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. 2020 Dec 28;15(12):e0244455.
doi: 10.1371/journal.pone.0244455. eCollection 2020.

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

Lavinia Kisten  1   2 , Vicki L Tolmay  1 , Isack Mathew  3 , Scott L Sydenham  4 , Eduard Venter  2
Affiliations

Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

Lavinia Kisten et al. PLoS One. .

Abstract

Russian wheat aphid (RWA; Diuraphis noxia Kurdjumov) resistance on the 1D chromosome of wheat has been the subject of intensive research. Conversely, the deployment of the Dn4 derived RWA resistant varieties diminished in recent years due to the overcoming of the resistance it imparts in the United States of America. However, this resistance has not been deployed in South Africa despite reports that Dn4 containing genotypes exhibited varying levels of resistance against the South African RWA biotypes. It is possible that there may be certain genetic differences within breeding lines or cultivars that influence the expression of resistance. The aim of this study was to identify single nucleotide polymorphism (SNP) markers associated with resistance to South African RWA biotypes. A panel of thirty-two wheat lines were phenotyped for RWA resistance using four South African RWA biotypes and a total of 181 samples were genotyped using the Illumina 9K SNP wheat chip. A genome wide association study using 7598 polymorphic SNPs showed that the population was clustered into two distinct subpopulations. Twenty-seven marker trait associations (MTA) were identified with an average linkage disequilibrium of 0.38 at 10 Mbp. Four of these markers were highly significant and three correlated with previously reported quantitative trait loci linked to RWA resistance in wheat. Twenty putative genes were annotated using the IWGSC RefSeq, three of which are linked to plant defence responses. This study identified novel chromosomal regions that contribute to RWA resistance and contributes to unravelling the complex genetics that control RWA resistance in wheat.

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Conflict of interest statement

Scott L. Sydenham is presently an employee of LongReach Plant Breeders Management Pty Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Population structure of the study panel.
A The two distinct clusters found in 169 wheat bulked samples used in this study. The green bars represent 102 winter-type bulked samples and the red bars represent 67 spring-type bulked samples. B Kinship matrix depicting relatedness among the genotypes.
Fig 2
Fig 2. Manhattan plot showing significant SNP markers associated with RWA resistance using CMLM with a FDR adjusted p-value of 0.05.
The horizontal green and red lines represent the threshold for genome wide significance (p < 0.000001) and FDR adjusted p < 0.0001, respectively.
Fig 3
Fig 3. Linkage disequilibrium (LD) among significant markers.
A Whole-genome LD decay plot against distance (Mbp) with smoothing curve. B Local LD among markers in significant association with Russian wheat aphid resistance.
Fig 4
Fig 4. Physical map of the wheat genome depicting the positions of putative candidate genes identified.
See this image and copyright information in PMC

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References

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