A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

Monika K. Michalak De Jimenez, Filippo M. Bassi, Farhad Ghavami, Kristin Simons, Rissa Dizon, Raed I. Seetan, Loai M. Alnemer, Anne M. Denton, Münevver Doǧramaci, Hana Šimková, Jaroslav Doležel, Kiran Seth, Ming Cheng Luo, Jan Dvorak, Yong Qiang Gu, Shahryar F. Kianian

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19 Scopus citations


The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs ae locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs ae locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."

Original languageEnglish (US)
Pages (from-to)19-32
Number of pages14
JournalFunctional and Integrative Genomics
Issue number1
StatePublished - Mar 2013
Externally publishedYes

Bibliographical note

Funding Information:
Acknowledgments The authors wish to thank Justin Hegstad and Allen Peckrul for their qualified technical help. This work was supported by funding from the National Science Foundation, Plant Genome Research Program (NSF-PGRP) grant No. IOS-0822100 to SFK. F.M.B was partially supported by Program Master and Back Regione Autonoma della Sardegna and Monsanto Beachell-Borlaug International Scholarship.


  • Alloplasmic
  • Cytoplasm substitution
  • Paleofusion
  • Species cytoplasm specific
  • Synteny
  • Wheat Zapper


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