Population structure and marker–trait association of salt tolerance in barley (Hordeum vulgare L.)

Elakhdar, Ammar; EL-Sattar, Mohamed Abd; Amer, Khairy; Rady, Assma; Kumamaru, Toshihiro

doi:10.1016/j.crvi.2016.06.006

Cited by 36 publications

(31 citation statements)

References 26 publications

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“…The diverse set consisted of 60 spring barley genotypes. The biological status, pedigree information, and population structure have been illustrated [ 90 ]. The list of all genotypes is presented in Table S1 .…”

Section: Methodsmentioning

confidence: 99%

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Moursi

Thabet

Amro

et al. 2020

Plants

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Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

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Section: Methodsmentioning

confidence: 99%

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Moursi

Thabet

Amro

et al. 2020

Plants

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“…Number of genotypes and the efficiency of markers for detecting alleles are relatively determine the PIC values. The PIC mean value was 0.513 which slightly higher than PIC value of 0.36 by Elakhdar et al (2016b), and lower than PIC value of 0.54 by Pasam et al (2014).…”

Section: Resultsmentioning

confidence: 55%

“…In the current study, about 2-8 alleles were detected per a locus with an average of 3.76 alleles (Table 3). This result is greater than 2.6/locus reported by Elakhdar et al (2016b), but lesser than 4 alleles/locus that found by Elakhdar et al (2018), and 6.29 alleles/locus found by Todorovska et al (2019). Size of amplified bands (from 80 to 1200bp) was estimated by comparing the PCR products with the known size of DNA fragments ladder.…”

Section: Resultsmentioning

confidence: 69%

Diversity Maintenance of Some Barley (Hordeum Spp) Genetic Resources Using SSR-Based Marker

2020

THE JAPS

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Barley is an important cereal crop cultivated in many parts of the world since ancient times. Genetic diversity was studied in a set of 16 barley (Hordeum spp) genotypes using 25 microsatellite (SSR) loci. A total of 94 different alleles distributed over all the seven chromosomes of barley. Out of these, 76 alleles were polymorphic with an average of 3.04 alleles/primer. Major allele frequency, gene diversity and PIC were estimated based on allele frequencies, having the mean values of 0.543, 0.571 and 0.513, respectively. Principal component analysis indicated the presence of high genetic variability among barley genotypes. ATACO, Canela, Local Abiad Sulaimani and Amal2 were identified to be highly distanced from other genotypes. The dendrogram created by hierarchical cluster analysis using the UPGMA algorithm was able to discriminate the genotypes into 7 groups according to their genetic distance. Both analyses parallel to principal coordinate analysis are indicating the close relatedness between Quinn, Zanbaka, Al-khair and Arta/3/Avar genotypes that exchange genetic material through continuous previous breeding programs. These values indicate high differentiation ability of SSR markers for genetic studies in barley and their utility for barley genetics and breeding.

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“…Additionally, compared to high throughput molecular markers such as SNPs, SSRs have their own advantages respected to population genetics 62 . The association between SSR markers and abiotic stresses tolerance such as salinity has been recognized and discussed in different plant species 39,63 . One of the main importance of the SSR markers, the inheritance of its alleles from the parents to the progeny which made them an efficient tool in marker-assisted selection breeding programs.…”

Section: Simple Sequence Repeat Analysismentioning

confidence: 99%

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

Ahmed

Alsamman

Mubarak

et al. 2019

Preprint

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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...

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Population structure and marker–trait association of salt tolerance in barley (Hordeum vulgare L.)

Cited by 36 publications

References 26 publications

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Diversity Maintenance of Some Barley (Hordeum Spp) Genetic Resources Using SSR-Based Marker

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

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