A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map

Guang Chen Fang, Barbara P. Blackmon, Margaret E. Staton, C. Dana Nelson, Thomas L. Kubisiak, Bode A. Olukolu, David Henry, Tatyana Zhebentyayeva, Christopher A. Saski, Chun Huai Cheng, Megan Monsanto, Stephen Ficklin, Michael Atkins, Laura L. Georgi, Abdelali Barakat, Nicholas Wheeler, John E. Carlson, Ronald Sederoff, Albert G. Abbott

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www. fagaceae. org/physical_maps.

Original languageEnglish (US)
Pages (from-to)525-537
Number of pages13
JournalTree Genetics and Genomes
Volume9
Issue number2
DOIs
StatePublished - Jan 1 2013

Fingerprint

Castanea mollissima
Bacterial Artificial Chromosomes
physical chromosome mapping
genome
Genome
bacterial artificial chromosomes
Fagaceae
probe
Gene Order
Quantitative Trait Loci
Expressed Sequence Tags
chromosome
Castanea
Genetic Markers
Clone Cells
expressed sequence tags
gene
linkage groups
blight
genetic marker

All Science Journal Classification (ASJC) codes

  • Forestry
  • Molecular Biology
  • Genetics
  • Horticulture

Cite this

Fang, G. C., Blackmon, B. P., Staton, M. E., Nelson, C. D., Kubisiak, T. L., Olukolu, B. A., ... Abbott, A. G. (2013). A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genetics and Genomes, 9(2), 525-537. https://doi.org/10.1007/s11295-012-0576-6
Fang, Guang Chen ; Blackmon, Barbara P. ; Staton, Margaret E. ; Nelson, C. Dana ; Kubisiak, Thomas L. ; Olukolu, Bode A. ; Henry, David ; Zhebentyayeva, Tatyana ; Saski, Christopher A. ; Cheng, Chun Huai ; Monsanto, Megan ; Ficklin, Stephen ; Atkins, Michael ; Georgi, Laura L. ; Barakat, Abdelali ; Wheeler, Nicholas ; Carlson, John E. ; Sederoff, Ronald ; Abbott, Albert G. / A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. In: Tree Genetics and Genomes. 2013 ; Vol. 9, No. 2. pp. 525-537.
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abstract = "Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www. fagaceae. org/physical_maps.",
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Fang, GC, Blackmon, BP, Staton, ME, Nelson, CD, Kubisiak, TL, Olukolu, BA, Henry, D, Zhebentyayeva, T, Saski, CA, Cheng, CH, Monsanto, M, Ficklin, S, Atkins, M, Georgi, LL, Barakat, A, Wheeler, N, Carlson, JE, Sederoff, R & Abbott, AG 2013, 'A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map', Tree Genetics and Genomes, vol. 9, no. 2, pp. 525-537. https://doi.org/10.1007/s11295-012-0576-6

A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. / Fang, Guang Chen; Blackmon, Barbara P.; Staton, Margaret E.; Nelson, C. Dana; Kubisiak, Thomas L.; Olukolu, Bode A.; Henry, David; Zhebentyayeva, Tatyana; Saski, Christopher A.; Cheng, Chun Huai; Monsanto, Megan; Ficklin, Stephen; Atkins, Michael; Georgi, Laura L.; Barakat, Abdelali; Wheeler, Nicholas; Carlson, John E.; Sederoff, Ronald; Abbott, Albert G.

In: Tree Genetics and Genomes, Vol. 9, No. 2, 01.01.2013, p. 525-537.

Research output: Contribution to journalArticle

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T1 - A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map

AU - Fang, Guang Chen

AU - Blackmon, Barbara P.

AU - Staton, Margaret E.

AU - Nelson, C. Dana

AU - Kubisiak, Thomas L.

AU - Olukolu, Bode A.

AU - Henry, David

AU - Zhebentyayeva, Tatyana

AU - Saski, Christopher A.

AU - Cheng, Chun Huai

AU - Monsanto, Megan

AU - Ficklin, Stephen

AU - Atkins, Michael

AU - Georgi, Laura L.

AU - Barakat, Abdelali

AU - Wheeler, Nicholas

AU - Carlson, John E.

AU - Sederoff, Ronald

AU - Abbott, Albert G.

PY - 2013/1/1

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N2 - Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www. fagaceae. org/physical_maps.

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