agricultural areas. Chickpea (Cicer arietinum L.) is an important grain legume that plays a significant role in the nutrition of the developing world. In this study, we used a chickpea subset collected from the genebank of the International Center for Agricultural Research in the Dry Area (ICARDA). This collection was selected by using the focused identification of germplasm strategy (FIGS). The subset included 138 genotypes which have been screened in the open field (Arish, Sinai, Egypt) and in the greenhouse (Giza, Egypt) by using the hydroponic system at 100 mM NaCl concentration. The experiment was laid out in randomized alpha lattice design in two replications. The molecular characterization was done by using sixteen SSR markers (collected from QTL conferred salinity tolerance in chickpea), 2,500 SNP and 3,031 DArT markers which have been developed and used for association study. The results indicated significant differences between the chickpea genotypes. Based on the average of the two hydroponic and field experiments, seven tolerant genotypes IGs (70782, 70430, 70764, 117703, 6057, 8447 and 70249) have been identified. The data analysis indicated one SSR (TAA170), three DArT (DART2393, DART769 and DART2009) and eleven SNP markers (SNP2021, SNP1268, SNP1451, SNP1487, SNP1667, SNP2095, SNP190, SNP2247 SNP1947, SNP2331 and SNP948) were associated with salinity tolerance. The flanking regions of these markers revealed genes with a known role in the salinity tolerance, which could be candidates for marker-assisted selection in chickpea breeding programs.

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Ahmed, S. M., Alsamman, A. M., Mubarak, M. H., Badawy, M. A., Kord, M. A., Momtaz, O. A., Hamwieh, A.. 2019-01-13. Dowsing for salinity tolerance related genes in chickpea through genome wide association and in silico PCR analysis. https://doi.org/10.1101/519744

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