• This record comes from PubMed

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

. 2023 ; 18 (1) : e0279737. [epub] 20230105

Language English Country United States Media electronic-ecollection

Document type Journal Article, Research Support, Non-U.S. Gov't

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.

See more in PubMed

Sato K. History and future perspectives of barley genomics. DNA Res. 2020;27. doi: 10.1093/dnares/dsaa023 PubMed DOI PMC

Abebe TD, Bauer AM, Léon J. Morphological diversity of Ethiopian barley (Hordeum vulgare L.) about geographic regions and altitudes. Hereditas. 2010;147: 154–164. doi: 10.1111/j.1601-5223.2010.02173.x PubMed DOI

Nixon-Darcus L, D’Andrea AC. Necessary for Life: Studies of Ancient and Modern Grinding Stones in Highland Ethiopia. African Archaeol Rev. 2017;34: 193–223. doi: 10.1007/s10437-017-9252-4 DOI

Tigerstedt PMA, Bjørnstad AS, Demissie A, Demissie A, Kilian A, Kleinhofs A, et al.. Communicated by The distinctness and diversity of Ethiopian barleys. Springer-Verlag; 1997.

Tadesse D, Asres T. On-farm diversity of barley landraces in North Western Ethiopia. Int J Biodivers Conserv. 2019;11.

Seid E, Eleni S, Faris H. Evaluation of genetic diversity in barley (Hordeum vulgare L.) from Wollo high land areas using agro-morphological traits and hordein. Afr J Biotechnol. 2015;14.

Girma M. Genetic erosion of barley in North Shewa Zone of Oromiya Region. Ethiop Int J Biodivers Conserv. 2014;6.

Eticha F, Woldeyesus S, Heinrich G. On-farm Diversity and Characterization of Barley (Hordeum vulgare L.) Landraces in the Highlands of West Shewa, Ethiopia. Ethnobotany Res Appl. 2010;8.

Assamere A, Mamuye A, Amare K, Fiseha M. Diversity, distribution, agronomic and post-harvest management of local barley (Hordeum vulgare L.) variety in South Wollo, Ethiopia. PLoS One. 2021;16: e0250899. doi: 10.1371/journal.pone.0250899 PubMed DOI PMC

Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, et al.. Genebank genomics highlights the diversity of a global barley collection. Nat Genet. 2019;51: 319–326. doi: 10.1038/s41588-018-0266-x PubMed DOI

Samberg LH, Fishman L, Allendorf FW. Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system. Evol Appl. 2013;6: 1133–1145. doi: 10.1111/eva.12091 PubMed DOI PMC

Purugganan MD, Fuller DQ. The nature of selection during plant domestication. Nature. 2009;457: 843–848. doi: 10.1038/nature07895 PubMed DOI

Mohammadi SA, Abdollahi Sisi N, Sadeghzadeh B. The influence of breeding history, origin, and growth type on the population structure of baisey as revealed by SSR markers. Sci Rep. 2020;10: 1–13. doi: 10.1038/s41598-020-75339-4 PubMed DOI PMC

Poets AM, Fang Z, Clegg MT, Morrell PL. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol. 2015;16: 173. doi: 10.1186/s13059-015-0712-3 PubMed DOI PMC

Casañas F, Simó J, Casals J, Prohens J. Toward an evolved concept of landrace. Front Plant Sci. 2017;8. doi: 10.3389/fpls.2017.00145 PubMed DOI PMC

Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, Schroeder JI. Genetic strategies for improving crop yields. Nature. 2019. pp. 109–118. doi: 10.1038/s41586-019-1679-0 PubMed DOI PMC

Glenn KC, Alsop B, Bell E, Goley M, Jenkinson J, Liu B, et al.. Bringing new plant varieties to market: Plant breeding and selection practices advance beneficial characteristics while minimizing unintended changes. Crop Science. Crop Science Society of America; 2017. pp. 2906–2921. doi: 10.2135/cropsci2017.03.0199 DOI

Aslan S, Forsberg NEG, Hagenblad J, Leino MW. Molecular genotyping of historical barley landraces reveals novel candidate regions for local adaption. Crop Sci. 2015;55: 2766–2776. doi: 10.2135/cropsci2015.02.0119 DOI

Ibrahim A, Harrison M, Meinke H, Fan Y, Johnson P, Zhou M. A regulator of early flowering in barley (Hordeum vulgare L.). PLoS One. 2018;13. doi: 10.1371/journal.pone.0200722 PubMed DOI PMC

Abdullaev RA, Alpatieva N V, Zveinek IA, Batasheva BA, Anisimova IN, Radchenko EE, et al.. Diversity of Dagestan Barleys for the Duration of the Period between Shooting and Earing Stages and Alleles in the Ppd-H1 and Ppd-H2 Loci. Springer. 2017;43: 3–7. doi: 10.3103/S1068367417020021 DOI

Malysheva-Otto L V., Röder MS. Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.). Mol Breed. 2006;18: 143–156. doi: 10.1007/s11032-006-9023-4 DOI

Contreras-Moreira B, Serrano-Notivoli R, Mohammed NE, Cantalapiedra CP, Beguería S, Casas AM, et al.. Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula. Mol Ecol. 2019;28: 1994–2012. doi: 10.1111/mec.15009 PubMed DOI PMC

Kumar P, Banjarey P, Malik R, Tikle AN, Verma RPSS, Vijayaraje R, et al.. Population structure and diversity assessment of barley (Hordeum vulgare L.) introduction from ICARDA. 2020;99. doi: 10.1007/s12041-020-01226-6 PubMed DOI

Darrier B, Russell J, Milner SG, Hedley PE, Shaw PD, Macaulay M, et al.. A Comparison of Mainstream Genotyping Platforms for the Evaluation and Use of Barley Genetic Resources. Front Plant Sci. 2019;0: 544. doi: 10.3389/fpls.2019.00544 PubMed DOI PMC

Tuvesson S, Von Post R, Von Post L, Dayteg C, Nilsson M, Forster BP. A high-throughput DNA extraction method for barley seed. Euphytica. 2003;130: 255–260. doi: 10.1023/A:1022863006134 DOI

Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, et al.. Development and evaluation of a barley 50k iSelect SNP array. Front Plant Sci. 2017;8: 1792. doi: 10.3389/fpls.2017.01792 PubMed DOI PMC

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, et al.. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544: 427–433. doi: 10.1038/nature22043 PubMed DOI

Wagner JO and FGB and MF and RK and PL and DM and PRM and RBO and GLS and PS and MHHS and ES and H. vegan: Community Ecology Package. R package; 2020. version 2.7–5

Granato ISC, Galli G, de Oliveira Couto EG, e Souza MB, Mendonça LF, Fritsche-Neto R. snpReady: a tool to assist breeders in genomic analysis. Mol Breed. 2018;38. doi: 10.1007/s11032-018-0844-8 DOI

Kamvar ZN, Tabima JF, unwald NJ. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2014;2014: 1–14. doi: 10.7717/peerj.281 PubMed DOI PMC

Jombart T, Ahmed I, Jombart T. and Ahmed I. new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27: 3070–3071. doi: 10.1093/bioinformatics/btr521 PubMed DOI PMC

R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2021. https://www.r-project.org/

Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo Á, Lareu M V. An overview of STRUCTURE: Applications, parameter settings, and supporting software. Front Genet. 2013;4. doi: 10.3389/fgene.2013.00098 PubMed DOI PMC

Evanno G, Regnaut S, ecology JG-M, 2005 undefined. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14: 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x PubMed DOI

Jakobsson M, Rosenberg NA. CLUMP: a cluster matching and permutation program for dealing with label switching and multimodality in the analysis of population structure. Bioinformatics. 2007;23: 1801–1806. doi: 10.1093/bioinformatics/btm233 PubMed DOI

Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8: 28–36. doi: 10.1111/2041-210X.12628 DOI

Wickham H. ggplot2. Wiley Interdiscip Rev Comput Stat. 2011;3: 180–185. doi: 10.1002/wics.147 DOI

Tadesse D, Derso B. The status and constraints of food barley production in the North Gondar highlands, North Western Ethiopia. Agric Food Secure. 2019;8. doi: 10.1186/s40066-018-0248-3 DOI

Daniel T, Tazebachew A. On-farm diversity of barley landraces in North Western Ethiopia. Int J Biodivers Conserv. 2019;11: 1–7. doi: 10.5897/ijbc2018.1247 DOI

Gadissa F, Abebe M, Worku B. Assessment on the Current State of On-Farm Diversity and Genetic Erosion in Barley (Hordeum vulgare L.) Landraces from Bale Highlands, Southeast. Ethiopia. Biomed Res Int. 2021; 23: 6677363. doi: 10.1155/2021/6677363 PubMed DOI PMC

Dessie AB, Abate TM, Mekie TM, Liyew YM. Crop diversification analysis on red pepper dominated smallholder farming system: evidence from northwest Ethiopia. Ecol Process. 2019;8. doi: 10.1186/s13717-019-0203-7 DOI

Tadesse D, Mekuria W, Asres T, Derso B. On-farm Characterization of Barley (Hordeum vulgare L.) Landraces in the Highlands of North Gondar, Ethiopia. Int J Sci Res Manag. 2018;6. doi: 10.18535/ijsrm/v6i6.ah01 DOI

Sansaloni C., Franco J., Santos B. et al.. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat Commun. 2020;11: 4572. doi: 10.1038/s41467-020-18404-w PubMed DOI PMC

Hailemichael S, Spade P. Ethnobotany, diverse food uses, claimed health benefits and implications on conservation of barley landraces in North Eastern Ethiopia highlands. J Ethnobiol Ethnomed. 2011;7. PubMed PMC

Chettri D., Anandan A., Nagireddy R., Sabarinathan S., & Sathyanarayana N. Genetic diversity in rice (Oryza sativa L.) landraces of Sikkim-Himalaya and early insight into their use in genome-wide association analysis. Plant Genetic Resource.2021,19(4), 347–356. doi: 10.1017/S1479262121000411 DOI

Zevallos E, Inga J, Alvarez F, Marmolejo K, Paitan R, Viza I, et al.. First signs of late blight resistance in traditional native potatoes of Pasco—Peru, a preliminary assay. Agric Food Secure. 2021;10:33. doi: 10.1186/S40066-021-00330-9 DOI

Garduño G, and C P-J of D, 2020 undefined. The on-farm diversity of maize cultivars and landraces in the Lacandon of Chiapas, Mexico. academicjournals.org. 12: 113–121. doi: 10.5897/JDAE2020.1170 DOI

Negisho K, Shibru S, Pillen K, Ordon F, Wehner G. Genetic diversity of Ethiopian durum wheat landraces. PLoS One. 2021;16. doi: 10.1371/journal.pone.0247016 PubMed DOI PMC

Zeng X, Guo Y, Xu Q, Mascher M, Guo G, Li S, et al.. Origin and evolution of qingke barley in Tibet. Nat Commun. 2018;9: 1–11. doi: 10.1038/s41467-018-07920-5 PubMed DOI PMC

De Haan S. Potato Diversity and Height: Multiple Dimensions of Farmer-Driven-in situ Conservation in the Andes. 2009; PhD thesis, Wageningen University, Wageningen.

Liu B, Ma G, Bussmann R, Bai K, Li J, et al.. Determining factors for the of hulless barley agroecosystem in the himalaya region—A from Northwest Yunnan, China. E. Global Ecol. Conserv.2019;18: e00600, doi: 10.1016/j.gecco.2019.e00600 DOI

Bauldry S. Structural Equation Modeling. Int Encycl Soc Behav Sci Second Ed. 2015; 615–620. doi: 10.1016/B978-0-08-097086-8.44055-9 DOI

Swarup S, Cargill E, Crosby K, … L F-C, 2021 undefined. is indispensable for plant breeding to improve crops. Wiley Online Libr. 2021;61: 839–852. doi: 10.1002/csc2.20377 DOI

Kumar P, Banjarey P, Malik R, Tikle AN, Verma RPS. Population structure and diversity assessment of barley (Hordeum vulgare L.) introduction from ICARDA. J Genet. 2020;99. doi: 10.1007/S12041-020-01226-6 PubMed DOI

Corbin LJ, Liu AYH, Bishop SC, Woolliams JA. Estimation of historical effective population size using linkage disequilibria with marker data. J Anim Breed Genet. 2012;129: 257–270. doi: 10.1111/j.1439-0388.2012.01003.x PubMed DOI

Tehseen M, Istipliler D, Kehel Z, Genes CS-, 2021 undefined. Genetic diversity and population structure analysis of Triticum aestivum L. Landrace panel from Afghanistan. mdpi.com. 2021, 25;12(3):340. doi: 10.3390/genes12030340 PubMed DOI PMC

Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, et al.. The USDA barley core collection: Genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 2014;9: 94688. doi: 10.1371/journal.pone.0094688 PubMed DOI PMC

Fricano A, Battaglia R, Mica E, Tondelli A, Crosatti C, Guerra D, et al.. Genetic Diversity for Barley Adaptation to Stressful Environments. Genomic Des Abiotic Stress Resist Cereal Crop. 2021; 153–191. doi: 10.1007/978-3-030-75875-2_4 DOI

Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, et al.. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 2019;52(2): 319–326. doi: 10.1038/s41588-018-0266-x PubMed DOI

Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, et al.. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature. 2020;588: 284–289. doi: 10.1038/s41586-020-2947-8 PubMed DOI PMC

Find record

Citation metrics

Loading data ...

Archiving options

Loading data ...