Genotyping-by-sequencing empowered genetic diversity analysis of Jordanian oat wild relative Avena sterilis

Al‐Hajaj, Nawal; Peterson, Gregory W.; Horbach, Carolee; Al-Shamaa, Khaled; Tinker, Nicholas A.; Fu, Yong‐Bi

doi:10.1007/s10722-018-0674-x

Cited by 6 publications

(5 citation statements)

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“…Also, the experimental cost for sampling genome-wide variants in this study was roughly $12,000, suggesting the feasibility of a wider application of GBS to characterize other perennial polyploid grass species. The results of the present study, along with those published in northern wheatgrass and wild oat [ 12 , 13 ], demonstrate the utility of GBS in molecular characterization of non-model plants with complex ploidy and genetic structures.…”

Section: Discussionsupporting

confidence: 76%

“…These results demonstrated the technical feasibility and effectiveness of GBS to sample genome-wide genetic variability in other perennial grass species with complex genomes. High resolution plant genetic diversity analysis, with 45,000 SNP markers spread over a genome, is more informative than with relatively few markers, like AFLP and SSR used in previous studies [ 1 , 12 , 18 , 38 , 39 , 40 ]. Also, the experimental cost for sampling genome-wide variants in this study was roughly $12,000, suggesting the feasibility of a wider application of GBS to characterize other perennial polyploid grass species.…”

Section: Discussionmentioning

confidence: 99%

“…To overcome these limitations, a GBS-based pipeline, called Haplotag, was developed by Tinker et al [ 9 ], which can generate tag-level haplotype and single nucleotide polymorphism (SNP) data for polyploid organisms. This approach has been successfully applied in the study of diploid and polyploid genomes in oat ( Avena sativa ) [ 10 , 11 , 12 ] and genetic diversity analysis of northern wheatgrass ( Elymus lanceolatus ssp. Lanceolatus ) [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

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Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

Baral

Coulman

Biligetu

et al. 2018

IJMS

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Molecular characterization of unsequenced plant species with complex genomes is now possible by genotyping-by-sequencing (GBS) using recent next generation sequencing technologies. This study represents the first use of GBS application to sample genome-wide variants of crested wheatgrass [Agropyron cristatum (L.) Gaertn.] and assess the genetic diversity present in 192 genotypes from 12 tetraploid lines. Bioinformatic analysis identified 45,507 single nucleotide polymorphism (SNP) markers in this outcrossing grass species. The model-based Bayesian analysis revealed four major clusters of the samples assayed. The diversity analysis revealed 15.8% of SNP variation residing among the 12 lines, and 12.1% SNP variation present among four genetic clusters identified by the Bayesian analysis. The principal coordinates analysis and dendrogram were able to distinguish four lines of Asian origin from Canadian cultivars and breeding lines. These results serve as a valuable resource for understanding genetic variability, and will aid in the genetic improvement of this outcrossing polyploid grass species for forage production. These findings illustrate the potential of GBS application in the characterization of non-model polyploid plants with complex genomes.

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Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

Baral

Coulman

Biligetu

et al. 2018

IJMS

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“…The presence of A. sterilis in all the habitats illustrated in Table 2 and Figure 2b aligns with Baum et al (1972) stating the high adaptability of the genus considered a weed to a wide range of diverse habitats. A study of the phenotypic diversity of the species from Jordan revealed significant variations in different population traits illustrating the importance of considering various population clusters for gene enrichment in oat crop improvement (Al-Hajaj et al, 2018).…”

Section: This Clearly Indicates the High Prevalence Of These Species ...mentioning

confidence: 99%

Surveying and mapping cereals and legumes wild relatives in Mount Hermon (Bekaa, Lebanon)

Sayde,

Chalak,

Baydoun

et al. 2024

Ecology and Evolution

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Crop Wild Relatives (CWR) should be highly prioritized, monitored, and conserved as they have an immense effect on sustainability and livelihood. In this study we aim to survey and map cereal and legume wild relatives of Fabaceae and Poaceae families. Mount Hermon, Bekaa side, Lebanon. A set of 46 CWR species were targeted based on desk selection analysis and prioritization by the International Center for Agricultural Research in Dry Areas genebank for their potential importance in breeding programs. A botanical survey of 17 sites of the various habitats of Mount Hermon was performed during April–June 2021 using a systematic transect/quadrate sampling method. Recorded genera and species were accurately georeferenced and then mapped with the DIVA‐GIS program. In total, 854 occurrences were observed belonging to 34 species of Fabaceae and 12 species of Poaceae. High H′ Shannon diversity values were recorded in three sites (Al Fakiaa, Sham El Hafour and Ain Ata‐ al Berke) of the Mount with values ranking between 2.45 and 2.83. This was confirmed by the richness distribution maps of genera and species. Richness distribution maps provide relevant clues on candidate sites for high concentrations of each of the species under study. At least the three sites, hosting 87% of the surveyed CWR's species, can be considered for further in situ conservation actions.

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“…Evolutionary changes in wild plants communities distributed over a range of different environments such as the progenitor of cultivated barley, are caused by a combination of gene ow, genetic drifts, and selective evolutionary forces (Levin 1988; Barrett and Kohn 1991), such as divergent selection and local adaptation (Linhart and Grant 1996;Gram and Sork 2001). Environmental gradients can create contrasting selective pressures due to intra-and inter-speci c competition (Fowler 1986;Linhart 1988) that shapes the genetic structure of plant populations because of environmental variables (Nevo 2001 The correlation between genetic structure and eco-geographical diversity may not hold for all species and habitats (Maxted et al 2008), such as wild oat in Jordan (Al-Hajaj et al 2018). The genetic structure of H. spontaneum had been characterized across its distribution range (Russell et al 2011;Jakob et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Phenotypic Evolution of The Wild Progenitor of Cultivated Barley (Hordeum Vulgare Subsp. Spontaneum (C. Koch) Thell.) Across Bioclimatic Regions In Jordan

Hajaj

Grando

Ababnah³

et al. 2021

Preprint

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Climate change affects the evolutionary potential and the survival of wild plant populations by acting on fitness traits. Resurrection approach was applied to investigate the phenotypic changes during the evolution of the wild progenitor of cultivated barley, Hordeum spontaneum K. Koch in Jordan. We compared 40 Hordeum spontaneum K. Koch populations collected in Jordan in 1991 with 40 Hordeum spontaneum K. Koch populations collected from the same sites in 2014. In the comparison we included seven Hordeum vulgare checks (one local landrace and six improved varieties). The analysis of the phenotypic data showed that the populations were aggregated according to their ecological geographical pattern in two groups with a significant (p < 0.0001) correlation between groups. Four heritable traits, namely plant height, biological yield, number of tillers, and awn length, determined the phenotypic structure of the populations. The two populations collected at 23 years distance, diverged in two distinctive phenotypic structure categories; a conserved structure and an evolved structure with a reduction in the phenotypic trait diversity in the population collected in 2014. These results reveal the value of combining phenotypic and environmental data to understand the evolution and adaptation of the population to climate change over a long period and the consequences on the wild progenitor of cultivated barley collection to avoid loss of genetic materials.

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Genotyping-by-sequencing empowered genetic diversity analysis of Jordanian oat wild relative Avena sterilis

Cited by 6 publications

References 46 publications

Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

Surveying and mapping cereals and legumes wild relatives in Mount Hermon (Bekaa, Lebanon)

Phenotypic Evolution of The Wild Progenitor of Cultivated Barley (Hordeum Vulgare Subsp. Spontaneum (C. Koch) Thell.) Across Bioclimatic Regions In Jordan

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