Dataset Information

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

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.

SUBMITTER: Kisten L

PROVIDER: S-EPMC7769470 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Kisten Lavinia L Tolmay Vicki L VL Mathew Isack I Sydenham Scott L SL Venter Eduard E

PloS one 20201228 12

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 bio ...[more]

PMID: 33370360

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Project description:BackgroundThe Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding.ResultsWe sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector.ConclusionsThis genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and advance functional and comparative genomics of insects and other organisms.

Project description:BackgroundProteins within aphid saliva play a crucial role as the molecular interface between aphids and their host plants. These salivary effectors modulate plant responses to favour aphid feeding and facilitate infestation. The identification of effectors from economically important pest species is central in understanding the molecular events during the aphid-plant interaction. The Russian wheat aphid (Diuraphis noxia, Kurdjumov) is one such pest that causes devastating losses to wheat and barley yields worldwide. Despite the severe threat to food security posed by D. noxia, the non-model nature of this pest and its host has hindered progress towards understanding this interaction. In this study, in the absence of a salivary gland transcriptome, whole-body transcriptomics data was mined to generate a candidate effector catalogue for D. noxia.ResultsMining the transcriptome identified 725 transcripts encoding putatively secreted proteins amongst which were transcripts specific to D. noxia. Six of the seven examined D. noxia putative effectors, termed DnE's (Diuraphis noxia effectors) exhibited salivary gland-specific expression. A comparative analysis between whole-body D. noxia transcriptome data versus the head and body transcriptomes from three other aphid species allowed us to define a catalogue of transcripts putatively upregulated in D. noxia head tissue. Five of these were selected for RT-qPCR confirmation, and were found to corroborate the differential expression predictions, with a further three confirmed to be highly expressed in D. noxia salivary gland tissue.ConclusionsDetermining a putative effector catalogue for D. noxia from whole-transcriptome data, particularly the identification of salivary-specific sequences potentially unique to D. noxia, provide the basis for future functional characterisation studies to gain further insight into this aphid-plant interaction. Furthermore, due to a lack of publicly available aphid salivary gland transcriptome data, the capacity to use comparative transcriptomics to compile a list of putative effector candidates from whole-body transcriptomics data will further the study of effectors in various aphid species.

Dataset Information

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

Publications

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

Similar Datasets

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