A high resolution radiation hybrid map of wheat chromosome 4A

Barbora Balcárková; Zeev Frenkel; Monika Škopová; Michael Abrouk; Ajay Kumar; Shiaoman Chao; Shahryar F. Kianian; Eduard Akhunov; Abraham B. Korol; Jaroslav Doležel; Miroslav Valárik

doi:10.3389/fpls.2016.02063

A high resolution radiation hybrid map of wheat chromosome 4A

Barbora Balcárková, Zeev Frenkel, Monika Škopová, Michael Abrouk, Ajay Kumar, Shiaoman Chao, Shahryar F. Kianian, Eduard Akhunov, Abraham B. Korol, Jaroslav Doležel, Miroslav Valárik

Plant Pathology

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12 Scopus citations

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.

Original language	English (US)
Article number	2063
Journal	Frontiers in Plant Science
Volume	7
DOIs	https://doi.org/10.3389/fpls.2016.02063
State	Published - Jan 10 2017

Bibliographical note

Publisher Copyright:
© 2017 Balcárková, Frenkel, Škopová, Abrouk, Kumar, Chao, Kianian, Akhunov, Korol, Doležel and Valárik.

Keywords

Chromosome deletion bin map
Endosperm radiation hybrid panel
Radiation hybrid map
SNP iSelect array
Triticum aestivum
Wheat chromosome 4A

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title = "A high resolution radiation hybrid map of wheat chromosome 4A",

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.",

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AU - Balcárková, Barbora

AU - Frenkel, Zeev

AU - Škopová, Monika

AU - Abrouk, Michael

AU - Kumar, Ajay

AU - Chao, Shiaoman

AU - Kianian, Shahryar F.

AU - Akhunov, Eduard

AU - Korol, Abraham B.

AU - Doležel, Jaroslav

AU - Valárik, Miroslav

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AB - 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.

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KW - Endosperm radiation hybrid panel

KW - Radiation hybrid map

KW - SNP iSelect array

KW - Triticum aestivum

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A high resolution radiation hybrid map of wheat chromosome 4A

Abstract

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Keywords

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