Population structure and diversity assessment of barley (Hordeum vulgare L.) introduction from ICARDA

Kumar, Pawan; Banjarey, Prabha; Malik, Rekha; Tikle, Ashok Narayanrao; Verma, Ramesh Pal Singh

doi:10.1007/s12041-020-01226-6

Cited by 10 publications

(7 citation statements)

References 26 publications

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“…When comparing Gumer vs. Ethiopia, FST was 0.40, and Nm was 0.38. Nm between Japan and USA was high, and genetic differentiation based on FST values was significant between the landraces among the different populations, which confirmed the dynamic genetic variation among the collected landraces [ 53 , 54 ]. The findings also confirm the presence of significant diversity in Ethiopia and Gumer barley landraces.…”

Section: Resultsmentioning

confidence: 62%

“…For example, European barley is grouped into three subpopulations based on the sequence of the photoperiod response gene ( Ppd-H1 ) [ 18 – 20 ]. Six different haplotypes were found in Asian barley populations, identified by the β-amylase gene ( Bmy1 ) at positions 115, 165, 233, 347, and 430, which allows adaptation and selection based on the preference for climate, and food [ 21 – 23 ]. Furthermore, the population structure of barley in different geographic locations indicates multiple selection pressures based on uses and growth environments [ 1 , 6 , 14 – 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and population structure of barley landraces from Southern Ethiopia’s Gumer district: Utilization for breeding and conservation

et al. 2023

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Barley is the fifth most important food crop in Ethiopia. The genetic relationship and population structure studies of barley are limited to gene bank collections. Therefore, this study fills a gap by investigating the selection, consumption, economic value, genetic diversity, and population structure of farm-collected barley from the Gumer district of the Gurage Zone, which has received little attention. The information on the use of barley in the study area was collected using semi-structured interviews and questionnaires. 124 households of 11 kebeles, the smallest community unit, were interviewed. Barley landraces collected were compared with those collected from Japan, the United States (USA), and other Ethiopian locations. Illumina iSelect (50K genotyping platform) was used to identify single nucleotide polymorphisms (SNP) (20,367). Thirty landraces were found in Gumer. Burdaenadenber had the highest on-farm Shannon index estimate (2.0), followed by Aselecha (1.97) and Enjefo (1.95). Aselecha and Fetazer had the highest (44%) and the lowest (29%) richness values, respectively. High and low Simpson index values were found in Aselecha (84%) and Wulbaragenateretero (79%), respectively. The neighbor-joining tree revealed that Gumer landraces formed a separate subcluster with a common ancestral node; a sister subcluster contained barley landraces from Japan. According to the population structure analysis, barley landraces from Gumer differed from Japan and the United States. The principal component analysis revealed that US barley was the most distant group from Gumer barley. The markers’ allele frequencies ranged from 0.10 to 0.50, with an average value of 0.28. The mean values of Nei’s gene diversity (0.38) and the polymorphic information content (0.30) indicated the presence of high genetic diversity in the samples. The clustering of accessions was not based on geographic origin. Significant genetic diversity calls for additional research and analysis of local barley diversity because the selection and use of barley in Ethiopia would have been affected by the preference of ethnic groups.

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Section: Resultsmentioning

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of barley landraces from Southern Ethiopia’s Gumer district: Utilization for breeding and conservation

et al. 2023

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“…The two kinds of molecular markers of SSR and SNP are the most commonly used in barley genetic diversity analysis [4][5][6][7][8]15,[26][27][28][29][30][31][32][33][34]. SSR markers were once very popular because of their good stability and easy operation.…”

Section: Discussionmentioning

confidence: 99%

“…SSR markers were once very popular because of their good stability and easy operation. However, the frequency of SSR markers in barley populations is always relatively low, and the number of loci that can be used for genetic diversity analysis is consequently limited [4][5][6]8,[27][28][29]31,34]. This makes SSRs less representative, and often means that they do not distinguish between different individuals with similar genetic backgrounds.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

Li¹,

Halford²,

Zong³

et al. 2023

Phyton

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Barley (Hordeum vulgare L.) is an important economic crop for food, feed and industrial raw materials. In the present research, 112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing (GBS), and the genetic diversity and population structure were analyzed. The results showed that 210,268 Single Nucleotide Polymorphisms (SNPs) were present in total, and the average poly-morphism information content (PIC) was 0.1642. Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups, with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups. Genotypes with similar or duplicated names were also investigated according to their genetic backgrounds and seed appearances. This study provided valuable information on barley landraces from the Shanghai region, and showed that all these barley landraces should be protected and used for future breeding programs.

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“…The genus Hordeum comprises more than 30 species. Some varieties are also found in this genus (Malysheva-Otto et al 2006;Forsberg et al 2019;Hagenblad and Morales 2020;Kumar et al 2020). Organelle genomes have been widely used in study of taxonomy, evolution and genetics (Wang et al 2016;Yang et al 2019;Wang et al 2020;Li, He, et al 2020).…”

Section: Tibetan Hulless Barley;mentioning

confidence: 99%

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

Ren

et al. 2021

Mitochondrial DNA Part B

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In the present study, the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum was sequenced, assembled and compared with closely related species. The chloroplast genome of Hordeum vulgare L. var. trifurcatum was composed of 84 protein-coding genes (PCG), 8 ribosomal RNA (rRNA) genes, and 38 transfer RNA (tRNA) genes. The Hordeum vulgare L. var. trifurcatum chloroplast genome is 136,485 bp in size, with the GC content of 38.32%. Phylogenetic analysis based on the combined chloroplast gene dataset indicated that the Hordeum vulgare L. var. trifurcatum exhibited a close relationship with Hordeum vulgare subsp. spontaneum and Hordeum vulgare subsp. vulgare.

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Population structure and diversity assessment of barley (Hordeum vulgare L.) introduction from ICARDA

Cited by 10 publications

References 26 publications

Genetic diversity and population structure of barley landraces from Southern Ethiopia’s Gumer district: Utilization for breeding and conservation

Genetic diversity and population structure of barley landraces from Southern Ethiopia’s Gumer district: Utilization for breeding and conservation

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

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