A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes

Massimo Iorizzo, Liangliang Gao, Harpartap Mann, Alessandra Traini, Maria Luisa Chiusano, Andrzej Killian, Riccardo Aversano, Domenico Carputo, James M. Bradeen

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. Results: Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. Conclusions: The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements.
Original languageEnglish
Article number123
Pages (from-to)1-9
Number of pages9
JournalBMC Genetics
Volume15
DOIs
Publication statusPublished - 2014

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Solanum
Solanum tuberosum
Genome
Technology
Lycopersicon esculentum
Chromosomes
Chromosome Mapping
Clone Cells

Cite this

Iorizzo, Massimo ; Gao, Liangliang ; Mann, Harpartap ; Traini, Alessandra ; Chiusano, Maria Luisa ; Killian, Andrzej ; Aversano, Riccardo ; Carputo, Domenico ; Bradeen, James M. / A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes. In: BMC Genetics. 2014 ; Vol. 15. pp. 1-9.
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title = "A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes",
abstract = "Background: Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. Results: Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. Conclusions: The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements.",
keywords = "Comparative genomics, DArT markers, Linkagemap, S. Bulbocastanum, S. Lycopersicum, S. Tuberosum",
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Iorizzo, M, Gao, L, Mann, H, Traini, A, Chiusano, ML, Killian, A, Aversano, R, Carputo, D & Bradeen, JM 2014, 'A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes', BMC Genetics, vol. 15, 123, pp. 1-9. https://doi.org/10.1186/s12863-014-0123-6

A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes. / Iorizzo, Massimo; Gao, Liangliang; Mann, Harpartap; Traini, Alessandra; Chiusano, Maria Luisa; Killian, Andrzej; Aversano, Riccardo; Carputo, Domenico; Bradeen, James M.

In: BMC Genetics, Vol. 15, 123, 2014, p. 1-9.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A DArT marker-based linkage map for Wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes

AU - Iorizzo, Massimo

AU - Gao, Liangliang

AU - Mann, Harpartap

AU - Traini, Alessandra

AU - Chiusano, Maria Luisa

AU - Killian, Andrzej

AU - Aversano, Riccardo

AU - Carputo, Domenico

AU - Bradeen, James M.

PY - 2014

Y1 - 2014

N2 - Background: Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. Results: Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. Conclusions: The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements.

AB - Background: Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. Results: Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. Conclusions: The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements.

KW - Comparative genomics

KW - DArT markers

KW - Linkagemap

KW - S. Bulbocastanum

KW - S. Lycopersicum

KW - S. Tuberosum

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UR - http://www.mendeley.com/research/dart-markerbased-linkage-map-wild-potato-solanum-bulbocastanum-facilitates-structural-comparisons-be

U2 - 10.1186/s12863-014-0123-6

DO - 10.1186/s12863-014-0123-6

M3 - Article

VL - 15

SP - 1

EP - 9

JO - BMC Genetics

JF - BMC Genetics

SN - 1471-2156

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