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

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 (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. IntroductionAbout 7.5 billion human share the same land, food and water resources. The global food demands are exponentially expanded while; the water scarcity will affect 1.8 billion people in 2025. One of the most crucial problems that face food security is salinity. According to FAO, over 6.5% of the world's land is affected, which is translated into 800 million HA of arable lands and expanding dramatically 1 . Filling the gap between the consumption and production require more research in order to enhance unprepared economic plant varieties to face such sudden environmental changes and unlock their ability to tolerance.Chickpea is one of the candidate cereal crops, which provides food with high nutritional value for an expanding world population. In addition, its global annual production is over 12 million tons. The chickpea production is centered in China (17%), India (12%), Russia and the USA (8%) 2 . Chickpea is sensitive to salinity which reduces its yield greatly 3 . Upon exposure to salt stress, the meristems accumulate salts in the vacuoles of the xylem 4 , to lower their osmotic potential till reaching high concentrations 5,6 . Other strategies to tolerate salinity can be by efficient osmotic adjustment, homeostasis, retention in root and mesophyll cells, and ROS detoxification 7,8 . The sodium (Na + ) accumulation in the cytoplasm dehydrates the cell by causing ion homeos...

Genome-wide identification and comprehensive study of anti-fungal genes in chickpea

“…Chickpea yield is significantly affected by both abiotic as well as biotic stress susceptibility (2,3). Fungal infections have been shown to destructive effects on the chickpea production compared to various diseases triggered by a wide range of pathogens.…”