Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

Hanan Sela; Caroline Loutre; Beat Keller; Alan Schulman; Eviatar Nevo; Abraham Korol; Tzion Fahima

doi:10.1007/s00122-010-1434-2

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

Hanan Sela, Caroline Loutre, Beat Keller, Alan Schulman, Eviatar Nevo, Abraham Korol, Tzion Fahima

Department of Evolutionary and Environmental Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Introduction: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). Results: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (d_S = 0.029, d_N = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (d_S = 0.069 vs. 0.029, d_N = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r² = 0.5 to r² = 0.1 within a 2-kb span. Conclusion: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.

Original language	English
Pages (from-to)	175-187
Number of pages	13
Journal	Theoretical And Applied Genetics
Volume	122
Issue number	1
DOIs	https://doi.org/10.1007/s00122-010-1434-2
State	Published - Jan 2011

Bibliographical note

Funding Information:
This work was supported by grants from the European Union’s Sixth Framework Programme (FP6) in the BioExploit project (No. CT-2005-513949). The authors acknowledge The Israel Science Foundation equipment grants #048/99, #1478/04, #1719/08. The authors wish to thank Ortal Mergi and Anne-Mari Narvanto for technical assistance.

ASJC Scopus subject areas

Biotechnology
Agronomy and Crop Science
Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s00122-010-1434-2

Cite this

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title = "Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations",

abstract = "Introduction: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). Results: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (dS = 0.029, dN = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (dS = 0.069 vs. 0.029, dN = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r2 = 0.5 to r2 = 0.1 within a 2-kb span. Conclusion: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.",

author = "Hanan Sela and Caroline Loutre and Beat Keller and Alan Schulman and Eviatar Nevo and Abraham Korol and Tzion Fahima",

note = "Funding Information: This work was supported by grants from the European Union{\textquoteright}s Sixth Framework Programme (FP6) in the BioExploit project (No. CT-2005-513949). The authors acknowledge The Israel Science Foundation equipment grants #048/99, #1478/04, #1719/08. The authors wish to thank Ortal Mergi and Anne-Mari Narvanto for technical assistance.",

year = "2011",

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doi = "10.1007/s00122-010-1434-2",

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T1 - Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

AU - Sela, Hanan

AU - Loutre, Caroline

AU - Keller, Beat

AU - Schulman, Alan

AU - Nevo, Eviatar

AU - Korol, Abraham

AU - Fahima, Tzion

N1 - Funding Information: This work was supported by grants from the European Union’s Sixth Framework Programme (FP6) in the BioExploit project (No. CT-2005-513949). The authors acknowledge The Israel Science Foundation equipment grants #048/99, #1478/04, #1719/08. The authors wish to thank Ortal Mergi and Anne-Mari Narvanto for technical assistance.

PY - 2011/1

Y1 - 2011/1

N2 - Introduction: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). Results: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (dS = 0.029, dN = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (dS = 0.069 vs. 0.029, dN = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r2 = 0.5 to r2 = 0.1 within a 2-kb span. Conclusion: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.

AB - Introduction: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). Results: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (dS = 0.029, dN = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (dS = 0.069 vs. 0.029, dN = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r2 = 0.5 to r2 = 0.1 within a 2-kb span. Conclusion: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.

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SN - 0040-5752

VL - 122

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JO - Theoretical And Applied Genetics

JF - Theoretical And Applied Genetics

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ER -

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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