A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

Marco Maccaferri, Maria A ngela Cane', Maria C. Sanguineti, Silvio Salvi, Maria C. Colalongo, Andrea Massi, Fran Clarke, Ron Knox, Curtis J. Pozniak, John M. Clarke, Tzion Fahima, Jorge Dubcovsky, Steven Xu, Karim Ammar, I. Karsai, Gyula Vida, Roberto Tuberosa

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

BACKGROUND: Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.

RESULTS: High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.

CONCLUSIONS: The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Original languageEnglish
Pages (from-to)873
Number of pages1
JournalBMC Genomics
Volume15
DOIs
Publication statusPublished - 2014

Fingerprint

Genome-Wide Association Study
Linkage Disequilibrium
Triticum
Genome
Genomics
Microsatellite Repeats
Chromosomes
Population
Tetraploidy
North America
Mexico
Genetic Recombination
Nucleotides
Technology

ASJC Scopus subject areas

  • Medicine(all)

Cite this

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. / Maccaferri, Marco; Cane', Maria A ngela; Sanguineti, Maria C.; Salvi, Silvio; Colalongo, Maria C.; Massi, Andrea; Clarke, Fran; Knox, Ron; Pozniak, Curtis J.; Clarke, John M.; Fahima, Tzion; Dubcovsky, Jorge; Xu, Steven; Ammar, Karim; Karsai, I.; Vida, Gyula; Tuberosa, Roberto.

In: BMC Genomics, Vol. 15, 2014, p. 873.

Research output: Contribution to journalArticle

Maccaferri, M, Cane', MAN, Sanguineti, MC, Salvi, S, Colalongo, MC, Massi, A, Clarke, F, Knox, R, Pozniak, CJ, Clarke, JM, Fahima, T, Dubcovsky, J, Xu, S, Ammar, K, Karsai, I, Vida, G & Tuberosa, R 2014, 'A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping', BMC Genomics, vol. 15, pp. 873. https://doi.org/10.1186/1471-2164-15-873
Maccaferri, Marco ; Cane', Maria A ngela ; Sanguineti, Maria C. ; Salvi, Silvio ; Colalongo, Maria C. ; Massi, Andrea ; Clarke, Fran ; Knox, Ron ; Pozniak, Curtis J. ; Clarke, John M. ; Fahima, Tzion ; Dubcovsky, Jorge ; Xu, Steven ; Ammar, Karim ; Karsai, I. ; Vida, Gyula ; Tuberosa, Roberto. / A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. In: BMC Genomics. 2014 ; Vol. 15. pp. 873.
@article{78308a4c80a043bf83657acd113bad6d,
title = "A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping",
abstract = "BACKGROUND: Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.RESULTS: High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology{\circledR} (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.CONCLUSIONS: The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.",
author = "Marco Maccaferri and Cane', {Maria A ngela} and Sanguineti, {Maria C.} and Silvio Salvi and Colalongo, {Maria C.} and Andrea Massi and Fran Clarke and Ron Knox and Pozniak, {Curtis J.} and Clarke, {John M.} and Tzion Fahima and Jorge Dubcovsky and Steven Xu and Karim Ammar and I. Karsai and Gyula Vida and Roberto Tuberosa",
year = "2014",
doi = "10.1186/1471-2164-15-873",
language = "English",
volume = "15",
pages = "873",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",

}

TY - JOUR

T1 - A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

AU - Maccaferri, Marco

AU - Cane', Maria A ngela

AU - Sanguineti, Maria C.

AU - Salvi, Silvio

AU - Colalongo, Maria C.

AU - Massi, Andrea

AU - Clarke, Fran

AU - Knox, Ron

AU - Pozniak, Curtis J.

AU - Clarke, John M.

AU - Fahima, Tzion

AU - Dubcovsky, Jorge

AU - Xu, Steven

AU - Ammar, Karim

AU - Karsai, I.

AU - Vida, Gyula

AU - Tuberosa, Roberto

PY - 2014

Y1 - 2014

N2 - BACKGROUND: Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.RESULTS: High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.CONCLUSIONS: The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

AB - BACKGROUND: Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.RESULTS: High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.CONCLUSIONS: The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

UR - http://www.scopus.com/inward/record.url?scp=84964313451&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84964313451&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-15-873

DO - 10.1186/1471-2164-15-873

M3 - Article

C2 - 25293821

AN - SCOPUS:84964313451

VL - 15

SP - 873

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

ER -