Domestication and crop evolution of wheat andbarley: Genes, genomics, and future directions
|
摘要
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of nextgeneration sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance(relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large,complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors,as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of nextgeneration sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance(relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large,complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors,as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of nextgeneration sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance(relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large,complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors,as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
引文
Abbo S,Lev-Yadun S,Gopher A(2012)Plant domestication and crop evolution in the near east:On events and processes.Crit Rev Plant Sci 31:241-257
Abbo S,van-Oss RP,Gopher A,Saranga Y,Ofner I,Peleg Z(2014)Plant domestication versus crop evolution:Aconceptual framework for cereals and grain legumes.Trends Plant Sci 19:351-360
A?berg E(1938)Hordeum agriocrithon nova sp.,a wild sixrowed barley.Ann Agric Coll Sweden 6:159-216
Allaby RG,Fuller DQ,Brown TA(2008)The genetic expectations of a protracted model for the origins of domesticated crops.Proc Natl Acad Sci USA 105:13982-13986
Allaby RG,Stevens C,Lucas L,Maeda O,Fuller DQ(2017)Geographic mosaics and changing rates of cereal domestication.Philos Trans R Soc B Biol Sci 372:20160429
Arranz-Otaegui A,Carretero LG,Ramsey MN,Fuller DQ,Richter T(2018)Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan.Proc Natl Acad Sci USA 115:7925-7930
Avni R,Nave M,Barad O,Baruch K,Twardziok SO,Gundlach H,Hale I,Mascher M,Spannagl M,Wiebe K,Jordan KW,Golan G,Deek J,Ben-Zvi B,Ben-Zvi G,Himmelbach A,MacLachlan RP,Sharpe AG,Fritz A,Ben-David R,Budak H,Fahima T,Korol A,Faris JD,Hernandez A,Mikel MA,Levy AA,Steffenson B,Maccaferri M,Tuberosa R,Cattivelli L,Faccioli P,Ceriotti A,Kashkush K,Pourkheirandish M,Komatsuda T,Eilam T,Sela H,Sharon A,Ohad N,Chamovitz DA,Mayer KFX,Stein N,Ronen G,Peleg Z,Pozniak CJ,Akhunov ED,Distelfeld A(2017)Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.Science 357:93-97
Azhaguvel P,Komatsuda T(2007)A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley.Ann Bot 100:1009-1015
Badr A,Muller K,Schafer R,El Rabey HE,Effgen S,Ibrahim HH,Pozzi C,Rohde W,Salamini F(2000)On the origin and domestication history of barley(Hordeum vulgare).Mol Biol Evol 17:499-510
Bayer MM,Rapazote-Flores P,Ganal M,Hedley PE,Macaulay M,Plieske J,Ramsay L,Russell J,Shaw PD,Thomas W,Waugh R(2017)Development and evaluation of a barley50k i Select SNP array.Front Plant Sci 8:1792
Beales J,Turner A,Griffiths S,Snape JW,Laurie DA(2007)A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat(Triticum aestivum L.).Theor Appl Genet 115:721-733
Blake NK,Lehfeldt BR,Lavin M,Talbert LE(1999)Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid:The B genome of wheat.Genome 42:351-360
Blatter RHE,Jacomet S,Schlumbaum A(2004)About the origin of European spelt(Triticum spelta L.):Allelic differentiation of the HMW Glutenin B1-1 and A1-2 subunit genes.Theor Appl Genet 108:360-367
Blattner FR,Badani Mendez AG(2001)RAPD data do not support a second centre of barley domestication in Morocco.Genet Resour Crop Evol 48:13-19
von Bothmer R,Jacobsen N,Baden C,Jorgensen R,LindeLaursen I(1995)An Ecogeographical Study of The Genus Hordeum,2nd edn.Rome:International Plant Genetic Resources Institute
B€orner A,Sch€afer M,Schmidt A,Grau M,Vorwald J(2005)Associations between geographical origin and morphological characters in bread wheat(Triticum aestivum L.).Plant Genet Resour 3:360-372
Brenchley R,Spannagl M,Pfeifer M,Barker GLA,D’Amore R,Allen AM,McKenzie N,Kramer M,Kerhornou A,Bolser D,Kay S,Waite D,Trick M,Bancroft I,Gu Y,Huo N,Luo M-C,Sehgal S,Gill B,Kianian S,Anderson O,Kersey P,Dvorak J,McCombie R,Hall A,Mayer KFX,Edwards KJ,Bevan MW,Hall N(2012)Analysis of the bread wheat genome using whole-genome shotgun sequencing.Nature 491:705-710
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
Chalupska D,Lee HY,Faris JD,Evrard A,Chalhoub B,Haselkorn R,Gornicki P(2008)Acc homoeoloci and the evolution of wheat genomes.Proc Natl Acad Sci USA 105:9691-9696
Chao S,Sharp PJ,Worland AJ,Warham EJ,Koebner RMD,Gale MD(1989)RFLP-based genetic maps of wheat homoeologous group 7 chromosomes.Theor Appl Genet 78:495-504
Chen FH,Dong GH,Zhang DJ,Liu XY,Jia X,An CB,Ma MM,Xie YW,Barton L,Ren XY,Zhao ZJ,Wu XH,Jones MK(2015)Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.Science 347:248-250
Chen QF,Yen C,Yang JL(1998)Chromosome location of the gene for brittle rachis in the Tibetan weedrace of common wheat.Genet Resour Crop Evol 45:407-410
Choo TM,Ho KM,Martin RA(2001)Genetic analysis of a hulless?covered cross of barley using doubled-haploid lines.Crop Sci 41:1021-1026
Civan P,Brown TA(2017)A novel mutation conferring the nonbrittle phenotype of cultivated barley.New Phytol 214:468-472
Civan P,Ivanicova Z,Brown TA(2013)Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the Fertile Crescent.PLoS ONE 8:e81955
Clavijo BJ,Venturini L,Schudoma C,Accinelli GG,Kaithakottil G,Wright J,Borrill P,Kettleborough G,Heavens D,Chapman H,Lipscombe J,Barker T,Lu F-H,McKenzie N,Raats D,Ramirez-Gonzalez RH,Coince A,Peel N,PercivalAlwyn L,Duncan O,Tr€osch J,Yu G,Bolser DM,Namaati G,Kerhornou A,Spannagl M,Gundlach H,Haberer G,Davey RP,Fosker C,Palma FD,Phillips AL,Millar AH,Kersey PJ,Uauy C,Krasileva KV,Swarbreck D,Bevan MW,Clark MD(2017)An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.Genome Res 27:885-896
Close TJ,Bhat PR,Lonardi S,Wu Y,Rostoks N,Ramsay L,Druka A,Stein N,Svensson JT,Wanamaker S,Bozdag S,Roose ML,Moscou MJ,Chao S,Varshney RK,Sz}ucs P,Sato K,Hayes PM,Matthews DE,Kleinhofs A,Muehlbauer GJ,DeYoung J,Marshall DF,Madishetty K,Fenton RD,Condamine P,Graner A,Waugh R(2009)Development and implementation of high-throughput SNP genotyping in barley.BMC Genomics 10:582
Comadran J,Kilian B,Russell J,Ramsay L,Stein N,Ganal M,Shaw P,Bayer M,Thomas W,Marshall D,Hedley P,Tondelli A,Pecchioni N,Francia E,Korzun V,Walther A,Waugh R(2012)Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley.Nat Genet 44:1388-1393
Dai F,Nevo E,Wu D,Comadran J,Zhou M,Qiu L,Chen Z,Beiles A,Chen G,Zhang G(2012)Tibet is one of the centers of domestication of cultivated barley.Proc Natl Acad Sci USA109:16969-16973
Debernardi JM,Lin H,Chuck G,Faris JD,Dubcovsky J(2017)microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability.Development 144:1966-1975
Distelfeld A,Korol A,Dubcovsky J,Uauy C,Blake T,Fahima T(2008)Colinearity between the barley grain protein content(GPC)QTL on chromosome arm 6HS and the wheat Gpc-B1 region.Mol Breed 22:25-38
Dixon LE,Greenwood JR,Bencivenga S,Zhang P,Cockram J,Mellers G,Ramm K,Cavanagh C,Swain SM,Boden SA(2018)TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat(Triticum aestivum L.).Plant Cell 30:563-581
Doebley JF,Gaut BS,Smith BD(2006)The molecular genetics of crop domestication.Cell 127:1309-1321
Dubcovsky J,Lijavetzky D,Appendino L,Tranquilli G(1998)Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement.Theor Appl Genet 97:968-975
Dubcovsky J,Dvorak J(2007)Genome plasticity a key factor in the success of polyploid wheat under domestication.Science 316:1862-1866
Dvorak J,Deal KR,Luo MC,You FM,von Borstel K,Dehghani H(2012)The origin of spelt and free-threshing hexaploid wheat.J Hered 103:426-441
Dvorak J,Terlizzi P,Zhang HB,Resta P(1993)The evolution of polyploid wheats:Identification of the A genome donor species.Genome 36:21-31
Elbaum R,Zaltzman L,Burgert I,Fratzl P(2007)The role of wheat awns in the seed dispersal unit.Science 316:884-886
Faris JD,Fellers JP,Brooks SA,Gill BS(2003)A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene.Genetics 164:311-321
Faris JD,Zhang Z,Chao S(2014)Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication.Gene 542:198-208
Faure S,Turner AS,Gruszka D,Christodoulou V,Davis SJ,von Korff M,Laurie DA(2012)Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley(Hordeum vulgare)to short growing seasons.Proc Natl Acad Sci USA 109:8328-8333
Fuller DQ(2007)Contrasting patterns in crop domestication and domestication rates:Recent achaeobotanical insights from the old world.Ann Bot 100:903-924
Gao L,Dorn K,Rife TW,Wang X,Lemes C,Clinesmith M,Silva P,Fritz A,Stein N,Mascher M,Poland J(2018)Completion of the‘Jagger’wheat genome leads to identification of Aegilops ventricosa 2NS translocation and its impact in wheat breeding.(https://pag.confex.com/pag/xxvi/meet ingapp.cgi/Paper/30261)
Glemin S,Scornavacca C,Dainat J,Burgarella C,Viader V,Ardisson M,Sarah G,Santoni S,David J,Ranwez V(2018)Pervasive hybridizations in the history of wheat relatives.bioRxiv 300848 doi:10.1101/300848
Golan G,Hendel E,Mendez Espitia GE,Schwartz N,Peleg Z(2018)Activation of seminal root primordia during wheat domestication reveals underlying mechanisms of plant resilience.Plant Cell Environ 41:755-766
Gorafi YSA,Kim JS,Elbashir AAE,Tsujimoto H(2018)A population of wheat multiple synthetic derivatives:An effective platform to explore,harness and utilize genetic diversity of Aegilops tauschii for wheat improvement.Theor Appl Genet 131:1615-1626
Groos C,Gay G,Perretant MR,Gervais L,Bernard M,Dedryver F,Charmet G(2002)Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white?red grain bread-wheat cross.Theor Appl Genet 104:39-47
Harlan JR,Zohary D(1966)Distribution of wild wheats and barley.Science 153:1074-1080
Harris DR(1989)An evolutionary continuum of people-plant interaction.In:Harris DR,Hillman GC,eds.Foraging and Farming:The Evolution of Plant Exploitation.Routledge,London.pp.11-26
Heun M,Abbo S,Lev-Yadun S,Gopher A(2012)A critical review of the protracted domestication model for Near-Eastern founder crops:Linear regression,long-distance gene flow,archaeological,and archaeobotanical evidence.J Exp Bot63:4333-4341
Heun M,Haldorsen S,Vollan K(2008)Reassessing domestication events in the Near East:Einkorn and Triticum urartu.Genome 51:444-451
Heun M,Sch€afer-Pregl R,Klawan D,Castagna R,Accerbi M,Borghi B,Salamini F(1997)Site of einkorn wheat domestication identified by DNA fingerprinting.Science278:1312-1314
Huang S,Steffenson B,Sela H,Stinebaugh K(2018)Resistance of Aegilops longissima to the rusts of wheat.Plant Dis 102:1124-1135
International Barley Genome Sequencing C(2012)A physical,genetic and functional sequence assembly of the barley genome.Nature 491:711-716
International Wheat Genome Sequencing Consortium(2014)A chromosome-based draft sequence of the hexaploid bread wheat Triticum aestivum genome.Science 345:1251788
International Wheat Genome Sequencing Consortium(2018)Shifting the limits in wheat research and breeding using a fully annotated reference genome.Science 361:eaar7191
Jakob SS,R€odder D,Engler JO,Shaaf S,€Ozkan H,Blattner FR,Kilian B(2014)Evolutionary history of wild barley(Hordeum vulgare subsp.spontaneum)analyzed using multilocus sequence data and paleodistribution modeling.Genome Biol Evol 6:685-702
Jia J,Zhao S,Kong X,Li Y,Zhao G,He W,Appels R,Pfeifer M,Tao Y,Zhang X,Jing R,Zhang C,Ma Y,Gao L,Gao C,Spannagl M,Mayer KFX,Li D,Pan S,Zheng F,Hu Q,Xia X,Li J,Liang Q,Chen J,Wicker T,Gou C,Kuang H,He G,Luo Y,Keller B,Xia Q,Lu P,Wang J,Zou H,Zhang R,Xu J,Gao J,Middleton C,Quan Z,Liu G,Wang J,International Wheat Genome Sequencing C,Yang H,Liu X,He Z,Mao L,Wang J(2013)Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.Nature 496:91-95
Jordan KW,Wang S,Lun Y,Gardiner LJ,MacLachlan R,Hucl P,Wiebe K,Wong D,Forrest KL,Sharpe AG,Sidebottom CH,Hall N,Toomajian C,Close T,Dubcovsky J,Akhunova A,Talbert L,Bansal UK,Bariana HS,Hayden MJ,Pozniak C,Jeddeloh JA,Hall A,Akhunov E(2015)A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.Genome Biol 16:48
Jorgensen C,Luo MC,Ramasamy R,Dawson M,Gill BS,Korol AB,Distelfeld A,Dvorak J(2017)A high-density genetic map of wild emmer wheat from the Karaca Dag region provides new evidence on the structure and evolution of wheat chromosomes.Front Plant Sci 8:1798
Kanazin V,Talbert H,See D,DeCamp P,Nevo E,Blake T(2002)Discovery and assay of single-nucleotide polymorphisms in barley(Hordeum vulgare).Plant Mol Biol 48:529-537
Kilian B,€Ozkan H,Kohl J,von Haeseler A,Barale F,Deusch O,Brandolini A,Yucel C,Martin W,Salamini F(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
Kilian B,€Ozkan H,Walther A,Kohl J,Dagan T,Salamini F,Martin W(2007)Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum(Einkorn)domestication:Implications for the origin of agriculture.Mol Biol Evol 24:2657-2668
Kjack JL,Witters RE(1974)Physiological activity of awns in isolines of Atlas Barley1.Crop Sci 14:243-248
Komatsuda T,Maxim P,Senthil N,Mano Y(2004)High-density AFLP map of nonbrittle rachis 1(btr1)and 2(btr2)genes in barley(Hordeum vulgare L.).Theor Appl Genet 109:986-995
Komatsuda T,Pourkheirandish M,He C,Azhaguvel P,Kanamori H,Perovic D,Stein N,Graner A,Wicker T,Tagiri A,Lundqvist U,Fujimura T,Matsuoka M,Matsumoto T,Yano M(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
Koren S,Schatz MC,Walenz BP,Martin J,Howard JT,Ganapathy G,Wang Z,Rasko DA,McCombie WR,Jarvis ED,Phillippy AM(2012)Hybrid error correction and de novo assembly of single-molecule sequencing reads.Nat Biotechnol 30:693-700
Kunert A,Naz AA,Dedeck O,Pillen K,Leon J(2007)AB-QTLanalysis in winter wheat:I.Synthetic hexaploid wheat(T.turgidum ssp.dicoccoides?T.tauschii)as a source of favourable alleles for milling and baking quality traits.Theor Appl Genet 115:683-695
Law CN,Sutka J,Worland AJ(1978)A Genetic study of daylength response in wheat.Heredity 41:185-191
Liller CB,Walla A,Boer MP,Hedley P,Macaulay M,Effgen S,von Korff M,van Esse GW,Koornneef M(2017)Fine mapping of a major QTL for awn length in barley using a multiparent mapping population.Theor Appl Genet 130:269-281
Ling H-Q,Zhao S,Liu D,Wang J,Sun H,Zhang C,Fan H,Li D,Dong L,Tao Y,Gao C,Wu H,Li Y,Cui Y,Guo X,Zheng S,Wang B,Yu K,Liang Q,Yang W,Lou X,Chen J,Feng M,Jian J,Zhang X,Luo G,Jiang Y,Liu J,Wang Z,Sha Y,Zhang B,Wu H,Tang D,Shen Q,Xue P,Zou S,Wang X,Liu X,Wang F,Yang Y,An X,Dong Z,Zhang K,Zhang X,Luo M-C,Dvorak J,Tong Y,Wang J,Yang H,Li Z,Wang D,Zhang A,Wang J(2013)Draft genome of the wheat A-genome progenitor Triticum urartu.Nature 496:87-90
Ling HQ,Ma B,Shi X,Liu H,Dong L,Sun H,Cao Y,Gao Q,Zheng S,Li Y,Yu Y,Du H,Qi M,Li Y,Lu H,Yu H,Cui Y,Wang N,Chen C,Wu H,Zhao Y,Zhang J,Li Y,Zhou W,Zhang B,Hu W,van Eijk MJT,Tang J,Witsenboer HMA,Zhao S,Li Z,Zhang A,Wang D,Liang C(2018)Genome sequence of the progenitor of wheat A subgenome Triticum urartu.Nature557:424-428
Longin CFH,W€urschum T(2016)Back to the Future-Tapping into ancient grains for food diversity.Trends Plant Sci 21:731-737
Luo MC,Gu YQ,Puiu D,Wang H,Twardziok SO,Deal KR,Huo N,Zhu T,Wang L,Wang Y,McGuire PE,Liu S,Long H,Ramasamy RK,Rodriguez JC,Van SL,Yuan L,Wang Z,Xia Z,Xiao L,Anderson OD,Ouyang S,Liang Y,Zimin AV,Pertea G,Qi P,Bennetzen JL,Dai X,Dawson MW,M€uller H-G,Kugler K,Rivarola-Duarte L,Spannagl M,Mayer KFX,Lu F-H,Bevan MW,Leroy P,Li P,You FM,Sun Q,Liu Z,Lyons E,Wicker T,Salzberg SL,Devos KM,Dvorak J(2017)Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.Nature 551:498-502
Luo MC,Yang ZL,You FM,Kawahara T,Waines JG,Dvorak J(2007)The structure of wild and domesticated emmer wheat populations,gene flow between them,and the site of emmer domestication.Theor Appl Genet 114:947-959
Maccaferri M,Sanguineti MC,Corneti S,Ortega JLA,Salem MB,Bort J,DeAmbrogio E,del Moral LFG,Demontis A,ElAhmed A,Maalouf F,Machlab H,Martos V,Moragues M,Motawaj J,Nachit M,Nserallah N,Ouabbou H,Royo C,Slama A,Tuberosa R(2008)Quantitative trait loci for grain yield and adaptation of durum wheat(Triticum durum Desf.)across a wide range of water availability.Genetics178:489-511
Marcussen T,Sandve SR,Heier L,Spannagl M,Pfeifer M,Jakobsen KS,Wulff BBH,Steuernagel B,Mayer KFX,Olsen OA(2014)Ancient hybridizations among the ancestral genomes of bread wheat.Science 345:1250092
Marino CL,Tuleen NA,Hart GE,Nelson JC,Sorrells ME,Lu YH,Leroy P,Lopes CR(1996)Molecular genetic maps of the group 6 chromosomes of hexaploid wheat(Triticum aestivum L.em.Thell.).Genome 39:359-366
Mascher M,Gundlach H,Himmelbach A,Beier S,Twardziok SO,Wicker T,Radchuk V,Dockter C,Hedley PE,Russell J,Bayer M,Ramsay L,Liu H,Haberer G,Zhang XQ,Zhang Q,Barrero RA,Li L,Taudien S,Groth M,Felder M,Hastie A,Simkova H,Stankova H,Vrana J,Chan S,Mu~noz-Amatria?n M,Ounit R,Wanamaker S,Bolser D,Colmsee C,Schmutzer T,Aliyeva-Schnorr L,Grasso S,Tanskanen J,Chailyan A,Sampath D,Heavens D,Clissold L,Cao S,Chapman B,Dai F,Han Y,Li H,Li X,Lin C,McCooke JK,Tan C,Wang P,Wang S,Yin S,Zhou G,Poland JA,Bellgard MI,Borisjuk L,Houben A,Dolezel J,Ayling S,Lonardi S,Kersey P,Langridge P,Muehlbauer GJ,Clark MD,Caccamo M,Schulman AH,Mayer KFX,Platzer M,Close TJ,Scholz U,Hansson M,Zhang G,Braumann I,Spannagl M,Li C,Waugh R,Stein N(2017)A chromosome conformation capture ordered sequence of the barley genome.Nature 544:427-433
Mascher M,Schuenemann VJ,Davidovich U,Marom N,Himmelbach A,H€ubner S,Korol A,David M,Reiter E,Riehl S,Schreiber M,Vohr SH,Green RE,Dawson IK,Russell J,Kilian B,Muehlbauer GJ,Waugh R,Fahima T,Krause J,Weiss E,Stein N(2016)Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.Nat Genet 48:1089-1093
Matus I,Corey A,Filichkin T,Hayes PM,Vales MI,Kling J,RieraLizarazu O,Sato K,Powell W,Waugh R(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
Maurer A,Draba V,Jiang Y,Schnaithmann F,Sharma R,Schumann E,Kilian B,Reif JC,Pillen K(2015)Modelling the genetic architecture of flowering time control in barley through nested association mapping.BMC Genomics 16:290
Mohler V,Lukman R,Ortiz-Islas S,William M,Worland AJ,van Beem J,Wenzel G(2004)Genetic and physical mapping of photoperiod insensitive gene Ppd-B1 in common wheat.Euphytica 138:33-40
Molina-Cano JL,Conde J(1980)Hordeum spontaneum C.Koch em.Bacht,collected in southern Morocco.Barley Genet Newsl 10:44-47
Mori N,Ishi T,Ishido T,Hirosawa S,Watatani H,Kawahara T,Nesbitt M,Belay G,Takumi S,Ogihara Y,Nakamura C(2003)Origins of domesticated emmer and common wheat inferred from chloroplast DNA fingerprinting.Tenth Int Wheat Genet Symp 2003:25-28
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
Morrell PL,Gonzales AM,Meyer KKT,Clegg MT(2014)Resequencing data indicate a modest effect of domestication on diversity in barley:A cultigen with multiple origins.J Hered 105:253-264
M€uller KJ,Romano N,Gerstner O,Garcia-Marotot F,Pozzi C,Salamini F,Rohde W(1995)The barley Hooded mutation caused by a duplication in a homeobox gene intron.Nature 374:727-730
M€uller T,Schierscher-Viret B,Fossati D,Brabant C,Schori A,Keller B,Krattinger SG(2018)Unlocking the diversity of genebanks:Whole-genome marker analysis of Swiss bread wheat and spelt.Theor Appl Genet 131:407-416
Muramatsu M(1963)Dosage effect of the spelta gene q of hexaploid wheat.Genetics 48:469-482
Nakamura S,Pourkheirandish M,Morishige H,Sameri M,Sato K,Komatsuda T(2017)Quantitative trait loci and maternal effects affecting the strong grain dormancy of wild barley(Hordeum vulgare ssp.spontaneum).Front Plant Sci 8:1840
Naz AA,Kunert A,Lind V,Pillen K,Leon J(2008)AB-QTLanalysis in winter wheat:II.Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population.Theor Appl Genet 116:1095-1104
Naz AA,Klaus M,Pillen K,Leon J(2015)Genetic analysis and detection of new QTL alleles for Septoria tritici blotch resistance using two advanced backcross wheat populations.Plant Breed 134:514-519
Nice LM,Steffenson BJ,Brown-Guedira GL,Akhunov ED,Liu C,Kono TJY,Morrell PL,Blake TK,Horsley RD,Smith KP,Muehlbauer GJ(2016)Development and genetic characterization of an advanced backcross-nested association mapping(AB-NAM)population of wild?cultivated barley.Genetics 203:1453-1467
Nielsen R(2000)Estimation of population parameters and recombination rates from single nucleotide polymorphisms.Genetics 154:931-942
Orabi J,Backes G,Wolday A,Yahyaoui A,Jahoor A(2007)The Horn of Africa as a centre of barley diversification and a potential domestication site.Theor Appl Genet 114:1117-1127
Osmont KS,Sibout R,Hardtke CS(2007)Hidden branches:Developments in root system architecture.Annu Rev Plant Biol 58:93-113
Ozkan H,Brandolini A,Pozzi C,Effgen S,Wunder J,Salamini F(2005)A reconsideration of the domestication geography of tetraploid wheats.Theor Appl Genet 110:1052-1060
€Ozkan H,Brandolini A,Sch€afer-Pregl R,Salamini F(2002)AFLPanalysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey.Mol Biol Evol 19:1797-1801
€Ozkan H,Willcox G,Graner A,Salamini F,Kilian B(2011)Geographic distribution and domestication of wild emmer wheat(Triticum dicoccoides).Genet Resour Crop Evol 58:11-53
Pankin A,Altm€uller J,Becker C,Korff M(2018)Targeted resequencing reveals genomic signatures of barley domestication.New Phytol 218:1247-1259
Pankin A,von Korff M(2017)Co-evolution of methods and thoughts in cereal domestication studies:A tale of barley(Hordeum vulgare).Curr Opin Plant Biol 36:15-21
Paterson AH,Lin YR,Li Z,Schertz KF,Doebley JF,Pinson SRM,Liu SC,Stansel JW,Irvine JE(1995)Convergent domestication of cereal crops by independent mutations at corresponding genetic loci.Science 269:1714-1718
Payne PI(1987)Genetics of wheat storage proteins and the effect of allelic variation on bread-making quality.Annu Rev Plant Physiol 38:141-153
Peng J,Sun D,Nevo E(2011)Wild emmer wheat,Triticum dicoccoides,occupies a pivotal position in wheat domestication process.Aust J Crop Sci 5:1127-1143
Piperno DR,Weiss E,Holst I,Nadel D(2004)Processing of wild cereal grains in the upper Palaeolithic revealed by starch grain analysis.Nature 430:670-673
Poets AM,Fang Z,Clegg MT,Morrell PL(2015)Barley landraces are characterized by geographically heterogeneous genomic origins.Genome Biol 16:173
Pont C,Salse J(2017)Wheat paleohistory created asymmetrical genomic evolution.Curr Opin Plant Biol 36:29-37
Pourkheirandish M,Hensel G,Kilian B,Senthil N,Chen G,Sameri M,Azhaguvel P,Sakuma S,Dhanagond S,Sharma R,Mascher M,Himmelbach A,Gottwald S,Nair Sudha K,Tagiri A,Yukuhiro F,Nagamura Y,Kanamori H,Matsumoto T,Willcox G,Middleton Christopher P,Wicker T,Walther A,Waugh R,Fincher Geoffrey B,Stein N,Kumlehn J,Sato K,Komatsuda T(2015)Evolution of the grain dispersal system in barley.Cell 162:527-539
Pourkheirandish M,Kanamori H,Wu J,Sakuma S,Blattner FR,Komatsuda T(2018)Elucidation of the origin of“agriocrithon”based on domestication genes questions the hypothesis that Tibet is one of the centers of barley domestication.Plant J 94:525-534
Purugganan MD,Fuller DF(2011)Archeaological data reveal slow rates of evolution during plant domestication.Evolution 65:171-183
Ram?rez-Gonzalez RH,Borrill P,Lang D,Harrington SA,Brinton J,Venturini L,Davey M,Jacobs J,van Ex F,Pasha A,Khedikar Y,Robinson SJ,Cory AT,Florio T,Concia L,Juery C,Shoonbeek H,Steuernagel B,Xiang D,Ridout CJ,Chalhoub B,Mayer KFX,Benhamed M,Latrasse D,Bendahmane A,IWGSC,Wulff BBH,Appels R,Tiwari V,Dalta R,Choulet F,Pozniak CJ,Provart NJ,Sharpe AG,Paux E,Spannagl M,Br€autigam A,Uauy C(2018)The transcriptional landscape of polyploid wheat.Science361:6089
Ramsay L,Comadran J,Druka A,Marshall DF,Thomas WTB,Macaulay M,MacKenzie K,Simpson C,Fuller J,Bonar N,Hayes PM,Lundqvist U,Franckowiak JD,Close TJ,Muehlbauer GJ,Waugh R(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
Ramsay L,Macaulay M,Ivanissevich S,MacLean K,Cardle L,Fuller J,Edwards KJ,Tuvesson S,Morgante M,Massari A,Maestri E,Marmiroli N,Sjakste T,Ganal M,Powell W,Waugh R(2000)A simple sequence repeat-based linkage map of barley.Genetics 156:1997-2005
Rebetzke GJ,Bonnett DG,Reynolds MP,Awns reduce grain number to increase grain size and harvestable yield in irrigated and rainfed spring wheat,J Exp Bot 67:2573-2586
Ren X,Nevo E,Sun D,Sun G(2013)Tibet as a potential domestication center of cultivated barley of China.PLoSONE 8:e62700
R€oder MS,Korzun V,Wendehake K,Plaschke J,Tixier MH,Leroy P,Ganal MW(1998)A microsatellite map of wheat.Genetics 149:2007-2023
Russell J,Zonneveld van M,Dawson IK,Booth A,Waugh R,Steffenson B(2014)Genetid diversity and ecological niche modelling of wild barley:Refugia,large-scale post-LGMrange expansion and limited mid-future climate threats.PLoS ONE 9:e86021
Russell J,Mascher M,Dawson IK,Kyriakidis S,Calixto C,Freund F,Bayer M,Milne I,Marshall-Griffiths T,Heinen S,Hofstad A,Sharma R,Himmelbach A,Knauft M,van Zonneveld M,Brown JWS,Schmid K,Kilian B,Muehlbauer GJ,Stein N,Waugh R(2016)Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation.Nat Genet48:1024-1030
Saisho D,Ishii M,Hori K,Sato K(2011)Natural variation of barley vernalization requirements:Implication of quantitative variation of winter growth habit as an adaptive trait in east Asia.Plant Cell Physiol 52:775-784
Sakuma S,Golan G,Guo Z,Ogawa T,Tagiri A,Sugimoto K,Bernhardt N,Brassac J,Mascher M,Hensel G,Ohnishi S,Jinno H,Yamashita Y,Ayalon I,Peleg Z,Schnurbusch T,Komatsuda T(2018)Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication.bioRxiv 434985doi:10.1101/434985
Salamini F,€Ozkan H,Brandolini A,Sch€afer-Pregl R,Martin W(2002)Genetics and geography of wild cereal domestication in the near east.Nat Rev Genet 3:429-441
Sanchez-Leon S,Gil-Humanes J,Ozuna Carmen V,Gimenez Mar?a J,Sousa C,Voytas Daniel F,Barro F(2017)Lowgluten,nontransgenic wheat engineered with CRISPR/Cas9.Plant Biotechnol J 16:902-910
Schmalenbach I,March TJ,Bringezu T,Waugh R,Pillen K(2011)High-resolution genotyping of wild barley introgression lines and fine-mapping of the threshability locus thresh-1using the Illumina GoldenGate assay.G3-Genes Genom Genet 1:187-196
Scott JC,Manisterski J,Sela H,Ben-Yehuda P,Steffenson BJ(2014)Resistance of Aegilops species from Israel to widely virulent African and Israeli races of the wheat stem rust pathogen.Plant Dis 98:1309-1320
Simons KJ,Fellers JP,Trick HN,Zhang Z,Tai YS,Gill BS,Faris JD(2006)Molecular characterization of the major wheat domestication gene Q.Genetics 172:547-555
Sood S,Kuraparthy V,Bai G,Gill BS(2009)The major threshability genes soft glume(sog)and tenacious glume(Tg),of diploid and polyploid wheat,trace their origin to independent mutations at non-orthologous loci.Theor Appl Genet 119:341-351
Sorensen AE(1986)Seed dispersal by adhesion.Annu Rev of Ecol Syst 17:443-463
Sourdille P,Cadalen T,Gay G,Gill B,Bernard M(2008)Molecular and physical mapping of genes affecting awning in wheat.Plant Breed 121:320-324
Steffenson BJ,Olivera P,Roy JK,Jin Y,Smith KP,Muehlbauer GJ(2007)A walk on the wild side:Mining wild wheat and barley collections for rust resistance genes.Aust J Agric Res 58:532-544
Stein JC,Yu Y,Copetti D,Zwickl DJ,Zhang L,Zhang C,Chougule K,Gao D,Iwata A,Goicoechea JL,Wei S,Wang J,Liao Y,Wang M,Jacquemin J,Becker C,Kudrna D,Zhang J,Londono CEM,Song X,Lee S,Sanchez P,Zuccolo A,Ammiraju JSS,Talag J,Danowitz A,Rivera LF,Gschwend AR,Noutsos C,Wu C-C,Kao S-M,Zeng J-W,Wei F-J,Zhao Q,Feng Q,El Baidouri M,Carpentier M-C,Lasserre E,Cooke R,Rosa Farias D,da Maia LC,dos Santos RS,Nyberg KG,McNally KL,Mauleon R,Alexandrov N,Schmutz J,Flowers D,Fan C,Weigel D,Jena KK,Wicker T,Chen M,Han B,Henry R,Hsing Y-C,Kurata N,de Oliveira AC,Panaud O,Jackson SA,Machado CA,Sanderson MJ,Long M,Ware D,Wing RA(2018)Genomes of 13 domesticated and wild rice relatives highlight genetic conservation,turnover and innovation across the genus Oryza.Nat Genet 50:285-296
Swanson-Wagner RA,Eichten SR,Kumari S,Tiffin P,Stein JC,Ware D,Springer NM(2010)Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.Genome Res 20:1-11
Taenzler B,Esposti RF,Vaccino P,Brandolini A,Effgen S,Heun M,Sch€AFer-Pregl R,Borghi B,Salamini F(2002)Molecular linkage map of Einkorn wheat:Mapping of storage-protein and soft-glume genes and bread-making quality QTLs.Genet Res 80:131-143
Taketa S,Amano S,Tsujino Y,Sato T,Saisho D,Kakeda K,Nomura M,Suzuki T,Matsumoto T,Sato K,Kanamori H,Kawasaki S,Takeda K(2008)Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway.Proc Natl Acad Sci USA 105:4062-4067
Tanksley SD,Nelson JC(1996)Advanced backcross QTLanalysis:A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines.Theor Appl Genet 92:191-203
Tiwari VK,Wang S,Sehgal S,Vrana J,Friebe B,Kubalakova M,Chhuneja P,Dolezel J,Akhunov E,Kalia B,Sabir J,Gill BS(2014)SNP discovery for mapping alien introgressions in wheat.BMC Genomics 15:273
Torada A,Amano Y(2002)Effect of seed coat color on seed dormancy in different environments.Euphytica 126:99-105
Trevaskis B,Bagnall DJ,Ellis MH,Peacock WJ,Dennis ES(2003)MADS box genes control vernalization-induced flowering in cereals.Proc Natl Acad Sci USA 100:13099-13104
Turner A,Beales J,Faure S,Dunford RP,Laurie DA(2005)The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley.Science 310:1031-1034
Uauy C,Distelfeld A,Fahima T,Blechl A,Dubcovsky J(2006)A NAC gene regulating senescence improves grain protein,zinc,and iron content in wheat.Science 314:1298
Varshney RK,Marcel TC,Ramsay L,Russell J,R€oder MS,Stein N,Waugh R,Langridge P,Niks RE,Graner A(2007)A high density barley microsatellite consensus map with 775 SSRloci.Theor Appl Genet 114:1091-1103
Vavilov NI,Freier F(1926)Studies on The Origin of Cultivated Plants.Trudi Po Prikl bot gen i Selek 16
Wang J,Luo MC,Chen Z,You FM,Wei Y,Zheng Y,Dvorak J(2013)Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat.New Phytol 198:925-937
Wang S,Wong D,Forrest K,Allen A,Chao S,Huang BE,Maccaferri M,Salvi S,Milner SG,Cattivelli L,Mastrangelo AM,Whan A,Stephen S,Barker G,Wieseke R,Plieske J,International Wheat Genome Sequencing C,Lillemo M,Mather D,Appels R,Dolferus R,Brown-Guedira G,Korol A,Akhunova AR,Feuillet C,Salse J,Morgante M,Pozniak C,Luo M-C,Dvorak J,Morell M,Dubcovsky J,Ganal M,Tuberosa R,Lawley C,Mikoulitch I,Cavanagh C,Edwards KJ,Hayden M,Akhunov E(2014)Characterization of polyploid wheat genomic diversity using a high-density90000 single nucleotide polymorphism array.Plant Biotechnol J 12:787-796
Watanabe N,Sugiyama K,Yamagishi Y,Sakata Y(2002)Comparative telosomic mapping of homoeologous genes for brittle rachis in tetraploid and hexaploid wheats.Hereditas 137:180-185
Wendler N,Mascher M,Himmelbach A,Johnston P,Pickering R,Stein N(2015)Bulbosum to Go:A toolbox to utilize Hordeum vulgare/bulbosum introgressions for breeding and beyond.Mol Plant 8:1507-1519
Wilhelm EP,Turner AS,Laurie DA(2009)Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat(Triticum durum Desf.).Theor Appl Genet 118:285-294
Winfield MO,Wilkinson PA,Allen AM,Barker GLA,Coghill JA,Burridge A,Hall A,Brenchley RC,D’Amore R,Hall N,Bevan MW,Richmond T,Gerhardt DJ,Jeddeloh JA,Edwards KJ(2012)Targeted re-sequencing of the allohexaploid wheat exome.Plant Biotechnol J 10:733-742
Yan L,Loukoianov A,Tranquilli G,Helguera M,Fahima T,Dubcovsky J(2003)Positional cloning of the wheat vernalization gene VRN1.Proc Natl Acad Sci USA 100:6263-6268
Yan L,Loukoianov A,Blechl A,Tranquilli G,Ramakrishna W,San Miguel P,Bennetzen JL,Echenique V,Dubcovsky J(2004)The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.Science 303:1640-1644
Yan L,Fu D,Li C,Blechl A,Tranquilli G,Bonafede M,Sanchez A,Valarik M,Yasuda S,Dubcovsky J(2006)The wheat and barley vernalization gene VRN3 is an orthologue of FT.Proc Natl Acad Sci USA 103:19581-19586
Yoshioka M,Iehisa JCM,Ohno R,Kimura T,Enoki H,Nishimura S,Nasuda S,Takumi S(2017)Three dominant awnless genes in common wheat:Fine mapping,interaction and contribution to diversity in awn shape and length.PLoSONE 12:e0176148
Yu G,Champouret N,Steuernagel B,Olivera PD,Simmons J,Williams C,Johnson R,Moscou MJ,Hernandez-Pinzon I,Green P,Sela H,Millet E,Jones JDG,Ward ER,Steffenson BJ,Wulff BBH(2017)Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis.Theor Appl Genet 130:1207-1222
Yu J,Holland JB,McMullen MD,Buckler ES(2008)Genetic design and statistical power of nested association mapping in maize.Genetics 178:539-551
Yuo T,Yamashita Y,Kanamori H,Matsumoto T,Lundqvist U,Sato K,Ichii M,Jobling SA,Taketa S(2012)A SHORTINTERNODES(SHI)family transcription factor gene regulates awn elongation and pistil morphology in barley.J Exp Bot 63:5223-5232
Zakhrabekova S,Gough P,Braumann I,M€uller AH,Lundqvist J,Ahmann K,Dockter C,Matyszczak I,Kurowska M,Druka A,Waugh R,Graner A,Stein N,Steuernagel B,Lundqvist U,Hansson M(2012)Induced mutations in circadian clock regulator Mat-a factilitated short-season adaptation and range extension in cultivated barley.Proc Natl Acad Sci USA 109:4326-4331
Zhang Z,Belcram H,Gornicki P,Charles M,Just J,Huneau C,Magdelenat G,Couloux A,Samain S,Gill BS,Rasmussen JB,Barbe V,Faris JD,Chalhoub B(2011)Duplication and partitioning in evolution and function of homoeologous Q;loci governing domestication characters in polyploid wheat.Proc Natl Acad Sci USA 108:18737-18742
Zhao G,Zou C,Li K,Wang K,Li T,Gao L,Zhang X,Wang H,Yang Z,Liu X,Jiang W,Mao L,Kong X,Jiao Y,Jia J(2017)The Aegilops tauschii genome reveals multiple impacts of transposons.Nat Plants 3:946-955
Zhao Q,Feng Q,Lu H,Li Y,Wang A,Tian Q,Zhan Q,Lu Y,Zhang L,Huang T,Wang Y,Fan D,Zhao Y,Wang Z,Zhou C,Chen J,Zhu C,Li W,Weng Q,Xu Q,Wang ZX,Wei X,Han B,Huang X(2018)Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.Nat Genet50:278-284
Zimin AV,Puiu D,Hall R,Kingan S,Clavijo BJ,Salzberg SL(2017a)The first near-complete assembly of the hexaploid bread wheat genome,Triticum aestivum.GigaScience 6:1-7
Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Mar Sc ais G,Yorke JA,Dvorak J,Salzberg SL(2017b)Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii,a progenitor of bread wheat,with the MaSuRCA mega-reads algorithm.Genome Res 27:787-792
Zohary D(1959)Is Hordeum agriocrithon the ancestor of sixrowed cultivated barley?Evolution 13:279-280
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 on Demand,Oxford,United Kingdom
Abbo S,van-Oss RP,Gopher A,Saranga Y,Ofner I,Peleg Z(2014)Plant domestication versus crop evolution:Aconceptual framework for cereals and grain legumes.Trends Plant Sci 19:351-360
A?berg E(1938)Hordeum agriocrithon nova sp.,a wild sixrowed barley.Ann Agric Coll Sweden 6:159-216
Allaby RG,Fuller DQ,Brown TA(2008)The genetic expectations of a protracted model for the origins of domesticated crops.Proc Natl Acad Sci USA 105:13982-13986
Allaby RG,Stevens C,Lucas L,Maeda O,Fuller DQ(2017)Geographic mosaics and changing rates of cereal domestication.Philos Trans R Soc B Biol Sci 372:20160429
Arranz-Otaegui A,Carretero LG,Ramsey MN,Fuller DQ,Richter T(2018)Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan.Proc Natl Acad Sci USA 115:7925-7930
Avni R,Nave M,Barad O,Baruch K,Twardziok SO,Gundlach H,Hale I,Mascher M,Spannagl M,Wiebe K,Jordan KW,Golan G,Deek J,Ben-Zvi B,Ben-Zvi G,Himmelbach A,MacLachlan RP,Sharpe AG,Fritz A,Ben-David R,Budak H,Fahima T,Korol A,Faris JD,Hernandez A,Mikel MA,Levy AA,Steffenson B,Maccaferri M,Tuberosa R,Cattivelli L,Faccioli P,Ceriotti A,Kashkush K,Pourkheirandish M,Komatsuda T,Eilam T,Sela H,Sharon A,Ohad N,Chamovitz DA,Mayer KFX,Stein N,Ronen G,Peleg Z,Pozniak CJ,Akhunov ED,Distelfeld A(2017)Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.Science 357:93-97
Azhaguvel P,Komatsuda T(2007)A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley.Ann Bot 100:1009-1015
Badr A,Muller K,Schafer R,El Rabey HE,Effgen S,Ibrahim HH,Pozzi C,Rohde W,Salamini F(2000)On the origin and domestication history of barley(Hordeum vulgare).Mol Biol Evol 17:499-510
Bayer MM,Rapazote-Flores P,Ganal M,Hedley PE,Macaulay M,Plieske J,Ramsay L,Russell J,Shaw PD,Thomas W,Waugh R(2017)Development and evaluation of a barley50k i Select SNP array.Front Plant Sci 8:1792
Beales J,Turner A,Griffiths S,Snape JW,Laurie DA(2007)A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat(Triticum aestivum L.).Theor Appl Genet 115:721-733
Blake NK,Lehfeldt BR,Lavin M,Talbert LE(1999)Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid:The B genome of wheat.Genome 42:351-360
Blatter RHE,Jacomet S,Schlumbaum A(2004)About the origin of European spelt(Triticum spelta L.):Allelic differentiation of the HMW Glutenin B1-1 and A1-2 subunit genes.Theor Appl Genet 108:360-367
Blattner FR,Badani Mendez AG(2001)RAPD data do not support a second centre of barley domestication in Morocco.Genet Resour Crop Evol 48:13-19
von Bothmer R,Jacobsen N,Baden C,Jorgensen R,LindeLaursen I(1995)An Ecogeographical Study of The Genus Hordeum,2nd edn.Rome:International Plant Genetic Resources Institute
B€orner A,Sch€afer M,Schmidt A,Grau M,Vorwald J(2005)Associations between geographical origin and morphological characters in bread wheat(Triticum aestivum L.).Plant Genet Resour 3:360-372
Brenchley R,Spannagl M,Pfeifer M,Barker GLA,D’Amore R,Allen AM,McKenzie N,Kramer M,Kerhornou A,Bolser D,Kay S,Waite D,Trick M,Bancroft I,Gu Y,Huo N,Luo M-C,Sehgal S,Gill B,Kianian S,Anderson O,Kersey P,Dvorak J,McCombie R,Hall A,Mayer KFX,Edwards KJ,Bevan MW,Hall N(2012)Analysis of the bread wheat genome using whole-genome shotgun sequencing.Nature 491:705-710
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
Chalupska D,Lee HY,Faris JD,Evrard A,Chalhoub B,Haselkorn R,Gornicki P(2008)Acc homoeoloci and the evolution of wheat genomes.Proc Natl Acad Sci USA 105:9691-9696
Chao S,Sharp PJ,Worland AJ,Warham EJ,Koebner RMD,Gale MD(1989)RFLP-based genetic maps of wheat homoeologous group 7 chromosomes.Theor Appl Genet 78:495-504
Chen FH,Dong GH,Zhang DJ,Liu XY,Jia X,An CB,Ma MM,Xie YW,Barton L,Ren XY,Zhao ZJ,Wu XH,Jones MK(2015)Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.Science 347:248-250
Chen QF,Yen C,Yang JL(1998)Chromosome location of the gene for brittle rachis in the Tibetan weedrace of common wheat.Genet Resour Crop Evol 45:407-410
Choo TM,Ho KM,Martin RA(2001)Genetic analysis of a hulless?covered cross of barley using doubled-haploid lines.Crop Sci 41:1021-1026
Civan P,Brown TA(2017)A novel mutation conferring the nonbrittle phenotype of cultivated barley.New Phytol 214:468-472
Civan P,Ivanicova Z,Brown TA(2013)Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the Fertile Crescent.PLoS ONE 8:e81955
Clavijo BJ,Venturini L,Schudoma C,Accinelli GG,Kaithakottil G,Wright J,Borrill P,Kettleborough G,Heavens D,Chapman H,Lipscombe J,Barker T,Lu F-H,McKenzie N,Raats D,Ramirez-Gonzalez RH,Coince A,Peel N,PercivalAlwyn L,Duncan O,Tr€osch J,Yu G,Bolser DM,Namaati G,Kerhornou A,Spannagl M,Gundlach H,Haberer G,Davey RP,Fosker C,Palma FD,Phillips AL,Millar AH,Kersey PJ,Uauy C,Krasileva KV,Swarbreck D,Bevan MW,Clark MD(2017)An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.Genome Res 27:885-896
Close TJ,Bhat PR,Lonardi S,Wu Y,Rostoks N,Ramsay L,Druka A,Stein N,Svensson JT,Wanamaker S,Bozdag S,Roose ML,Moscou MJ,Chao S,Varshney RK,Sz}ucs P,Sato K,Hayes PM,Matthews DE,Kleinhofs A,Muehlbauer GJ,DeYoung J,Marshall DF,Madishetty K,Fenton RD,Condamine P,Graner A,Waugh R(2009)Development and implementation of high-throughput SNP genotyping in barley.BMC Genomics 10:582
Comadran J,Kilian B,Russell J,Ramsay L,Stein N,Ganal M,Shaw P,Bayer M,Thomas W,Marshall D,Hedley P,Tondelli A,Pecchioni N,Francia E,Korzun V,Walther A,Waugh R(2012)Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley.Nat Genet 44:1388-1393
Dai F,Nevo E,Wu D,Comadran J,Zhou M,Qiu L,Chen Z,Beiles A,Chen G,Zhang G(2012)Tibet is one of the centers of domestication of cultivated barley.Proc Natl Acad Sci USA109:16969-16973
Debernardi JM,Lin H,Chuck G,Faris JD,Dubcovsky J(2017)microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability.Development 144:1966-1975
Distelfeld A,Korol A,Dubcovsky J,Uauy C,Blake T,Fahima T(2008)Colinearity between the barley grain protein content(GPC)QTL on chromosome arm 6HS and the wheat Gpc-B1 region.Mol Breed 22:25-38
Dixon LE,Greenwood JR,Bencivenga S,Zhang P,Cockram J,Mellers G,Ramm K,Cavanagh C,Swain SM,Boden SA(2018)TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat(Triticum aestivum L.).Plant Cell 30:563-581
Doebley JF,Gaut BS,Smith BD(2006)The molecular genetics of crop domestication.Cell 127:1309-1321
Dubcovsky J,Lijavetzky D,Appendino L,Tranquilli G(1998)Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement.Theor Appl Genet 97:968-975
Dubcovsky J,Dvorak J(2007)Genome plasticity a key factor in the success of polyploid wheat under domestication.Science 316:1862-1866
Dvorak J,Deal KR,Luo MC,You FM,von Borstel K,Dehghani H(2012)The origin of spelt and free-threshing hexaploid wheat.J Hered 103:426-441
Dvorak J,Terlizzi P,Zhang HB,Resta P(1993)The evolution of polyploid wheats:Identification of the A genome donor species.Genome 36:21-31
Elbaum R,Zaltzman L,Burgert I,Fratzl P(2007)The role of wheat awns in the seed dispersal unit.Science 316:884-886
Faris JD,Fellers JP,Brooks SA,Gill BS(2003)A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene.Genetics 164:311-321
Faris JD,Zhang Z,Chao S(2014)Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication.Gene 542:198-208
Faure S,Turner AS,Gruszka D,Christodoulou V,Davis SJ,von Korff M,Laurie DA(2012)Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley(Hordeum vulgare)to short growing seasons.Proc Natl Acad Sci USA 109:8328-8333
Fuller DQ(2007)Contrasting patterns in crop domestication and domestication rates:Recent achaeobotanical insights from the old world.Ann Bot 100:903-924
Gao L,Dorn K,Rife TW,Wang X,Lemes C,Clinesmith M,Silva P,Fritz A,Stein N,Mascher M,Poland J(2018)Completion of the‘Jagger’wheat genome leads to identification of Aegilops ventricosa 2NS translocation and its impact in wheat breeding.(https://pag.confex.com/pag/xxvi/meet ingapp.cgi/Paper/30261)
Glemin S,Scornavacca C,Dainat J,Burgarella C,Viader V,Ardisson M,Sarah G,Santoni S,David J,Ranwez V(2018)Pervasive hybridizations in the history of wheat relatives.bioRxiv 300848 doi:10.1101/300848
Golan G,Hendel E,Mendez Espitia GE,Schwartz N,Peleg Z(2018)Activation of seminal root primordia during wheat domestication reveals underlying mechanisms of plant resilience.Plant Cell Environ 41:755-766
Gorafi YSA,Kim JS,Elbashir AAE,Tsujimoto H(2018)A population of wheat multiple synthetic derivatives:An effective platform to explore,harness and utilize genetic diversity of Aegilops tauschii for wheat improvement.Theor Appl Genet 131:1615-1626
Groos C,Gay G,Perretant MR,Gervais L,Bernard M,Dedryver F,Charmet G(2002)Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white?red grain bread-wheat cross.Theor Appl Genet 104:39-47
Harlan JR,Zohary D(1966)Distribution of wild wheats and barley.Science 153:1074-1080
Harris DR(1989)An evolutionary continuum of people-plant interaction.In:Harris DR,Hillman GC,eds.Foraging and Farming:The Evolution of Plant Exploitation.Routledge,London.pp.11-26
Heun M,Abbo S,Lev-Yadun S,Gopher A(2012)A critical review of the protracted domestication model for Near-Eastern founder crops:Linear regression,long-distance gene flow,archaeological,and archaeobotanical evidence.J Exp Bot63:4333-4341
Heun M,Haldorsen S,Vollan K(2008)Reassessing domestication events in the Near East:Einkorn and Triticum urartu.Genome 51:444-451
Heun M,Sch€afer-Pregl R,Klawan D,Castagna R,Accerbi M,Borghi B,Salamini F(1997)Site of einkorn wheat domestication identified by DNA fingerprinting.Science278:1312-1314
Huang S,Steffenson B,Sela H,Stinebaugh K(2018)Resistance of Aegilops longissima to the rusts of wheat.Plant Dis 102:1124-1135
International Barley Genome Sequencing C(2012)A physical,genetic and functional sequence assembly of the barley genome.Nature 491:711-716
International Wheat Genome Sequencing Consortium(2014)A chromosome-based draft sequence of the hexaploid bread wheat Triticum aestivum genome.Science 345:1251788
International Wheat Genome Sequencing Consortium(2018)Shifting the limits in wheat research and breeding using a fully annotated reference genome.Science 361:eaar7191
Jakob SS,R€odder D,Engler JO,Shaaf S,€Ozkan H,Blattner FR,Kilian B(2014)Evolutionary history of wild barley(Hordeum vulgare subsp.spontaneum)analyzed using multilocus sequence data and paleodistribution modeling.Genome Biol Evol 6:685-702
Jia J,Zhao S,Kong X,Li Y,Zhao G,He W,Appels R,Pfeifer M,Tao Y,Zhang X,Jing R,Zhang C,Ma Y,Gao L,Gao C,Spannagl M,Mayer KFX,Li D,Pan S,Zheng F,Hu Q,Xia X,Li J,Liang Q,Chen J,Wicker T,Gou C,Kuang H,He G,Luo Y,Keller B,Xia Q,Lu P,Wang J,Zou H,Zhang R,Xu J,Gao J,Middleton C,Quan Z,Liu G,Wang J,International Wheat Genome Sequencing C,Yang H,Liu X,He Z,Mao L,Wang J(2013)Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation.Nature 496:91-95
Jordan KW,Wang S,Lun Y,Gardiner LJ,MacLachlan R,Hucl P,Wiebe K,Wong D,Forrest KL,Sharpe AG,Sidebottom CH,Hall N,Toomajian C,Close T,Dubcovsky J,Akhunova A,Talbert L,Bansal UK,Bariana HS,Hayden MJ,Pozniak C,Jeddeloh JA,Hall A,Akhunov E(2015)A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.Genome Biol 16:48
Jorgensen C,Luo MC,Ramasamy R,Dawson M,Gill BS,Korol AB,Distelfeld A,Dvorak J(2017)A high-density genetic map of wild emmer wheat from the Karaca Dag region provides new evidence on the structure and evolution of wheat chromosomes.Front Plant Sci 8:1798
Kanazin V,Talbert H,See D,DeCamp P,Nevo E,Blake T(2002)Discovery and assay of single-nucleotide polymorphisms in barley(Hordeum vulgare).Plant Mol Biol 48:529-537
Kilian B,€Ozkan H,Kohl J,von Haeseler A,Barale F,Deusch O,Brandolini A,Yucel C,Martin W,Salamini F(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
Kilian B,€Ozkan H,Walther A,Kohl J,Dagan T,Salamini F,Martin W(2007)Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum(Einkorn)domestication:Implications for the origin of agriculture.Mol Biol Evol 24:2657-2668
Kjack JL,Witters RE(1974)Physiological activity of awns in isolines of Atlas Barley1.Crop Sci 14:243-248
Komatsuda T,Maxim P,Senthil N,Mano Y(2004)High-density AFLP map of nonbrittle rachis 1(btr1)and 2(btr2)genes in barley(Hordeum vulgare L.).Theor Appl Genet 109:986-995
Komatsuda T,Pourkheirandish M,He C,Azhaguvel P,Kanamori H,Perovic D,Stein N,Graner A,Wicker T,Tagiri A,Lundqvist U,Fujimura T,Matsuoka M,Matsumoto T,Yano M(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
Koren S,Schatz MC,Walenz BP,Martin J,Howard JT,Ganapathy G,Wang Z,Rasko DA,McCombie WR,Jarvis ED,Phillippy AM(2012)Hybrid error correction and de novo assembly of single-molecule sequencing reads.Nat Biotechnol 30:693-700
Kunert A,Naz AA,Dedeck O,Pillen K,Leon J(2007)AB-QTLanalysis in winter wheat:I.Synthetic hexaploid wheat(T.turgidum ssp.dicoccoides?T.tauschii)as a source of favourable alleles for milling and baking quality traits.Theor Appl Genet 115:683-695
Law CN,Sutka J,Worland AJ(1978)A Genetic study of daylength response in wheat.Heredity 41:185-191
Liller CB,Walla A,Boer MP,Hedley P,Macaulay M,Effgen S,von Korff M,van Esse GW,Koornneef M(2017)Fine mapping of a major QTL for awn length in barley using a multiparent mapping population.Theor Appl Genet 130:269-281
Ling H-Q,Zhao S,Liu D,Wang J,Sun H,Zhang C,Fan H,Li D,Dong L,Tao Y,Gao C,Wu H,Li Y,Cui Y,Guo X,Zheng S,Wang B,Yu K,Liang Q,Yang W,Lou X,Chen J,Feng M,Jian J,Zhang X,Luo G,Jiang Y,Liu J,Wang Z,Sha Y,Zhang B,Wu H,Tang D,Shen Q,Xue P,Zou S,Wang X,Liu X,Wang F,Yang Y,An X,Dong Z,Zhang K,Zhang X,Luo M-C,Dvorak J,Tong Y,Wang J,Yang H,Li Z,Wang D,Zhang A,Wang J(2013)Draft genome of the wheat A-genome progenitor Triticum urartu.Nature 496:87-90
Ling HQ,Ma B,Shi X,Liu H,Dong L,Sun H,Cao Y,Gao Q,Zheng S,Li Y,Yu Y,Du H,Qi M,Li Y,Lu H,Yu H,Cui Y,Wang N,Chen C,Wu H,Zhao Y,Zhang J,Li Y,Zhou W,Zhang B,Hu W,van Eijk MJT,Tang J,Witsenboer HMA,Zhao S,Li Z,Zhang A,Wang D,Liang C(2018)Genome sequence of the progenitor of wheat A subgenome Triticum urartu.Nature557:424-428
Longin CFH,W€urschum T(2016)Back to the Future-Tapping into ancient grains for food diversity.Trends Plant Sci 21:731-737
Luo MC,Gu YQ,Puiu D,Wang H,Twardziok SO,Deal KR,Huo N,Zhu T,Wang L,Wang Y,McGuire PE,Liu S,Long H,Ramasamy RK,Rodriguez JC,Van SL,Yuan L,Wang Z,Xia Z,Xiao L,Anderson OD,Ouyang S,Liang Y,Zimin AV,Pertea G,Qi P,Bennetzen JL,Dai X,Dawson MW,M€uller H-G,Kugler K,Rivarola-Duarte L,Spannagl M,Mayer KFX,Lu F-H,Bevan MW,Leroy P,Li P,You FM,Sun Q,Liu Z,Lyons E,Wicker T,Salzberg SL,Devos KM,Dvorak J(2017)Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.Nature 551:498-502
Luo MC,Yang ZL,You FM,Kawahara T,Waines JG,Dvorak J(2007)The structure of wild and domesticated emmer wheat populations,gene flow between them,and the site of emmer domestication.Theor Appl Genet 114:947-959
Maccaferri M,Sanguineti MC,Corneti S,Ortega JLA,Salem MB,Bort J,DeAmbrogio E,del Moral LFG,Demontis A,ElAhmed A,Maalouf F,Machlab H,Martos V,Moragues M,Motawaj J,Nachit M,Nserallah N,Ouabbou H,Royo C,Slama A,Tuberosa R(2008)Quantitative trait loci for grain yield and adaptation of durum wheat(Triticum durum Desf.)across a wide range of water availability.Genetics178:489-511
Marcussen T,Sandve SR,Heier L,Spannagl M,Pfeifer M,Jakobsen KS,Wulff BBH,Steuernagel B,Mayer KFX,Olsen OA(2014)Ancient hybridizations among the ancestral genomes of bread wheat.Science 345:1250092
Marino CL,Tuleen NA,Hart GE,Nelson JC,Sorrells ME,Lu YH,Leroy P,Lopes CR(1996)Molecular genetic maps of the group 6 chromosomes of hexaploid wheat(Triticum aestivum L.em.Thell.).Genome 39:359-366
Mascher M,Gundlach H,Himmelbach A,Beier S,Twardziok SO,Wicker T,Radchuk V,Dockter C,Hedley PE,Russell J,Bayer M,Ramsay L,Liu H,Haberer G,Zhang XQ,Zhang Q,Barrero RA,Li L,Taudien S,Groth M,Felder M,Hastie A,Simkova H,Stankova H,Vrana J,Chan S,Mu~noz-Amatria?n M,Ounit R,Wanamaker S,Bolser D,Colmsee C,Schmutzer T,Aliyeva-Schnorr L,Grasso S,Tanskanen J,Chailyan A,Sampath D,Heavens D,Clissold L,Cao S,Chapman B,Dai F,Han Y,Li H,Li X,Lin C,McCooke JK,Tan C,Wang P,Wang S,Yin S,Zhou G,Poland JA,Bellgard MI,Borisjuk L,Houben A,Dolezel J,Ayling S,Lonardi S,Kersey P,Langridge P,Muehlbauer GJ,Clark MD,Caccamo M,Schulman AH,Mayer KFX,Platzer M,Close TJ,Scholz U,Hansson M,Zhang G,Braumann I,Spannagl M,Li C,Waugh R,Stein N(2017)A chromosome conformation capture ordered sequence of the barley genome.Nature 544:427-433
Mascher M,Schuenemann VJ,Davidovich U,Marom N,Himmelbach A,H€ubner S,Korol A,David M,Reiter E,Riehl S,Schreiber M,Vohr SH,Green RE,Dawson IK,Russell J,Kilian B,Muehlbauer GJ,Waugh R,Fahima T,Krause J,Weiss E,Stein N(2016)Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.Nat Genet 48:1089-1093
Matus I,Corey A,Filichkin T,Hayes PM,Vales MI,Kling J,RieraLizarazu O,Sato K,Powell W,Waugh R(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
Maurer A,Draba V,Jiang Y,Schnaithmann F,Sharma R,Schumann E,Kilian B,Reif JC,Pillen K(2015)Modelling the genetic architecture of flowering time control in barley through nested association mapping.BMC Genomics 16:290
Mohler V,Lukman R,Ortiz-Islas S,William M,Worland AJ,van Beem J,Wenzel G(2004)Genetic and physical mapping of photoperiod insensitive gene Ppd-B1 in common wheat.Euphytica 138:33-40
Molina-Cano JL,Conde J(1980)Hordeum spontaneum C.Koch em.Bacht,collected in southern Morocco.Barley Genet Newsl 10:44-47
Mori N,Ishi T,Ishido T,Hirosawa S,Watatani H,Kawahara T,Nesbitt M,Belay G,Takumi S,Ogihara Y,Nakamura C(2003)Origins of domesticated emmer and common wheat inferred from chloroplast DNA fingerprinting.Tenth Int Wheat Genet Symp 2003:25-28
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
Morrell PL,Gonzales AM,Meyer KKT,Clegg MT(2014)Resequencing data indicate a modest effect of domestication on diversity in barley:A cultigen with multiple origins.J Hered 105:253-264
M€uller KJ,Romano N,Gerstner O,Garcia-Marotot F,Pozzi C,Salamini F,Rohde W(1995)The barley Hooded mutation caused by a duplication in a homeobox gene intron.Nature 374:727-730
M€uller T,Schierscher-Viret B,Fossati D,Brabant C,Schori A,Keller B,Krattinger SG(2018)Unlocking the diversity of genebanks:Whole-genome marker analysis of Swiss bread wheat and spelt.Theor Appl Genet 131:407-416
Muramatsu M(1963)Dosage effect of the spelta gene q of hexaploid wheat.Genetics 48:469-482
Nakamura S,Pourkheirandish M,Morishige H,Sameri M,Sato K,Komatsuda T(2017)Quantitative trait loci and maternal effects affecting the strong grain dormancy of wild barley(Hordeum vulgare ssp.spontaneum).Front Plant Sci 8:1840
Naz AA,Kunert A,Lind V,Pillen K,Leon J(2008)AB-QTLanalysis in winter wheat:II.Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population.Theor Appl Genet 116:1095-1104
Naz AA,Klaus M,Pillen K,Leon J(2015)Genetic analysis and detection of new QTL alleles for Septoria tritici blotch resistance using two advanced backcross wheat populations.Plant Breed 134:514-519
Nice LM,Steffenson BJ,Brown-Guedira GL,Akhunov ED,Liu C,Kono TJY,Morrell PL,Blake TK,Horsley RD,Smith KP,Muehlbauer GJ(2016)Development and genetic characterization of an advanced backcross-nested association mapping(AB-NAM)population of wild?cultivated barley.Genetics 203:1453-1467
Nielsen R(2000)Estimation of population parameters and recombination rates from single nucleotide polymorphisms.Genetics 154:931-942
Orabi J,Backes G,Wolday A,Yahyaoui A,Jahoor A(2007)The Horn of Africa as a centre of barley diversification and a potential domestication site.Theor Appl Genet 114:1117-1127
Osmont KS,Sibout R,Hardtke CS(2007)Hidden branches:Developments in root system architecture.Annu Rev Plant Biol 58:93-113
Ozkan H,Brandolini A,Pozzi C,Effgen S,Wunder J,Salamini F(2005)A reconsideration of the domestication geography of tetraploid wheats.Theor Appl Genet 110:1052-1060
€Ozkan H,Brandolini A,Sch€afer-Pregl R,Salamini F(2002)AFLPanalysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey.Mol Biol Evol 19:1797-1801
€Ozkan H,Willcox G,Graner A,Salamini F,Kilian B(2011)Geographic distribution and domestication of wild emmer wheat(Triticum dicoccoides).Genet Resour Crop Evol 58:11-53
Pankin A,Altm€uller J,Becker C,Korff M(2018)Targeted resequencing reveals genomic signatures of barley domestication.New Phytol 218:1247-1259
Pankin A,von Korff M(2017)Co-evolution of methods and thoughts in cereal domestication studies:A tale of barley(Hordeum vulgare).Curr Opin Plant Biol 36:15-21
Paterson AH,Lin YR,Li Z,Schertz KF,Doebley JF,Pinson SRM,Liu SC,Stansel JW,Irvine JE(1995)Convergent domestication of cereal crops by independent mutations at corresponding genetic loci.Science 269:1714-1718
Payne PI(1987)Genetics of wheat storage proteins and the effect of allelic variation on bread-making quality.Annu Rev Plant Physiol 38:141-153
Peng J,Sun D,Nevo E(2011)Wild emmer wheat,Triticum dicoccoides,occupies a pivotal position in wheat domestication process.Aust J Crop Sci 5:1127-1143
Piperno DR,Weiss E,Holst I,Nadel D(2004)Processing of wild cereal grains in the upper Palaeolithic revealed by starch grain analysis.Nature 430:670-673
Poets AM,Fang Z,Clegg MT,Morrell PL(2015)Barley landraces are characterized by geographically heterogeneous genomic origins.Genome Biol 16:173
Pont C,Salse J(2017)Wheat paleohistory created asymmetrical genomic evolution.Curr Opin Plant Biol 36:29-37
Pourkheirandish M,Hensel G,Kilian B,Senthil N,Chen G,Sameri M,Azhaguvel P,Sakuma S,Dhanagond S,Sharma R,Mascher M,Himmelbach A,Gottwald S,Nair Sudha K,Tagiri A,Yukuhiro F,Nagamura Y,Kanamori H,Matsumoto T,Willcox G,Middleton Christopher P,Wicker T,Walther A,Waugh R,Fincher Geoffrey B,Stein N,Kumlehn J,Sato K,Komatsuda T(2015)Evolution of the grain dispersal system in barley.Cell 162:527-539
Pourkheirandish M,Kanamori H,Wu J,Sakuma S,Blattner FR,Komatsuda T(2018)Elucidation of the origin of“agriocrithon”based on domestication genes questions the hypothesis that Tibet is one of the centers of barley domestication.Plant J 94:525-534
Purugganan MD,Fuller DF(2011)Archeaological data reveal slow rates of evolution during plant domestication.Evolution 65:171-183
Ram?rez-Gonzalez RH,Borrill P,Lang D,Harrington SA,Brinton J,Venturini L,Davey M,Jacobs J,van Ex F,Pasha A,Khedikar Y,Robinson SJ,Cory AT,Florio T,Concia L,Juery C,Shoonbeek H,Steuernagel B,Xiang D,Ridout CJ,Chalhoub B,Mayer KFX,Benhamed M,Latrasse D,Bendahmane A,IWGSC,Wulff BBH,Appels R,Tiwari V,Dalta R,Choulet F,Pozniak CJ,Provart NJ,Sharpe AG,Paux E,Spannagl M,Br€autigam A,Uauy C(2018)The transcriptional landscape of polyploid wheat.Science361:6089
Ramsay L,Comadran J,Druka A,Marshall DF,Thomas WTB,Macaulay M,MacKenzie K,Simpson C,Fuller J,Bonar N,Hayes PM,Lundqvist U,Franckowiak JD,Close TJ,Muehlbauer GJ,Waugh R(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
Ramsay L,Macaulay M,Ivanissevich S,MacLean K,Cardle L,Fuller J,Edwards KJ,Tuvesson S,Morgante M,Massari A,Maestri E,Marmiroli N,Sjakste T,Ganal M,Powell W,Waugh R(2000)A simple sequence repeat-based linkage map of barley.Genetics 156:1997-2005
Rebetzke GJ,Bonnett DG,Reynolds MP,Awns reduce grain number to increase grain size and harvestable yield in irrigated and rainfed spring wheat,J Exp Bot 67:2573-2586
Ren X,Nevo E,Sun D,Sun G(2013)Tibet as a potential domestication center of cultivated barley of China.PLoSONE 8:e62700
R€oder MS,Korzun V,Wendehake K,Plaschke J,Tixier MH,Leroy P,Ganal MW(1998)A microsatellite map of wheat.Genetics 149:2007-2023
Russell J,Zonneveld van M,Dawson IK,Booth A,Waugh R,Steffenson B(2014)Genetid diversity and ecological niche modelling of wild barley:Refugia,large-scale post-LGMrange expansion and limited mid-future climate threats.PLoS ONE 9:e86021
Russell J,Mascher M,Dawson IK,Kyriakidis S,Calixto C,Freund F,Bayer M,Milne I,Marshall-Griffiths T,Heinen S,Hofstad A,Sharma R,Himmelbach A,Knauft M,van Zonneveld M,Brown JWS,Schmid K,Kilian B,Muehlbauer GJ,Stein N,Waugh R(2016)Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation.Nat Genet48:1024-1030
Saisho D,Ishii M,Hori K,Sato K(2011)Natural variation of barley vernalization requirements:Implication of quantitative variation of winter growth habit as an adaptive trait in east Asia.Plant Cell Physiol 52:775-784
Sakuma S,Golan G,Guo Z,Ogawa T,Tagiri A,Sugimoto K,Bernhardt N,Brassac J,Mascher M,Hensel G,Ohnishi S,Jinno H,Yamashita Y,Ayalon I,Peleg Z,Schnurbusch T,Komatsuda T(2018)Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication.bioRxiv 434985doi:10.1101/434985
Salamini F,€Ozkan H,Brandolini A,Sch€afer-Pregl R,Martin W(2002)Genetics and geography of wild cereal domestication in the near east.Nat Rev Genet 3:429-441
Sanchez-Leon S,Gil-Humanes J,Ozuna Carmen V,Gimenez Mar?a J,Sousa C,Voytas Daniel F,Barro F(2017)Lowgluten,nontransgenic wheat engineered with CRISPR/Cas9.Plant Biotechnol J 16:902-910
Schmalenbach I,March TJ,Bringezu T,Waugh R,Pillen K(2011)High-resolution genotyping of wild barley introgression lines and fine-mapping of the threshability locus thresh-1using the Illumina GoldenGate assay.G3-Genes Genom Genet 1:187-196
Scott JC,Manisterski J,Sela H,Ben-Yehuda P,Steffenson BJ(2014)Resistance of Aegilops species from Israel to widely virulent African and Israeli races of the wheat stem rust pathogen.Plant Dis 98:1309-1320
Simons KJ,Fellers JP,Trick HN,Zhang Z,Tai YS,Gill BS,Faris JD(2006)Molecular characterization of the major wheat domestication gene Q.Genetics 172:547-555
Sood S,Kuraparthy V,Bai G,Gill BS(2009)The major threshability genes soft glume(sog)and tenacious glume(Tg),of diploid and polyploid wheat,trace their origin to independent mutations at non-orthologous loci.Theor Appl Genet 119:341-351
Sorensen AE(1986)Seed dispersal by adhesion.Annu Rev of Ecol Syst 17:443-463
Sourdille P,Cadalen T,Gay G,Gill B,Bernard M(2008)Molecular and physical mapping of genes affecting awning in wheat.Plant Breed 121:320-324
Steffenson BJ,Olivera P,Roy JK,Jin Y,Smith KP,Muehlbauer GJ(2007)A walk on the wild side:Mining wild wheat and barley collections for rust resistance genes.Aust J Agric Res 58:532-544
Stein JC,Yu Y,Copetti D,Zwickl DJ,Zhang L,Zhang C,Chougule K,Gao D,Iwata A,Goicoechea JL,Wei S,Wang J,Liao Y,Wang M,Jacquemin J,Becker C,Kudrna D,Zhang J,Londono CEM,Song X,Lee S,Sanchez P,Zuccolo A,Ammiraju JSS,Talag J,Danowitz A,Rivera LF,Gschwend AR,Noutsos C,Wu C-C,Kao S-M,Zeng J-W,Wei F-J,Zhao Q,Feng Q,El Baidouri M,Carpentier M-C,Lasserre E,Cooke R,Rosa Farias D,da Maia LC,dos Santos RS,Nyberg KG,McNally KL,Mauleon R,Alexandrov N,Schmutz J,Flowers D,Fan C,Weigel D,Jena KK,Wicker T,Chen M,Han B,Henry R,Hsing Y-C,Kurata N,de Oliveira AC,Panaud O,Jackson SA,Machado CA,Sanderson MJ,Long M,Ware D,Wing RA(2018)Genomes of 13 domesticated and wild rice relatives highlight genetic conservation,turnover and innovation across the genus Oryza.Nat Genet 50:285-296
Swanson-Wagner RA,Eichten SR,Kumari S,Tiffin P,Stein JC,Ware D,Springer NM(2010)Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.Genome Res 20:1-11
Taenzler B,Esposti RF,Vaccino P,Brandolini A,Effgen S,Heun M,Sch€AFer-Pregl R,Borghi B,Salamini F(2002)Molecular linkage map of Einkorn wheat:Mapping of storage-protein and soft-glume genes and bread-making quality QTLs.Genet Res 80:131-143
Taketa S,Amano S,Tsujino Y,Sato T,Saisho D,Kakeda K,Nomura M,Suzuki T,Matsumoto T,Sato K,Kanamori H,Kawasaki S,Takeda K(2008)Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway.Proc Natl Acad Sci USA 105:4062-4067
Tanksley SD,Nelson JC(1996)Advanced backcross QTLanalysis:A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines.Theor Appl Genet 92:191-203
Tiwari VK,Wang S,Sehgal S,Vrana J,Friebe B,Kubalakova M,Chhuneja P,Dolezel J,Akhunov E,Kalia B,Sabir J,Gill BS(2014)SNP discovery for mapping alien introgressions in wheat.BMC Genomics 15:273
Torada A,Amano Y(2002)Effect of seed coat color on seed dormancy in different environments.Euphytica 126:99-105
Trevaskis B,Bagnall DJ,Ellis MH,Peacock WJ,Dennis ES(2003)MADS box genes control vernalization-induced flowering in cereals.Proc Natl Acad Sci USA 100:13099-13104
Turner A,Beales J,Faure S,Dunford RP,Laurie DA(2005)The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley.Science 310:1031-1034
Uauy C,Distelfeld A,Fahima T,Blechl A,Dubcovsky J(2006)A NAC gene regulating senescence improves grain protein,zinc,and iron content in wheat.Science 314:1298
Varshney RK,Marcel TC,Ramsay L,Russell J,R€oder MS,Stein N,Waugh R,Langridge P,Niks RE,Graner A(2007)A high density barley microsatellite consensus map with 775 SSRloci.Theor Appl Genet 114:1091-1103
Vavilov NI,Freier F(1926)Studies on The Origin of Cultivated Plants.Trudi Po Prikl bot gen i Selek 16
Wang J,Luo MC,Chen Z,You FM,Wei Y,Zheng Y,Dvorak J(2013)Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat.New Phytol 198:925-937
Wang S,Wong D,Forrest K,Allen A,Chao S,Huang BE,Maccaferri M,Salvi S,Milner SG,Cattivelli L,Mastrangelo AM,Whan A,Stephen S,Barker G,Wieseke R,Plieske J,International Wheat Genome Sequencing C,Lillemo M,Mather D,Appels R,Dolferus R,Brown-Guedira G,Korol A,Akhunova AR,Feuillet C,Salse J,Morgante M,Pozniak C,Luo M-C,Dvorak J,Morell M,Dubcovsky J,Ganal M,Tuberosa R,Lawley C,Mikoulitch I,Cavanagh C,Edwards KJ,Hayden M,Akhunov E(2014)Characterization of polyploid wheat genomic diversity using a high-density90000 single nucleotide polymorphism array.Plant Biotechnol J 12:787-796
Watanabe N,Sugiyama K,Yamagishi Y,Sakata Y(2002)Comparative telosomic mapping of homoeologous genes for brittle rachis in tetraploid and hexaploid wheats.Hereditas 137:180-185
Wendler N,Mascher M,Himmelbach A,Johnston P,Pickering R,Stein N(2015)Bulbosum to Go:A toolbox to utilize Hordeum vulgare/bulbosum introgressions for breeding and beyond.Mol Plant 8:1507-1519
Wilhelm EP,Turner AS,Laurie DA(2009)Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat(Triticum durum Desf.).Theor Appl Genet 118:285-294
Winfield MO,Wilkinson PA,Allen AM,Barker GLA,Coghill JA,Burridge A,Hall A,Brenchley RC,D’Amore R,Hall N,Bevan MW,Richmond T,Gerhardt DJ,Jeddeloh JA,Edwards KJ(2012)Targeted re-sequencing of the allohexaploid wheat exome.Plant Biotechnol J 10:733-742
Yan L,Loukoianov A,Tranquilli G,Helguera M,Fahima T,Dubcovsky J(2003)Positional cloning of the wheat vernalization gene VRN1.Proc Natl Acad Sci USA 100:6263-6268
Yan L,Loukoianov A,Blechl A,Tranquilli G,Ramakrishna W,San Miguel P,Bennetzen JL,Echenique V,Dubcovsky J(2004)The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.Science 303:1640-1644
Yan L,Fu D,Li C,Blechl A,Tranquilli G,Bonafede M,Sanchez A,Valarik M,Yasuda S,Dubcovsky J(2006)The wheat and barley vernalization gene VRN3 is an orthologue of FT.Proc Natl Acad Sci USA 103:19581-19586
Yoshioka M,Iehisa JCM,Ohno R,Kimura T,Enoki H,Nishimura S,Nasuda S,Takumi S(2017)Three dominant awnless genes in common wheat:Fine mapping,interaction and contribution to diversity in awn shape and length.PLoSONE 12:e0176148
Yu G,Champouret N,Steuernagel B,Olivera PD,Simmons J,Williams C,Johnson R,Moscou MJ,Hernandez-Pinzon I,Green P,Sela H,Millet E,Jones JDG,Ward ER,Steffenson BJ,Wulff BBH(2017)Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis.Theor Appl Genet 130:1207-1222
Yu J,Holland JB,McMullen MD,Buckler ES(2008)Genetic design and statistical power of nested association mapping in maize.Genetics 178:539-551
Yuo T,Yamashita Y,Kanamori H,Matsumoto T,Lundqvist U,Sato K,Ichii M,Jobling SA,Taketa S(2012)A SHORTINTERNODES(SHI)family transcription factor gene regulates awn elongation and pistil morphology in barley.J Exp Bot 63:5223-5232
Zakhrabekova S,Gough P,Braumann I,M€uller AH,Lundqvist J,Ahmann K,Dockter C,Matyszczak I,Kurowska M,Druka A,Waugh R,Graner A,Stein N,Steuernagel B,Lundqvist U,Hansson M(2012)Induced mutations in circadian clock regulator Mat-a factilitated short-season adaptation and range extension in cultivated barley.Proc Natl Acad Sci USA 109:4326-4331
Zhang Z,Belcram H,Gornicki P,Charles M,Just J,Huneau C,Magdelenat G,Couloux A,Samain S,Gill BS,Rasmussen JB,Barbe V,Faris JD,Chalhoub B(2011)Duplication and partitioning in evolution and function of homoeologous Q;loci governing domestication characters in polyploid wheat.Proc Natl Acad Sci USA 108:18737-18742
Zhao G,Zou C,Li K,Wang K,Li T,Gao L,Zhang X,Wang H,Yang Z,Liu X,Jiang W,Mao L,Kong X,Jiao Y,Jia J(2017)The Aegilops tauschii genome reveals multiple impacts of transposons.Nat Plants 3:946-955
Zhao Q,Feng Q,Lu H,Li Y,Wang A,Tian Q,Zhan Q,Lu Y,Zhang L,Huang T,Wang Y,Fan D,Zhao Y,Wang Z,Zhou C,Chen J,Zhu C,Li W,Weng Q,Xu Q,Wang ZX,Wei X,Han B,Huang X(2018)Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.Nat Genet50:278-284
Zimin AV,Puiu D,Hall R,Kingan S,Clavijo BJ,Salzberg SL(2017a)The first near-complete assembly of the hexaploid bread wheat genome,Triticum aestivum.GigaScience 6:1-7
Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Mar Sc ais G,Yorke JA,Dvorak J,Salzberg SL(2017b)Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii,a progenitor of bread wheat,with the MaSuRCA mega-reads algorithm.Genome Res 27:787-792
Zohary D(1959)Is Hordeum agriocrithon the ancestor of sixrowed cultivated barley?Evolution 13:279-280
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 on Demand,Oxford,United Kingdom