Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach

Abstract Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent mark...

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Main Authors: Said Dadshani, Boby Mathew, Agim Ballvora, Annaliese S. Mason, Jens Léon
Format: Article
Language:English
Published: Nature Publishing Group 2021-03-01
Series:Scientific Reports
Online Access:https://doi.org/10.1038/s41598-021-85226-1
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spelling doaj-3955e2f6d3964ea2a83b8b73b7f1f2d12021-03-11T12:18:28ZengNature Publishing GroupScientific Reports2045-23222021-03-0111111210.1038/s41598-021-85226-1Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approachSaid Dadshani0Boby Mathew1Agim Ballvora2Annaliese S. Mason3Jens Léon4Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of BonnBayer CropScienceInstitute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of BonnInstitute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of BonnInstitute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of BonnAbstract Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this translocation. A “selective sweep” for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.https://doi.org/10.1038/s41598-021-85226-1
collection DOAJ
language English
format Article
sources DOAJ
author Said Dadshani
Boby Mathew
Agim Ballvora
Annaliese S. Mason
Jens Léon
spellingShingle Said Dadshani
Boby Mathew
Agim Ballvora
Annaliese S. Mason
Jens Léon
Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
Scientific Reports
author_facet Said Dadshani
Boby Mathew
Agim Ballvora
Annaliese S. Mason
Jens Léon
author_sort Said Dadshani
title Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
title_short Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
title_full Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
title_fullStr Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
title_full_unstemmed Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
title_sort detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
publisher Nature Publishing Group
series Scientific Reports
issn 2045-2322
publishDate 2021-03-01
description Abstract Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this translocation. A “selective sweep” for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.
url https://doi.org/10.1038/s41598-021-85226-1
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