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

• Published in: Functional & integrative genomics Vol. 13; no. 1; pp. 19 - 32
• Main Authors: Michalak de Jimenez, Monika K, Bassi, Filippo M, Ghavami, Farhad, Simons, Kristin, Dizon, Rissa, Seetan, Raed I, Alnemer, Loai M, Denton, Anne M, Doğramacı, Münevver, Šimková, Hana, Doležel, Jaroslav, Seth, Kiran, Luo, Ming-Cheng, Dvorak, Jan, Gu, Yong Qiang, Kianian, Shahryar F
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-03-2013; Springer Nature B.V
• Subjects: alpha Radiation; Animal Genetics and Genomics; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Brachypodium distachyon; Cell Biology; Centromere - genetics; Centromeres; chromosome mapping; Chromosomes; Chromosomes, Plant - genetics; Conservation; Cytoplasm; Evolution; Evolutionary conservation; Gene mapping; genes; Genes, Plant; Genetic Loci; Genetic Markers; Genomics; Genotype & phenotype; Grasses; hybrids; Life Sciences; loci; Microbial Genetics and Genomics; nuclear-cytoplasmic interactions; Original Paper; Oryza sativa; Phenotyping; Plant Genetics and Genomics; Plant populations; Radiation Hybrid Mapping; Sorghum bicolor; Speciation; Synteny; Telomere - genetics; Triticum - genetics; Triticum aestivum; Wheat; Paleofusion; Species cytoplasm specific; Wheat Zapper; Alloplasmic; Cytoplasm substitution; Synteny
• ISSN: 1438-793X; 1438-7948
• DOI: 10.1007/s10142-013-0318-3

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.”