Abstract
Wild and cultivated barley are characterized by a high level of genetic diversity and a pronounced geographic population structure. Numerous studies using a diversity of markers showed that the centre of diversity of both wild and cultivated barley is in the Western part of the Fertile Crescent where the species was presumably domesticated. Comparisons of geographic diversity patterns suggested additional centres of domestication, of which the Eastern part of the Fertile Crescent (Iran or Himalaya), are most strongly supported. In wild barley, the geographic distribution of genetic and phenotypic diversity largely follows a neutral isolation by distance pattern, but common-garden experiments and environmental association studies indicate that local adaptation by natural selection also had a significant influence on these patterns but, so far no strong candidate genes for local adaptation were identified. Cultivated barley landraces and elite material have a significantly reduced level of genetic diversity compared to wild barley which also shows significant geographic differentiation and evidence for local adaptation. Several major domestication genes have already been cloned and patterns of diversity largely confirm the hypotheses that these genes were exposed to strong domestication-related selection that caused a reduction of diversity in these genes. Ex situ genebank collections of wild and domesticated barley were used to define core collections that have been phenotyped and genotyped to facilitate allele mining and introgression into elite varieties. The future utilization of barley genetic diversity will be facilitated by a good reference genome. The rapid progress of sequencing technologies and modern breeding methods like genomic selection and genome editing will contribute to an efficient utilization of barley genetic diversity.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Alonso-Blanco C, Andrade J, Becker C et al (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166:481–491. https://doi.org/10.1016/j.cell.2016.05.063
Alqudah AM, Sharma R, Pasam RK et al (2014) Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley. PLoS One 9:e113120. https://doi.org/10.1371/journal.pone.0113120
Andolfatto P, Nordborg M (1998) The effect of gene conversion on intralocus associations. Genetics 148:1397–1399
Aslan S, Forsberg NEG, Hagenblad J, Leino MW (2015) Molecular genotyping of historical barley landraces reveals novel candidate regions for local adaption. Crop Sci 55:2766. https://doi.org/10.2135/cropsci2015.02.0119
Backes G, Orabi J, Wolday A et al (2008) High genetic diversity revealed in barley (Hordeum vulgare) collected from small-scale farmer’s fields in Eritrea. Genet Res Crop Evol 56:85–97. https://doi.org/10.1007/s10722-008-9347-5
Badr A, M K, Sch R et al (2000) On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol 17:499–510. https://doi.org/10.1093/oxfordjournals.molbev.a026330
Bedada G, Westerbergh A, Nevo E et al (2014) DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel. Heredity 112:646–655. https://doi.org/10.1038/hdy.2014.2
Bélanger S, Clermont I, Esteves P, Belzile F (2016a) Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach. Theor Appl Genet 129:1393–1404. https://doi.org/10.1007/s00122-016-2711-5
Bélanger S, Esteves P, Clermont I et al (2016b) Genotyping-by-sequencing on pooled samples and its use in measuring segregation bias during the course of androgenesis in barley. Plant Genome 9. https://doi.org/10.3835/plantgenome2014.10.0073
Bengtsson T, Manninen O, Jahoor A, Orabi J, PPP Barley Consortium (2017) Genetic diversity, population structure and linkage disequilibrium in Nordic spring barley (Hordeum vulgare L. subsp. vulgare). Genet Resour Crop Evol 64(8):2021–2033
Bevan MW, Uauy C, Wulff BB et al (2017) Genomic innovation for crop improvement. Nature 543:346–354
Blattner FR, Badani Méndez AG (2001) RAPD data do not support a second centre of barley domestication in Morocco. Genet Res Crop Evol 48:13–19. https://doi.org/10.1023/a:1011299021969
Brown TA, Jones MK, Powell W, Allaby RG (2009) The complex origins of domesticated crops in the Fertile Crescent. Trends Ecol Evol 24:103–109. https://doi.org/10.1016/j.tree.2008.09.008
Caldwell K, Russell J, Langridge P, Powell W (2005) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567. https://doi.org/10.1534/genetics.104.038489
Chen X, Hackett CA, Niks RE et al (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley. PLoS One 5:e8598. https://doi.org/10.1371/journal.pone.0008598
Civáň P, Brown TA (2017) A novel mutation conferring the nonbrittle phenotype of cultivated barley. New Phyt 214:468–472. https://doi.org/10.1111/nph.14377
Clegg M, Brown A, Whitfeld P (1984) Chloroplast DNA diversity in wild and cultivated barley: implications for genetic conservation. Genet Res 43:339–343
Close TJ, Bhat PR, Lonardi S et al (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582. https://doi.org/10.1186/1471-2164-10-582
Comadran J, Kilian B, Russell J et al (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44:1388–1392. https://doi.org/10.1038/ng.2447
Dai F, Nevo E, Wu D et al (2012) Tibet is one of the centers of domestication of cultivated barley. Proc Natl Acad Sci USA 109:16969–16973. https://doi.org/10.1073/pnas.1215265109
Dai F, Chen Z-H, Wang X et al (2014) Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley. Proc Natl Acad Sci USA 111:13403–13408. https://doi.org/10.1073/pnas.1414335111
Dawson IK, Russell J, Powell W et al (2015) Barley: a translational model for adaptation to climate change. New Phyt 206:913–931. https://doi.org/10.1111/nph.13266
Dekkers JC, Hospital F, others (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22–32
Dempewolf H, Baute G, Anderson J et al (2017) Past and future use of wild relatives in crop breeding. Crop Sci 57:1070. https://doi.org/10.2135/cropsci2016.10.0885
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321. https://doi.org/10.1016/j.cell.2006.12.006
Ellis R, Forster B, Robinson D et al (2000) Wild barley: a source of genes for crop improvement in the 21st century? J Exp Bot 51:9–17. https://doi.org/10.1093/jexbot/51.342.9
Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578. https://doi.org/10.1111/j.1471-8286.2007.01758.x
Fan Y, Shabala S, Ma Y et al (2015) Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits. BMC Genomics 16:43. https://doi.org/10.1186/s12864-015-1243-8
Fang Z, Gonzales AM, Clegg MT et al (2014) Two genomic regions contribute disproportionately to geographic differentiation in wild barley. Genes Genomes Genet 4:1193–1203
Fischbeck G (2003) Diversification through breeding. In: Developments in plant genetics and breeding. Elsevier, pp 29–52
Forsberg NEG, Russell J, Macaulay M et al (2014) Farmers without borders-genetic structuring in century old barley (Hordeum vulgare). Heredity 114:195–206. https://doi.org/10.1038/hdy.2014.83
Friedt W, Horsley RD, Harvey BL et al (2011) Barley breeding history, progress, objectives, and technology. In: Barley. Wiley-Blackwell, pp 160–220
Fuller DQ, Asouti E, Purugganan MD (2011a) Cultivation as slow evolutionary entanglement: comparative data on rate and sequence of domestication. Veg Hist Archaeobot 21:131–145. https://doi.org/10.1007/s00334-011-0329-8
Fuller DQ, Willcox G, Allaby RG (2011b) Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the near east. World Archaeol 43:628–652. https://doi.org/10.1080/00438243.2011.624747
Gawenda I, Thorwarth P, Günther T et al (2015) Genome-wide association studies in elite varieties of German winter barley using single-marker and haplotype-based methods. Plant Breed 134:28–39. https://doi.org/10.1111/pbr.12237
Gross BL, Olsen KM (2010) Genetic perspectives on crop domestication. Trends Plant Sci 15:529–537. https://doi.org/10.1016/j.tplants.2010.05.008
Günther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195:205–220. https://doi.org/10.1534/genetics.113.152462
Guo G, Dondup D, Zhang L et al (2014) Identification of SNPs in barley (Hordeum vulgare L.) by deep sequencing of six reduced representation libraries. Crop J 2:419–425. https://doi.org/10.1016/j.cj.2014.06.008
Gupta PK, Sharma S, Kumar S et al (2004) Adaptive ribosomal DNA polymorphism in wild barley at a mosaic microsite, Newe Ya’ar in Israel. Plant Sci 166:1555–1563
Gurushidze M, Hiekel S, Otto I et al (2017) Site-directed mutagenesis in barley by expression of TALE nuclease in embryogenic pollen. In: Biotechnologies for plant mutation breeding. Springer, pp 113–128
Harlan HV, Martini ML (1938) The effect of natural selection in a mixture of barley varieties. J Agric Res 57(3)
Harlan J, Zohary D (1966) Distrbution of wild wheats and barley. Science 153:1074–1080
Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169:2335–2352. https://doi.org/10.1534/genetics.104.036947
Hofinger BJ, Russel Joanne R, Bass CG et al (2011) An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Mol Ecol 17:3653–3668. https://doi.org/10.1111/j.1365-294x.2011.05201.x
Hu S, Lübberstedt T (2015) Getting the ‘MOST’ out of crop improvement. Trends Plant Sci 20:372–379. https://doi.org/10.1016/j.tplants.2015.03.002
Huang Q, Beharav A, Youchun U et al (2002) Mosaic microecological differential stess causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Ya’ar, Israel. Genome 45:1216–1229
Hübner S, Höffken M, Oren E et al (2009) Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Mol Ecol 18:1523–1536. https://doi.org/10.1111/j.1365-294x.2009.04106.x
Hübner S, Bdolach E, Ein-Gedy S et al (2012a) Phenotypic landscapes: phenological patterns in wild and cultivated barley. J Evol Biol 26:163–174. https://doi.org/10.1111/jeb.12043
Hübner S, Günther T, Flavell A et al (2012b) Islands and streams: clusters and gene flow in wild barley populations from the Levant. Mol Ecol 21:1115–1129. https://doi.org/10.1111/j.1365-294x.2011.05434.x
Ingvarsson PK, Eckert C (2002) A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution 56:2368. https://doi.org/10.1554/0014-3820(2002)056[2368:ampogd]2.0.co;2
Inostroza L, del Pozo A, Matus I et al (2008) Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol Breed 23:365–376. https://doi.org/10.1007/s11032-008-9239-6
Jakob SS, Rödder D, Engler JO et al (2014) Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling. Genome Biol Evol 6:685–702. https://doi.org/10.1093/gbe/evu047
Jilal A, Grando S, Henry RJ et al (2008) Genetic diversity of ICARDA’s worldwide barley landrace collection. Genet Res Crop Evol 55:1221–1230. https://doi.org/10.1007/s10722-008-9322-1
Jones H, Leigh FJ, Mackay I et al (2008) Population-based resequencing reveals that the flowering time adaptation of cultivated barley originated east of the Fertile Crescent. Mol Biol Evol 25:2211–2219. https://doi.org/10.1093/molbev/msn167
Kalendar R, Tanskanen J, Immonen S et al (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607. https://doi.org/10.1073/pnas.110587497
Kalladan R, Worch S, Rolletschek H et al (2013) Identification of quantitative trait loci contributing to yield and seed quality parameters under terminal drought in barley advanced backcross lines. Mol Breed 32:71–90. https://doi.org/10.1007/s11032-013-9853-9
Kapusi E, Corcuera-Gómez M, Melnik S, Stoger E (2017) Heritable genomic fragment deletions and small indels in the putative engase gene induced by CRISPR/Cas9 in barley. Front Plant Sci 8:540. https://doi.org/10.3389/fpls.2017.00540
Kilian B, Ozkan H, Kohl J et al (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics 276:230–241. https://doi.org/10.1007/s00438-006-0136-6
Knüpffer H (2009) Triticeae genetic resources in ex situ genebank collections. In: Genetics and genomics of the triticeae. Springer, pp 31–79
Komatsuda T, Pourkheirandish M, He C et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104:1424–1429. https://doi.org/10.1073/pnas.0608580104
Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL (2016) The role of deleterious substitutions in crop genomes. Mol Biol Evol 33:2307–2317. https://doi.org/10.1093/molbev/msw102
Lenser T, Theißen G (2013) Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci 18:704–714. https://doi.org/10.1016/j.tplants.2013.08.007
Lev E, Kislev ME, Bar-Yosef O (2005) Mousterian vegetal food in Kebara Cave, Mt. Carmel. J Archaeol Sci 32:475–484. https://doi.org/10.1016/j.jas.2004.11.006
Li J-Y, Wang J, Zeigler RS (2014) The 3,000 rice genomes project: new opportunities and challenges for future rice research. GigaScience 3:8. https://doi.org/10.1186/2047-217x-3-8
Lin M, Cai S, Wang S et al (2015) Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theor Appl Genet 128:1385–1395. https://doi.org/10.1007/s00122-015-2513-1
Liu H, Bayer M, Druka A et al (2014) An evaluation of genotyping by sequencing (GBS) to map the breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics 15:104. https://doi.org/10.1186/1471-2164-15-104
Long NV, Dolstra O, Malosetti M et al (2013) Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 126:2335–2351. https://doi.org/10.1007/s00122-013-2139-0
Mamo BE, Barber BL, Steffenson BJ (2014) Genome-wide association mapping of zinc and iron concentration in barley landraces from Ethiopia and Eritrea. J Cereal Sci 60:497–506. https://doi.org/10.1016/j.jcs.2014.08.007
Maroof MAS, Allard RW, Zhang QF (1990) Genetic diversity and ecogeographical differentiation among ribosomal DNA alleles in wild and cultivated barley. Proc Natl Acad Sci USA 87:8486–8490. https://doi.org/10.1073/pnas.87.21.8486
Mascher M, Wu S, Amand PS et al (2013) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 8:e76925. https://doi.org/10.1371/journal.pone.0076925
Mascher M, Gundlach H, Himmelbach A et al (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433. https://doi.org/10.1038/nature22043
Matus I, Corey A, Filichkin T et al (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Genome 46:1010–1023. https://doi.org/10.1139/g03-080
Maurer A, Draba V, Pillen K (2016) Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping. J Exp Bot 67:2507–2518. https://doi.org/10.1093/jxb/erw070
McCouch S, Baute GJ, Bradeen J et al (2013) Agriculture: feeding the future. Nature 499:23–24
Molina-Cano JL, Fra-Mon P, Salcedo G et al (1987) Morocco as a possible domestication center for barley: biochemical and agromorphological evidence. Theor Appl Genet 73:531–536. https://doi.org/10.1007/bf00289190
Molina-Cano JL, Moralejo M, Igartua E, Romagosa I (1999) Further evidence supporting Morocco as a centre of origin of barley. Theor Appl Genet 98:913–918. https://doi.org/10.1007/s001220051150
Mora F, Quitral YA, Matus I et al (2016) SNP-based QTL mapping of 15 complex traits in barley under rain-fed and well-watered conditions by a mixed modeling approach. Front Plant Sci 7:909. https://doi.org/10.3389/fpls.2016.00909
Moragues M, Comadran J, Waugh R et al (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theor Appl Genet 120:1525–1534. https://doi.org/10.1007/s00122-010-1273-1
Morrell PL, Clegg MT (2007) Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci USA 104:3289–3294. https://doi.org/10.1073/pnas.0611377104
Morrell PL, Lundy KE, Clegg MT (2003) Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proc Natl Acad Sci USA 100:10812–10817. https://doi.org/10.1073/pnas.1633708100
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102:2442–2447. https://doi.org/10.1534/genetics.105.054502
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2006) Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173:1705–1723. https://doi.org/10.1534/genetics.105.054502
Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13(2):85–96. https://doi.org/10.1038/nrg3097
Morrell PL, Gonzales AM, Meyer KK, Clegg MT (2013) Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins. J Heredity 105:253–264. https://doi.org/10.1093/jhered/est083
Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB et al (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9:e94688. https://doi.org/10.1371/journal.pone.0094688
Nakamura S, Pourkheirandish M, Morishige H, Kubo Y, Nakamura M, Ichimura K, Seo S, Kanamori H, Wu J, Ando T, Hensel G, Sameri M, Stein N, Sato K, Matsumoto T, Yano M, Komatsuda T (2016) Mitogen-activated protein kinase kinase 3 regulates seed dormancy in barley. Curr Biol 26:775–781. https://doi.org/10.1016/j.cub.2016.01.024
Neale D, Saghai-Maroof M, Allard R et al (1988) Chloroplast DNA diversity in populations of wild and cultivated barley. Genetics 120:1105–1110
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Nevo E (1995) Asian, African and American biota meet at ‘Evolution Canyon’ Israel: local tests of global biodiversity and genetic diversity patterns. Proc Roy Soc B 262:149–155
Nevo E (2014) Evolution of wild barley at “Evolution Canyon”: adaptation, speciation, possible domestication, and improvement
Nevo E, Beharav A, Meyer R et al (2005) Genomic microsatellite adaptive divergence of wild barley by microclimatic stress in ‘Evolution Canyon’, Israel. Biol J Linn Soc 84:205–224
Nevo E, Fu Y-B, Pavlicek T et al (2012) Evolution of wild cereals during 28 years of global warming in Israel. Proc Natl Acad Sci USA 109:3412–3415. https://doi.org/10.1073/pnas.1121411109
Nice LM, Steffenson BJ, Brown-Guedira GL et al (2016) Development and genetic characterization of an advanced backcross-nested association mapping (AB-NAM) population of wild × cultivated barley. Genetics 203:1453–1467. https://doi.org/10.1534/genetics.116.190736
Orabi J, Backes G, Wolday A et al (2007) The Horn of Africa as a centre of barley diversification and a potential domestication site. Theor Appl Genet 114:1117–1127. https://doi.org/10.1007/s00122-007-0505-5
Østerberg JT, Xiang W, Olsen LI et al (2017) Accelerating the domestication of new crops: feasibility and approaches. Trends Plant Sci 22:373–384. https://doi.org/10.1016/j.tplants.2017.01.004
Owuor ED, Fahima T, Beharav A et al (1999) RAPD divergence caused by microsite edaphic selection in wild barley. Genetica 105:177–192. https://doi.org/10.1023/A:1003781711908
Pankin A, Altmüller J, Becker C, von Korff M (2017) Targeted re-sequencing reveals the genetic signatures and the reticulate history of barley domestication. bioRxiv 070078
Pasam RK, Sharma R, Malosetti M et al (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16. https://doi.org/10.1186/1471-2229-12-16
Pasam RK, Sharma R, Walther A et al (2014) Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates. PLoS One 9:e116164. https://doi.org/10.1371/journal.pone.0116164
Paterson AH, Lin Y-R, Li Z et al (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–1718. https://doi.org/10.1126/science.269.5231.1714
Pillen K, Zacharias A, Léon J (2003) Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor Appl Genet 107:340–352. https://doi.org/10.1007/s00122-003-1253-9
Poets AM, Fang Z, Clegg MT, Morrell PL (2015a) Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol 16:173. https://doi.org/10.1186/s13059-015-0712-3
Poets AM, Mohammadi M, Seth K et al (2015b) The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations. Genes Genomes Genet 6:609–622. https://doi.org/10.1534/g3.115.024349
Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253. https://doi.org/10.1371/journal.pone.0032253
Potokina E, Druka A, Luo Z et al (2008) Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant J 53:90–101. https://doi.org/10.1111/j.1365-313x.2007.03315.x
Pourkheirandish M, Komatsuda T (2007) The importance of barley genetics and domestication in a global perspective. Annals Bot 100:999–1008. https://doi.org/10.1093/aob/mcm139
Pourkheirandish M, Hensel G, Kilian B et al (2015) Evolution of the grain dispersal system in barley. Cell 162:527–539. https://doi.org/10.1016/j.cell.2015.07.002
Ramsay L, Comadran J, Druka A et al (2011) INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene teosinte branched 1. Nat Genet 43:169–172. https://doi.org/10.1038/ng.745
Riehl S, Zeidi M, Conard NJ (2013) Emergence of agriculture in the foothills of the Zagros mountains of Iran. Science 341:65–67. https://doi.org/10.1126/science.1236743
Russell J, Dawson IK, Flavell AJ et al (2011) Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes. New Phyt 191:564–578. https://doi.org/10.1111/j.1469-8137.2011.03704.x
Russell J, van Zonneveld M, Dawson IK et al (2014) Genetic diversity and ecological niche modelling of wild barley: refugia, large-scale post-LGM range expansion and limited mid-future climate threats? PLoS One 9:e86021. https://doi.org/10.1371/journal.pone.0086021
Russell J, Mascher M, Dawson IK et al (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48:1024–1030. https://doi.org/10.1038/ng.3612
Saisho D, Purugganan MD (2007) Molecular phylogeography of domesticated barley traces expansion of agriculture in the old world. Genetics 177:1765–1776. https://doi.org/10.1534/genetics.107.079491
Salamini F, Özkan H, Brandolini A et al (2002) Genetics and geography of wild cereal domestication in the Near East. Nat Rev Genet 3:429–441
Sannemann W, Huang BE, Mathew B, Léon J (2015) Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept. Mol Breed 35:86. https://doi.org/10.1007/s11032-015-0284-7
Sato K, Yamane M, Yamaji N, Kanamori H, Tagiri A, Schwerdt JG, Fincher GB, Matsumoto T, Takeda K, Komatsuda T (2016) Alanine aminotransferase controls seed dormancy in barley. Nat Commun 7:11625. https://doi.org/10.1038/ncomms11625
Sayed MA, Hamada A, Lèon J, Naz AA (2016) Genetic mapping reveals novel exotic QTL alleles for seminal root architecture in barley advanced backcross double haploid population. Euphytica 213:2. https://doi.org/10.1007/s10681-016-1809-9
Schaart JG, van de Wiel CC, Lotz LA, Smulders MJ (2016) Opportunities for products of new plant breeding techniques. Trends Plant Sci 21:438–449. https://doi.org/10.1016/j.tplants.2015.11.006
Schmalenbach I, Körber N, Pillen K (2008) Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. Theor Appl Genet 117:1093–1106. https://doi.org/10.1007/s00122-008-0847-7
Schmid KJ, Thorwarth P (2014) Genomic selection in barley breeding. In: Biotechnological approaches to barley improvement. Springer, pp 367–378
Schnaithmann F, Kopahnke D, Pillen K (2014) A first step toward the development of a barley NAM population and its utilization to detect QTLs conferring leaf rust seedling resistance. Theor Appl Genet 127:1513–1525. https://doi.org/10.1007/s00122-014-2315-x
Shi J, Lai J (2015) Patterns of genomic changes with crop domestication and breeding. Curr Opin Plant Biol 24:47–53. https://doi.org/10.1016/j.pbi.2015.01.008
Snow L, Brody T (1984) Genetic variation of Hordeum spontaneum in Israel, ecogeographical races detected by trait measurements. Plant Syst Evol 145:15–28
Somers D, Gyenis L, Yun S et al (2007) Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50:714–723. https://doi.org/10.1139/g07-054
Spies A, Korzun V, Bayles R et al (2012) Allele mining in barley genetic resources reveals genes of race-non-specific powdery mildew resistance. Front Plant Sci 2. https://doi.org/10.3389/fpls.2011.00113
Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43:1160–1163. https://doi.org/10.1038/ng.942
Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066. https://doi.org/10.1126/science.277.5329.1063
Tanno K, Willcox G (2011) Distinguishing wild and domestic wheat and barley spikelets from early holocene sites in the Near East. Veg Hist Archaeobot 21:107–115. https://doi.org/10.1007/s00334-011-0316-0
Thormann I, Reeves P, Thumm S et al (2017) Changes in barley (Hordeum vulgare L. subsp. vulgare) genetic diversity and structure in Jordan over a period of 31 years. Plant Genet Resour. https://doi.org/10.1017/s1479262117000028
Thorwarth P, Ahlemeyer J, Bochard A-M et al (2017) Genomic prediction ability for yield-related traits in German winter barley elite material. Theor Appl Genet. https://doi.org/10.1007/s00122-017-2917-1
Tondelli A, Xu X, Moragues M et al (2013) Structural and temporal variation in genetic diversity of European spring two-row barley cultivars and association mapping of quantitative traits. Plant Genome. https://doi.org/10.3835/plantgenome2013.03.0007
Turner A (2005) The pseudo-response regulator ppd-h1 provides adaptation to photoperiod in barley. Science 310:1031–1034. https://doi.org/10.1126/science.1117619
Turpeinen T, Tenhola T, Manninen O et al (2001) Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in Israel. Mol Ecol 10:1577–1591
Verhoeven KJ, Vanhala TK, Biere A, Nevo E, van Damme JM (2004) The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats. Evolution 58(2):270–283
Vitti JJ, Grossman SR, Sabeti PC (2013) Detecting natural selection in genomic data. Ann Rev Genet 47:97–120. https://doi.org/10.1146/annurev-genet-111212-133526
Volis S, Ward D, ad BYAIS, Zur V, Mendlinger S (2001) Tests for adaptive rapd variation in population genetic structure of wild barley, Hordeum spontaneum Koch. Biol J Linn Soc 4:289–303
Volis S, Mendlinger S, Turuspekov Y, Esnazarov U (2002) Phenotypic and allozyme variation in Mediterranean and desert populations of wild barley, Hordeum spontaneum Koch. Evolution 56:1403–1415
Volis S, Zaretsky M, Shulgina I (2009) Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal. Heredity 105:384–393. https://doi.org/10.1038/hdy.2009.168
Volis S, Zaretsky M, Shulgina I (2010) Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal. Heredity 105(4):384
Volis S, Shulgina I, Zaretsky M, Koren O (2011) Epistasis in natural populations of a predominantly selfing plant. Heredity 106(2):300
von Korff M, Wang H, Leon J, Pillen K (2006) AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor Appl Genet 112:1221–1231. https://doi.org/10.1007/s00122-006-0223-4
Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF (2005) The origin of the naked grains of maize. Nature 436:714–719. https://doi.org/10.1038/nature03863
Wei YM, Baum BR, Nevo E, Zheng YL (2005) Does domestication mimic speciation? 1. A population-genetic analysis of Hordeum spontaneum and Hordeum vulgare based on AFLP and evolutionary considerations. Can J Bot 83:1496–1512. https://doi.org/10.1139/b05-151
Weigel D, Nordborg M (2015) Population genomics for understanding adaptation in wild plant species. Ann Rev Genet 49:315–338. https://doi.org/10.1146/annurev-genet-120213-092110
Wendler N, Mascher M, Himmelbach A et al (2015) Bulbosum to go: a toolbox to utilize Hordeum vulgare/bulbosum introgressions for breeding and beyond. Mol Plant 8:1507–1519. https://doi.org/10.1016/j.molp.2015.05.004
Willcox G (2005) The distribution, natural habitats and availability of wild cereals in relation to their domestication in the near east: multiple events, multiple centres. Veg Hist Archaeobot 14:534–541. https://doi.org/10.1007/s00334-005-0075-x
Wright SI, Bi IV, Schroeder SG et al (2005) The effects of artificial selection on the maize genome. Science 308:1310–1314. https://doi.org/10.1126/science.1107891
Yang P, Habekuß A, Hofinger BJ et al (2016) Sequence diversification in recessive alleles of two host factor genes suggests adaptive selection for bymovirus resistance in cultivated barley from East Asia. Theor Appl Genet 130:331–344. https://doi.org/10.1007/s00122-016-2814-z
Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–989
Zohary D, Hopf M, Weiss E (2012) Domestication of plants in the Old World: the origin and spread of domesticated plants in Southwest Asia, Europe, and the Mediterranean Basin. Oxford University Press, Oxford
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Schmid, K., Kilian, B., Russell, J. (2018). Barley Domestication, Adaptation and Population Genomics. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_17
Download citation
DOI: https://doi.org/10.1007/978-3-319-92528-8_17
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-92527-1
Online ISBN: 978-3-319-92528-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)