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. 2021 Mar 15;16(3):e0248405.
doi: 10.1371/journal.pone.0248405. eCollection 2021.

Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection

Hadeer M Aboshady  1   2   3   4 , Nathalie Mandonnet  4 , Anna M Johansson  3 , Elisabeth Jonas  3 , Jean-Christophe Bambou  4
Affiliations

Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection

Hadeer M Aboshady et al. PLoS One. .

Abstract

Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig 1
Fig 1
Venn diagram for SNP (a) deletion (b) and insertion (c) variants identified in samples from the resistant and susceptible group.
Fig 2
Fig 2. Single nucleotide polymorphism (SNP) distribution among genes.
Fig 3
Fig 3. Insertions and deletions (indels) identified among genes using the data from resistant (R) and susceptible (S) kids.
Fig 4
Fig 4. Variant effect prediction in resistant and susceptible animals.
Fig 5
Fig 5. Gene ontology for genes containing variants for data from the resistant and susceptible genotypes.
Fig 6
Fig 6. KEGG pathways for genes containing genomic variants in the data from the resistant and susceptible animals.
Fig 7
Fig 7. Number of genomic variants for each gene in the T cell receptor signalling pathway in the resistant animals.
See this image and copyright information in PMC

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