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

Said Dadshani,Boby Mathew,Agim Ballvora,Annaliese S Mason,Jens Léon

doi:10.1038/s41598-021-85226-1

Said Dadshani, Boby Mathew + Show 3 more

Open Access

https://doi.org/10.1038/s41598-021-85226-1

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Journal: Scientific Reports	Publication Date: Mar 9, 2021
Citations: 19	License type: open-access

Affiliation: University of Bonn, Bayer (Germany)

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.

Highlights

Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions
The aim of the present study is to estimate the potential of a linkage disequilibrium (LD)-corrected wheat map for use in genome-wide association studies (GWAS) approaches and for detection of signatures that are related to the breeding progress of German cultivars
A total of 81,655 single nucleotide polymorphism (SNP) marker were aligned to the wheat reference genome assembly RefSeq v1.025, of which 54,389 markers aligned to physical positions on the assembled pseudomolecules

Summary

Introduction

Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. Population genetics and genome-wide association studies (GWAS) are comprehensive approaches to assess genomic diversity and detect signatures of past or ongoing selection in breeding at the molecular level[10,11,12]. Analyzing a set of winter wheat cultivars representing 50 years of German breeding history, Lichthardt et al (2020) were able to identify a co-evolution effect determining sink and source allocation in plants which affected grain yield potential. Studying changes of allele frequency within these panels in the course of breeding history allows us to trace the origin of beneficial alleles and identify valuable sources of genetic variation that may have been neglected during the breeding process. By identification and selection of genotypes containing alleles of interest these alleles can be re-introduced into modern c ultivars[26]

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