1.
Matsuoka Y, Nasuda S. Durum wheat as a candidate for the unknown female progenitor of bread
wheat: an empirical study with a highly fertile F1 hybrid with Aegilops tauschii Coss. Theor Appl Genet.
2004; 109: 1710–1717. https://doi.org/10.1007/s00122-004-1806-6 PMID: 15448900
2.
Pumphrey M, Bai J, Laudencia-Chingcuanco D, Anderson O, Gill BS. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics. 2009; 181: 1147–
1157. https://doi.org/10.1534/genetics.108.096941 PMID: 19104075
3.
Mestiri I, Chague´ V, Tanguy A-M, Huneau C, Huteau V, Belcram H, et al. Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol. 2010; 186: 86–101. https://doi.org/10.1111/j.1469-8137.2010.03186.x PMID:
20149116
PLOS ONE | https://doi.org/10.1371/journal.pone.0284408 April 27, 2023
23 / 27
PLOS ONE
Phenotypic effects of Am genomes in nascent synthetic hexaploids from crosses between durum and wild einkorn
4.
Chague´ V, Just J, Mestiri I, Balzergue S, Tanguy A-M, Huneau C, et al. Genome-wide gene expression
changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol. 2010; 187: 1181–
1194. https://doi.org/10.1111/j.1469-8137.2010.03339.x PMID: 20591055
5.
Zhang H, Bian Y, Gou X, Zhu B, Xu C, Qi B, et al. Persistent whole-chromosome aneuploidy is generally
associated with nascent allohexaploid wheat. Proc Natl Acad Sci U S A. 2013; 110: 3447–3452. https://
doi.org/10.1073/pnas.1300153110 PMID: 23401544
6.
Jones H, Gosman N, Horsnell R, Rose GA, Everest LA, Bentley AR, et al. Strategy for exploiting exotic
germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss.
example. Theor Appl Genet. 2013; 126: 1793–1808. https://doi.org/10.1007/s00122-013-2093-x PMID:
23558983
7.
Li A, Liu D, Yang W, Kishii M, Mao L. Synthetic hexaploid wheat: yesterday, today, and tomorrow. Proc
Est Acad Sci Eng. 2018; 4: 552–558. https://doi.org/10.1016/j.eng.2018.07.001
8.
Takumi S, Mitta S, Komura S, Ikeda TM, Matsunaka H, Sato K, et al. Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars. PLoS One. 2020; 15: e0228397. https://doi.org/10.1371/journal.pone.
0228397 PMID: 31986184
9.
Dvorak J, McGuire PE, Cassidy B. Apparent sources of the A genomes of wheats inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome.
1988; 30: 680–689. https://doi.org/10.1139/g88-115
10.
Volante A, Barabaschi D, Marino R, Brandolini A. Genome-wide association study for morphological,
phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum). G3.
2021;11. https://doi.org/10.1093/g3journal/jkab281 PMID: 34849796
11.
Fricano A, Brandolini A, Rossini L, Sourdille P, Wunder J, Effgen S, et al. Crossability of Triticum urartu
and Triticum monococcum wheats, homoeologous recombination, and description of a panel of interspecific introgression lines. G3. 2014; 4: 1931–1941. https://doi.org/10.1534/g3.114.013623 PMID:
25147190
12.
Heun M, Scha¨fer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, et al. Site of einkorn wheat
domestication identified by DNA fingerprinting. Science. 1997; 278: 1312–1314. https://doi.org/10.
1126/science.278.5341.1312
13.
Kilian B, Ozkan H, Walther A, Kohl J, Dagan T, Salamini F, et al. 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. 2007; 24: 2657–2668.
https://doi.org/10.1093/molbev/msm192 PMID: 17898361
14.
Pour-Aboughadareh A, Mahmoudi M, Moghaddam M, Ahmadi J, Mehrabi AA, Alavikia SS. Agro-morphological and molecular variability in Triticum boeoticum accessions from Zagros Mountains, Iran.
Genet Resour Crop Evol. 2017; 64: 545–556. https://doi.org/10.1007/s10722-016-0381-4
15.
Ma H, Singh RP, Mujeeb-Kazi A. Resistance to stripe rust in durum wheats, A-genome diploids, and
their amphiploids. Euphytica. 1997; 94: 279–286. https://doi.org/10.1023/A:1002979706378.
16.
Rogers WJ, Rogers WJ, Miller TE, Payne PI, Seekings JA, Sayers EJ, et al. Introduction to bread wheat
(Triticum aestivum L.) and assessment for bread-making quality of alleles from T. boeoticum Boiss.
ssp. thaoudar at Glu-A1 encoding two high-molecular-weight subunits of glutenin. Euphytica. 1997; 93:
19–29. https://doi.org/10.1023/a:1002991206350
17.
Shi AN, Leath S, Murphy JP. A major gene for powdery mildew resistance transferred to common
wheat from wild einkorn wheat. Phytopathology. 1998; 88: 144–147. https://doi.org/10.1094/PHYTO.
1998.88.2.144 PMID: 18944983
18.
Anker CC, Niks RE. Prehaustorial resistance to the wheat leaf rust fungus, Puccinia triticina, in Triticum
monococcum (s.s.). Euphytica. 2001; 117: 209–215. https://doi.org/10.1023/A:1026577307163
19.
Chhuneja P, Kaur S, Garg T, Ghai M, Kaur S, Prashar M, et al. Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor Appl Genet.
2008; 116: 313–324. https://doi.org/10.1007/s00122-007-0668-0 PMID: 17989954
20.
Chhuneja P, Kumar K, Stirnweis D, Hurni S, Keller B, Dhaliwal HS, et al. Identification and mapping of
two powdery mildew resistance genes in Triticum boeoticum L. Theor Appl Genet. 2012; 124: 1051–
1058. https://doi.org/10.1007/s00122-011-1768-4 PMID: 22198205
21.
Hovhannisyan NA, Dulloo ME, Yesayan AH, Knu¨pffer H, Amri A. Tracking of powdery mildew and leaf
rust resistance genes in Triticum boeoticum and T. urartu, wild relatives of common wheat. Czech J
Genet Plant Breed. 2011; 47: 45–57. https://doi.org/10.17221/127/2010-cjgpb
22.
Sultan MARF, Hui L, Yang LJ, Xian ZH. Assessment of drought tolerance of some Triticum L. species
through physiological indices. Czech J Genet Plant Breed. 2012; 48: 178–184. https://doi.org/10.17221/
21/2012-cjgpb
PLOS ONE | https://doi.org/10.1371/journal.pone.0284408 April 27, 2023
24 / 27
PLOS ONE
Phenotypic effects of Am genomes in nascent synthetic hexaploids from crosses between durum and wild einkorn
23.
Gill RS, Dhaliwal HS, Multani DS. Synthesis and evaluation of Triticum durum—T. monococcum amphiploids. Theor Appl Genet. 1988; 75: 912–916. https://doi.org/10.1007/bf00258053
24.
Megyeri M, Miko´ P, Molna´r I, Kova´cs G. Development of synthetic amphiploids based on Triticum turgidum × T. monococcum crosses to improve the adaptability of cereals. Acta Agron Hungar. 2011; 59:
267–274. https://doi.org/10.1556/aagr.59.2011.3.11
25.
Li H, Liu X, Zhang M, Feng Z, Liu D, Ayliffe M, et al. Development and identification of new synthetic T.
turgidum–T. monococcum amphiploids. Plant Genetic Resources 2018; 16: 555–563. https://doi.org/
10.1017/s1479262118000175
26.
Miko´ P, Megyeri M, Farkas A, Molna´r I, Molna´r-La´ng M. Molecular cytogenetic identification and phenotypic description of a new synthetic amphiploid, Triticum timococcum (AtAtGGAmAm). Genet Resour
Crop Evol. 2015; 62: 55–66. https://doi.org/10.1007/s10722-014-0135-0 PMID: 26412939
27.
Liu X, Yang H, Zhang M, Liu X, Peng T, Hao M, et al. Molecular cytogenetic identification of a new synthetic amphiploid (Triticum timococcum, AtAtGGAmAm) with a seed setting rate comparable with that of
natural Triticum zhukovskyi. Plant Breeding. 2022; 141: 558–565. https://doi.org/10.1111/pbr.13030
28.
Chen S, Hegarty J, Shen T, Hua L, Li H, Luo J, et al. Stripe rust resistance gene Yr34 (synonym Yr48) is
located within a distal translocation of Triticum monococcum chromosome 5AmL into common wheat.
Theor Appl Genet. 2021; 134: 2197–2211. https://doi.org/10.1007/s00122-021-03816-z PMID:
33791822
29.
Elkot AFA, Chhuneja P, Kaur S, Saluja M, Keller B, Singh K. Marker assisted transfer of two powdery
mildew resistance genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.). PLoS One. 2015; 10: e0128297. https://doi.org/10.1371/journal.pone.0128297 PMID:
26066332
30.
Takumi S, Naka Y, Morihiro H, Matsuoka Y. Expression of morphological and flowering time variation
through allopolyploidization: an empirical study with 27 wheat synthetics and their parental Aegilops
tauschii accessions. Plant Breed. 2009; 128: 585–590. https://doi.org/10.1111/j.1439-0523.2009.
01630.x
31.
Kajimura T, Murai K, Takumi S. Distinct genetic regulation of flowering time and grain-filling period
based on empirical study of D-genome diversity in synthetic hexaploid wheat lines. Breed Sci. 2011; 61:
130–141. https://doi.org/10.1270/jsbbs.61.130
32.
Okada M, Ikeda TM, Yoshida K, Takumi S. Effect of the U genome on grain hardness in nascent synthetic hexaploids derived from interspecific hybrids between durum wheat and Aegilops umbellulata. J
Cereal Sci. 2018; 83: 153–161. https://doi.org/10.1016/j.jcs.2018.08.011
33.
Okada M, Michikawa A, Yoshida K, Nagaki K, Ikeda TM, Takumi S. Phenotypic effects of the U-genome
variation in nascent synthetic hexaploids derived from interspecific crosses between durum wheat and
its diploid relative Aegilops umbellulata. PLoS One. 2020; 15: e0231129. https://doi.org/10.1371/
journal.pone.0231129 PMID: 32240263
34.
Okamoto Y, Nguyen AT, Yoshioka M, Iehisa JCM, Takumi S. Identification of quantitative trait loci controlling grain size and shape in the D genome of synthetic hexaploid wheat lines. Breed Sci. 2013; 63:
423–429. https://doi.org/10.1270/jsbbs.63.423 PMID: 24399915
35.
Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum
aestivum L.). Theor Appl Genet. 2004; 109: 1105–1114. https://doi.org/10.1007/s00122-004-1740-7
PMID: 15490101
36.
Torada A, Koike M, Mochida K, Ogihara Y. SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet. 2006; 112: 1042–1051. https://doi.org/10.
1007/s00122-006-0206-5 PMID: 16450184
37.
Nishijima R, Iehisa JCM, Matsuoka Y, Takumi S. The cuticular wax inhibitor locus Iw2 in wild diploid
wheat Aegilops tauschii: phenotypic survey, genetic analysis, and implications for the evolution of common wheat. BMC Plant Biol. 2014; 14: 246. https://doi.org/10.1186/s12870-014-0246-y PMID:
25224598
38.
Kamvar ZN, Tabima JF, Gru¨nwald NJ. Poppr: an R package for genetic analysis of populations with
clonal, partially clonal, and/or sexual reproduction. PeerJ. 2014; 2: e281. https://doi.org/10.7717/peerj.
281 PMID: 24688859
39.
Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in
R. Bioinformatics. 2019; 35: 526–528. https://doi.org/10.1093/bioinformatics/bty633 PMID: 30016406
40.
Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype
data. Genetics. 2000; 155: 945–959. https://doi.org/10.1093/genetics/155.2.945 PMID: 10835412
41.
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software
STRUCTURE: a simulation study. Mol Ecol. 2005; 14: 2611–2620. https://doi.org/10.1111/j.1365294X.2005.02553.x PMID: 15969739
PLOS ONE | https://doi.org/10.1371/journal.pone.0284408 April 27, 2023
25 / 27
PLOS ONE
Phenotypic effects of Am genomes in nascent synthetic hexaploids from crosses between durum and wild einkorn
42.
Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012; 4: 359–361. https://
doi.org/10.1007/s12686-011-9548-7
43.
Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with
label switching and multimodality in analysis of population structure. Bioinformatics. 2007; 23: 1801–
1806. https://doi.org/10.1093/bioinformatics/btm233 PMID: 17485429
44.
Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC. Metaphase and interphase fluorescence in situ
hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci U S
A. 1995; 92: 4487–4491. https://doi.org/10.1073/pnas.92.10.4487 PMID: 7753830
45.
Michikawa A, Yoshida K, Okada M, Sato K, Takumi S. Genome-wide polymorphisms from RNA
sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat. Mol Genet Genomics. 2019; 294: 1327–1341. https://doi.org/10.1007/
s00438-019-01581-9 PMID: 31187273
46.
Tanabata T, Shibaya T, Hori K, Ebana K, Yano M. SmartGrain: high-throughput phenotyping software
for measuring seed shape through image analysis. Plant Physiol. 2012; 160: 1871–1880. https://doi.
org/10.1104/pp.112.205120 PMID: 23054566
47.
Okamoto Y, Kajimura T, Ikeda TM, Takumi S. Evidence from principal component analysis for improvement of grain shape- and spikelet morphology-related traits after hexaploid wheat speciation. Genes
Genet Syst. 2012; 87: 299–310. https://doi.org/10.1266/ggs.87.299 PMID: 23412632
48.
Bu¨rkner P-C. brms: An R package for Bayesian multilevel models using Stan. J Stat Softw. 2017; 80: 1–
28. https://doi.org/10.18637/jss.v080.i01
49.
Baillot N, Girousse C, Allard V, Piquet-Pissaloux A, Le Gouis J. Different grain-filling rates explain grainweight differences along the wheat ear. PLoS One. 2018; 13: e0209597. https://doi.org/10.1371/
journal.pone.0209597 PMID: 30596702
50.
Fick SE, Hijmans RJ. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas.
Int J Climatol. 2017; 37: 4302–4315. https://doi.org/10.1002/joc.5086
51.
Gaines CS, Finney PF, Fleege LM, Andrews LC. Predicting a hardness measurement using the singlekernel characterization system. Cereal Chem. 1996, 73: 278–283.
52.
Zeller FJ, Cermeno MC, Miller TE. Cytological analysis on the distribution and origin of the alien chromosome pair conferring blue aleurone color in several European common wheat (Triticum aestivum L.)
strains. Theor Appl Genet. 1991; 81: 551–558. https://doi.org/10.1007/BF00219448 PMID: 24221323
53.
Zhou Y, Zhao X, Li Y, Xu J, Bi A, Kang L, et al. Triticum population sequencing provides insights into
wheat adaptation. Nat Genet. 2020; 52: 1412–1422. https://doi.org/10.1038/s41588-020-00722-w
PMID: 33106631
54.
Takumi S, Nishioka E, Morihiro H, Kawahara T, Matsuoka Y. Natural variation of morphological traits in
wild wheat progenitor Aegilops tauschii Coss. Breed Sci. 2009; 59: 579–588. https://doi.org/10.1270/
jsbbs.59.579
55.
Miki Y, Ikeda TM, Yoshida K, Takumi S. Identification of a hard kernel texture line of synthetic allohexaploid wheat reducing the puroindoline accumulation on the D genome from Aegilops tauschii. J Cereal
Sci. 2020; 93: 102964. https://doi.org/10.1016/j.jcs.2020.102964
Lachman J, Martinek P, Kotı´kova´ Z, Orsa´k M, Sˇulc M. Genetics and chemistry of pigments in wheat
grain—A review. J Cereal Sci. 2017; 74: 145–154. https://doi.org/10.1016/j.jcs.2017.02.007
56.
57.
Liu X, Zhang M, Jiang X, Li H, Jia Z, Hao M, et al. TbMYC4A is a candidate gene controlling the blue
aleurone trait in a wheat-Triticum boeoticum substitution line. Front Plant Sci. 2021; 12: 762265. https://
doi.org/10.3389/fpls.2021.762265 PMID: 34804098
58.
Shipp J, Abdel-Aal E-SM. Food applications and physiological effects of anthocyanins as functional
food ingredients. Open Food Sci J. 2010; 4: 7–22. https://doi.org/10.2174/1874256401004010007
59.
Hermsen JGT. Hybrid dwarfness in wheat. Euphytica. 1967; 16: 134–162. https://doi.org/10.1007/
BF00043448
60.
Tikhenko N, Rutten T, Tsvetkova N, Voylokov A, Bo¨rner A. Hybrid dwarfness in crosses between wheat
(Triticum aestivum L.) and rye (Secale cereale L.): a new look at an old phenomenon. Plant Biol. 2015;
17: 320–326. https://doi.org/10.1111/plb.12237 PMID: 25251214
61.
Mizuno N, Hosogi N, Park P, Takumi S. Hypersensitive response-like reaction is associated with hybrid
necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii coss. PLoS One. 2010;
5: e11326. https://doi.org/10.1371/journal.pone.0011326 PMID: 20593003
62.
Okada M, Yoshida K, Takumi S. Hybrid incompatibilities in interspecific crosses between tetraploid
wheat and its wild diploid relative Aegilops umbellulata. Plant Mol Biol. 2017; 95: 625–645. https://doi.
org/10.1007/s11103-017-0677-6 PMID: 29090430
PLOS ONE | https://doi.org/10.1371/journal.pone.0284408 April 27, 2023
26 / 27
PLOS ONE
Phenotypic effects of Am genomes in nascent synthetic hexaploids from crosses between durum and wild einkorn
63.
Bomblies K, Lempe J, Epple P, Warthmann N, Lanz C, Dangl JL, et al. Autoimmune response as a
mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol. 2007; 5: e236.
https://doi.org/10.1371/journal.pbio.0050236 PMID: 17803357
64.
Chae E, Bomblies K, Kim S-T, Karelina D, Zaidem M, Ossowski S, et al. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell. 2014; 159: 1341–
1351. https://doi.org/10.1016/j.cell.2014.10.049 PMID: 25467443
65.
Chen C, Chen H, Lin Y-S, Shen J-B, Shan J-X, Qi P, et al. A two-locus interaction causes interspecific
hybrid weakness in rice. Nat Commun. 2014; 5: 3357. https://doi.org/10.1038/ncomms4357 PMID:
24556665
66.
Alca´zar R, von Reth M, Bautor J, Chae E, Weigel D, Koornneef M, et al. Analysis of a plant complex
resistance gene locus underlying immune-related hybrid incompatibility and its occurrence in nature.
PLoS Genet. 2014; 10: e1004848. https://doi.org/10.1371/journal.pgen.1004848 PMID: 25503786
PLOS ONE | https://doi.org/10.1371/journal.pone.0284408 April 27, 2023
27 / 27
...