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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #346176

Research Project: Genetic Improvement of Durum and Spring Wheat for Quality and Resistance to Diseases and Pests

Location: Cereal Crops Research

Title: A high resolution radiation hybrid map of wheat chromosome 4A

Author
item BALCARKOVA, BARBORA - Institute Of Experimental Botany
item FRENKEL, ZEEV - University Of Haifa
item SKOPOVA, MONIKA - Institute Of Experimental Botany
item ABROUK, MICHAEL - Institute Of Experimental Botany
item KUMAR, AJAY - North Dakota State University
item Chao, Shiaoman
item Kianian, Shahryar
item AKHUNOV, EDUARD - Kansas State University
item KOROL, ABRAHAM - University Of Haifa
item DOLEZEL, JAROSLAV - Institute Of Experimental Botany
item VALARIK, MIROSLAV - Institute Of Experimental Botany

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/26/2016
Publication Date: 1/10/2017
Citation: Balcarkova, B., Frenkel, Z., Skopova, M., Abrouk, M., Kumar, A., Chao, S., Kianian, S., Akhunov, E., Korol, A., Dolezel, J., Valarik, M. 2017. A high resolution radiation hybrid map of wheat chromosome 4A. Frontiers in Plant Science. 7:2063. https://doi.org/10.3389/fpls.2016.02063.

Interpretive Summary: Bread wheat has a large and complex genome with low recombination levels at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers and impedes obtaining of high-quality reference genome sequence, prerequisite to better understanding of its genes and their functions. Radiation hybrid (RH) mapping is an alternative approach. In this approach a chromosome is broken into random fragments using radiation. Then, the presence or absence of a marker is screened to generate a radiation hybrid population. Here we report on the construction of high-density and high-resolution RH map of chromosome 4A supported by high-density chromosome deletion map. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.

Technical Abstract: Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.