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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Autores principales:	Said Dadshani, Boby Mathew, Agim Ballvora, Annaliese S. Mason, Jens Léon
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3955e2f6d3964ea2a83b8b73b7f1f2d1
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spelling	oai:doaj.org-article:3955e2f6d3964ea2a83b8b73b7f1f2d12021-12-02T13:34:32ZDetection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach10.1038/s41598-021-85226-12045-2322https://doaj.org/article/3955e2f6d3964ea2a83b8b73b7f1f2d12021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85226-1https://doaj.org/toc/2045-2322Abstract 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.Said DadshaniBoby MathewAgim BallvoraAnnaliese S. MasonJens LéonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Said Dadshani Boby Mathew Agim Ballvora Annaliese S. Mason Jens Léon Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
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.
format	article
author	Said Dadshani Boby Mathew Agim Ballvora Annaliese S. Mason Jens Léon
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 Portfolio
publishDate	2021
url	https://doaj.org/article/3955e2f6d3964ea2a83b8b73b7f1f2d1
work_keys_str_mv	AT saiddadshani detectionofbreedingsignaturesinwheatusingalinkagedisequilibriumcorrectedmappingapproach AT bobymathew detectionofbreedingsignaturesinwheatusingalinkagedisequilibriumcorrectedmappingapproach AT agimballvora detectionofbreedingsignaturesinwheatusingalinkagedisequilibriumcorrectedmappingapproach AT annaliesesmason detectionofbreedingsignaturesinwheatusingalinkagedisequilibriumcorrectedmappingapproach AT jensleon detectionofbreedingsignaturesinwheatusingalinkagedisequilibriumcorrectedmappingapproach
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Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach

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