Assessment of genetic diversity in Egyptian barley (Hordeum vulgare L.) genotypes using SSR and SNP markers

Elakhdar, Ammar; Kumamaru, Toshihiro; Qualset, C. O.; Brueggeman, Robert; Amer, Khairy; Capo-chichi, L. J. A.

doi:10.1007/s10722-018-0666-x

Cited by 23 publications

(29 citation statements)

References 41 publications

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“…Numerous studies revealed different levels of genetic diversity in accessions from various geographic origins [5][6][7][8][9][10]. A considerably higher level of genetic diversity and the number of haplotypes was found in wild barley accessions and landraces compared to present-day cultivated barley genotypes [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

et al. 2021

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Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

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Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

et al. 2021

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“…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: 70%

“…Due to limited genetic variation among modern crop species, efficient use of the available genetic variation of local and non-adapted modern cultivars is necessary for germplasm maintenance, and for improving different crops (Russell et al, 1997;Tanksley and McCouch, 1997;Frankham et al, 2010;Chen et al, 2020), since the development of new improved genotypes requires the exploration and characterization of genetic diversity in available germplasm (Elakhdar et al, 2018). This diversity study may improve the efficiency of germplasm management operations, preventing the loss of allelic diversity through random genetic drift (Russell et al, 1997;Frankham et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

“…SSR markers have been extensively used in barley genetic diversity (Elakhdar et al, 2016a;Ferreira et al, 2016;Elakhdar et al, 2018;Arya et al, 2019), Association mapping (Jamali et al, 2017) linkage mapping and phylogenetic analysis (Lakew et al, 2013;Zhang et al, 2014). Among different DNA marker types used in barley, microsatellites have proven to be the markers of choice for genetic diversity studies for this plant species (Wang et al, 2010;Hua et al, 2015;Todorovska et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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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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“…Population genetics addresses variations in allele frequencies among and within populations. Several studies using molecular markers have been performed to investigate the genetic diversity in different barley germplasm collections, such as global barley germplasm (Malysheva-Otto et al ., 2006; Milner et al ., 2019), or mixtures of the wild and domesticated barley accessions to reveal genomic signatures of barley domestication (Pankin et al ., 2018; Zeng et al ., 2018), or compare the local and exotic cultivated barley germplasms within a location (Usubaliev et al ., 2013; Bengtsson et al ., 2017; Elakhdar et al ., 2018).…”

Section: Introductionmentioning

confidence: 99%

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

Zhang¹,

Luan²,

Zang³

et al. 2020

Plant Genet. Resour.

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Starch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

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Assessment of genetic diversity in Egyptian barley (Hordeum vulgare L.) genotypes using SSR and SNP markers

Cited by 23 publications

References 41 publications

Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

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

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

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