Genomics studies in wild species of wheat have been limited due to the lack of references; however, new technologies and bioinformatics tools have much potential to promote genomic research. The wheat-Haynaldia villosa translocation line T6VS·6AL has been widely used as a backbone parent of wheat breeding in China. Therefore, revealing the genome structure of translocation chromosome 6VS·6AL will clarify how this chromosome formed and will help to determine how it affects agronomic traits. In this study, chromosome flow sorting, NGS sequencing and Chicago long-range linkage assembly were innovatively used to produce the assembled sequences of 6VS·6AL, and gene prediction and genome structure characterization at the molecular level were effectively performed. The analysis discovered that the short arm of 6VS·6AL was actually composed of a large distal segment of 6VS, a small proximal segment of 6AS and the centromere of 6A, while the collinear region in 6VS corresponding to 230-260 Mb of 6AS-Ta was deleted when the recombination between 6VS and 6AS occurred. In addition to the molecular mechanism of the increased grain weight and enhanced spike length produced by the translocation chromosome, it may be correlated with missing GW2-V and an evolved NRT-V cluster. Moreover, a fine physical bin map of 6VS was constructed by the high-throughput developed 6VS-specific InDel markers and a series of newly identified small fragment translocation lines involving 6VS. This study will provide essential information for mining of new alien genes carried by the 6VS·6AL translocation chromosome.

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czech Republic

National Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics Institute Nanjing Agricultural University JCIC MCP Nanjing China

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Arraiano, L.S. , Chartrain, L. , Bossolini, E. , Slatter, H.N. , Keller, B. and Brown, J.K.M. (2007) A gene in European wheat cultivars for resistance to an African isolate of

Avni, R. , Nave, M. , Barad, O. , Baruch, K. , Twardziok, S.O. , Gundlach, H. , Hale, I. PubMed

Blanco, A. , Simeone, R. , Tanzarella, O.A. and Greco, B. (1983) Morphology and chromosome pairing of a hybrid between PubMed

Brenchley, R. , Spannagl, M. , Pfeifer, M. , Barker, G.L.A. , D’Amore, R. , Allen, A.M. , McKenzie, N. PubMed PMC

Cao, A. , Xing, L. , Wang, X. , Yang, X. , Wang, W. , Sun, Y. , Qian, C. PubMed PMC

Castro, A.M. , Vasicek, A. , Manifiesto, M. , Giménez, D.O. , Tacaliti, M.S. , Dobrovolskaya, O. , Röder, M.S.

Chen, P. and Liu, D. (1982) Cytogenetic studies of hybrid progenies between Triticum aestivum and Haynaldia villosa. Journal of Nanjing Agricultural College 4, 1–16.

Chen, P.D. , Qi, L.L. , Zhou, B. , Zhang, S.Z. and Liu, D.J. (1995) Development and molecular cytogenetic analysis of wheat‐ PubMed

Chen, P. , You, C. , Hu, Y. , Chen, S. , Zhou, B. , Cao, A. and Wang, X. (2013) Radiation‐induced translocations with reduced

Clavijo, B.J. , Venturini, L. , Schudoma, C. , Accinelli, G.G. , Kaithakottil, G. , Wright, J. , Borrill, P. PubMed PMC

De Pace, C. , Vaccino, P. , Cionini, G. , Pasquini, M. , Bizzarri, M. and Qualset, C.O. (2011) Dasypyrum. In Wild Crop Relatives: Genomic and Breeding Resources, Cereals, Vol 1, chapter 4 ( Kole, C. , ed), pp. 185–292.Heidelberg: Springer.

Du, P. , Zhuang, L. , Wang, Y. , Yuan, L. , Wang, Q. , Wang, D. , Dawadondup PubMed

Guo, J. , Shi, W. , Zhang, Z. , Cheng, J. , Sun, D. , Yu, J. , Li, X. PubMed PMC

Guo, Z. , Chen, D. , Alqudah, A.M. , Roder, M.S. , Ganal, M.W. and Schnurbusch, T. (2017) Genome‐wide association analyses of 54 traits identified multiple loci for the determination of floret fertility in wheat. New Phytol. 214, 257–270. PubMed

Gupta, P.K. , Rustgi, S. and Kumar, N. (2006) Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants. Genome, 49, 565–571. PubMed

Holzapfel, J. , Voss, H.H. , Miedaner, T. , Korzun, V. , Haberle, J. , Schweizer, G. , Mohler, V. PubMed

IWGSC . (2014) A chromosome‐based draft sequence of the hexaploid bread wheat ( PubMed

IWGSC . (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361, 7191. PubMed

Jia, J. , Zhao, S. , Kong, X. , Li, Y. , Zhao, G. , He, W. , Appels, R. PubMed

Krzywinski, M. , Schein, J. , Birol, I. , Connors, J. , Gascoyne, R. , Horsman, D. , Jones, S.J. PubMed PMC

Li, H. , Chen, X. , Xin, Z.Y. , Ma, Y.Z. , Xu, H.J. , Chen, X.Y. and Jia, X. (2005) Development and identification of wheat–

Ling, H.Q. , Zhao, S. , Liu, D. , Wang, J. , Sun, H. and Al, E. (2013) Draft genome of the wheat A‐genome progenitor PubMed

Liu, C. , Qi, L. , Liu, W. , Zhao, W. , Wilson, J. , Friebe, B. and Gill, B.S. (2011) Development of a set of compensating PubMed

Lopes, M.S. , Reynolds, M.P. , McIntyre, C.L. , Mathews, K.L. , Jalal Kamali, M.R. , Mossad, M. , Feltaous, Y. PubMed

Lukaszewski, A.J. (1988) A comparison of several approaches in the development of disomic alien addition lines of wheat. In: Proceedings of the 7th International Wheat Genetics Symposium, vol 1 ( Miller, T.E. and Koebner, R.M.D. , eds) , pp. 363–367. Cambridge, UK: Institute of Plant Sciences Research.

Luo, M.C. , Gu, Y.Q. , You, F.M. , Deal, K.R. , Ma, Y. , Hu, Y. , Huo, N. PubMed PMC

Luo, M.C. , Gu, Y.Q. , Puiu, D. , Wang, H. , Twardziok, S.O. , Deal, K.R. , Huo, N. PubMed PMC

Mago, R. , Bariana, H.S. , Dundas, I.S. , Spielmeyer, W. , Lawrence, G.J. , Pryor, A.J. and Ellis, J.G. (2005) Development of PCR markers for the selection of wheat stem rust resistance genes Sr24 and Sr26 in diverse wheat germplasm. Theor. Appl. Genet. 111, 496–504. PubMed

Monte, J.V. , McIntyre, C.L. and Gustafson, J.P. (1993) Analysis of phylogenetic relationships in the Triticeae tribe using RFLPs. Theor. Appl. Genet. 86, 649–655. PubMed

Paux, E. , Roger, D. , Badaeva, E. , Gay, G. , Bernard, M. , Sourdille, P. and Feuillet, C. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC‐end sequencing on chromosome 3B. Plant J. 48, 463–474. PubMed

Rohringer, R. , Kim, W.K. and Samborski, D.J. (1979) A histological study of interactions between avirulent races of stem rust and wheat containing resistance genes

Sears, E.R. (1953) Addition of the genome of

Simmonds, J. , Scott, P. , Leverington‐Waite, M. , Turner, A.S. , Brinton, J. , Korzun, V. , Snape, J. PubMed PMC

Simons, K. , Abate, Z. , Chao, S. , Zhang, W. , Rouse, M. , Jin, Y. , Elias, E. PubMed PMC

Spielmeyer, W. , Hyles, J. , Joaquim, P. , Azanza, F. , Bonnett, D. , Ellis, M.E. , Moore, C. PubMed

Su, Z. , Hao, C. , Wang, L. , Dong, Y. and Zhang, X. (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat ( PubMed

Sun, H. , Song, J. , Lei, J. , Song, X. , Dai, K. , Xiao, J. , Yuan, C. PubMed

Sun, X.Y. , Wu, K. , Zhao, Y. , Kong, F.M. , Han, G.Z. , Jiang, H.M. , Huang, X.J.

Tahmasebi, S. , Heidari, B. , Pakniyat, H. and McIntyre, C.L. (2017) Mapping QTLs associated with agronomic and physiological traits under terminal drought and heat stress conditions in wheat ( PubMed

Tanaka, Y. , Tsuda, M. , Yasumoto, K. , Terachi, T. and Yamagishi, H. (2014) The complete mitochondrial genome sequence of PubMed

Thind, A.K. , Wicker, T. , Simkova, H. , Fossati, D. , Moullet, O. , Brabant, C. , Vrana, J. PubMed

Thind, A.K. , Wicker, T. , Muller, T. , Ackermann, P.M. , Steuernagel, B. , Wulff, B.B.H. , Spannagl, M. PubMed PMC

Tiwari, V.K. , Wang, S. , Danilova, T. , Koo, D.H. and Gill, B.S. (2016) Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5Mg of PubMed

Wang, H. , Dai, K. , Xiao, J. , Yuan, C. , Zhao, R. , Dolezel, J. , Wu, Y. PubMed PMC

Wang, Y. , Hou, J. , Liu, H. , Li, T. , Wang, K. , Hao, C. , Liu, H. PubMed PMC

Wu, X. , Chang, X. and Jing, R. (2012) Genetic insight into yield‐associated traits of wheat grown in multiple rain‐fed environments. PLoS One, 7, e31249. PubMed PMC

Xiao, J. , Wan, W. , Li, M. , Yu, Z. , Zhang, X. , Liu, J. , Holušová, K. DOI

Xing, L. , Di, Z. , Yang, W. , Liu, J. , Li, M. , Wang, X. , Cui, C. PubMed PMC

Xing, L. , Hu, P. , Liu, J. , Witek, K. , Zhou, S. , Xu, J. , Zhou, W. PubMed

Zhang, P. , He, Z. , Tian, X. , Gao, F. , Xu, D. , Liu, J. , Wen, W.

Zhang, P. , Li, W. , Fellers, J. , Friebe, B. and Gill, B.S. (2004) BAC‐FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma, 112, 288–299. PubMed

Zhang, R. , Fan, Y. , Kong, L. , Wang, Z. , Wu, J. , Xing, L. , Cao, A. PubMed

Zhang, W. , Zhang, R. , Feng, Y. , Bie, T. and Chen, P. (2013) Distribution of highly repeated DNA sequences in

Zhang, X. , Ma, L. and Zheng, J. (2017b) Characteristics of genes selected by domestication and iIntensive breeding in crop plants. Acta Agronomica Sinica, 2, 157–170.

Zhang, X. , Wei, X. , Xiao, J. , Yuan, C. , Wu, Y. , Cao, A. , Xing, L.

Zhao, G. , Zou, C. , Li, K. , Wang, K. , Li, T. , Gao, L. , Zhang, X. PubMed

Zimin, A.V. , Puiu, D. , Hall, R. , Kingan, S. , Clavijo, B.J. and Salzberg, S.L. (2017) The first near‐complete assembly of the hexaploid bread wheat genome, PubMed PMC

Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes