Study on the Association between LRRC8B Gene InDel and Sheep Body Conformation Traits

Zhang, Jiaqiang; Zhansaya, Toremurat; Liang, Yilin; Cheng, Jie; Sun, Zhenzhen; Huang, Yangming; Liu, Junxia; Chaogetu, BUREN; Ren, Gang; Chen, Hong

doi:10.3390/genes14020356

Cited by 3 publications

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

Niciura,

Cardoso,

Ibelli

et al. 2024

Parasites Vectors

View full text Add to dashboard Cite

Background The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control. Methods Eggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content. Results The heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep. Conclusions The present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep. Graphical Abstract

show abstract

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

Niciura,

Cardoso,

Ibelli

et al. 2024

Parasites Vectors

View full text Add to dashboard Cite

show abstract

Multi-omics elucidated parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

Niciura,

Cardoso,

Ibelli

et al. 2023

Preprint

View full text Add to dashboard Cite

Background: The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying parasite resistance. Haemonchus contortus, the predominant sheep parasite species in the tropics, results in significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control measures due to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota effects, modulates host immunity can guide selection decisions to breed more resistant animals. This understanding can also refine management practices and inform the development of new therapeutics for long-term helminth control. Results: Egg per gram (EPG) counts were obtained in Morada Nova sheep subjected to two artificial infections with H. contortus, and used as a proxy to select animals with high resistance or susceptibility. The GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between groups based on RNA-seq of the abomasum. From 50K SNP genotyping, EPG heritability estimate was 0.12, and a genome-wide association study (GWAS) identified regions on chromosomes 2 and 11 harboring candidate genes for resistance, immune response, body weight, and adaptation. Trans-eQTLs between significant variants and differentially expressed transcripts were found. Amplicon sequence variants (ASVs) from PCR amplification and sequencing of bacterial and archaeal 16S rRNA genes in sheep feces and rumen generated functional co-expression modules correlated with resistance to H. contortus, showing enrichment in pathways of response to bacterium, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera, Prevotellaceae family, and Verrucomicrobiota. In RNA-seq of H. contortus, some mitochondrial, collagen- and cuticle-related genes were expressed only in parasites retrieved from susceptible sheep. Conclusions: This study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota and the H. contortus parasite. These findings can assist with the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus in sheep.

show abstract

SNP-Based and Kmer-Based eQTL Analysis Using Transcriptome Data

Ge,

Li,

Zhang

2024

Animals

View full text Add to dashboard Cite

Traditional expression quantitative trait locus (eQTL) mapping associates single nucleotide polymorphisms (SNPs) with gene expression, where the SNPs are derived from large-scale whole-genome sequencing (WGS) data or transcriptome data. While WGS provides a high SNP density, it also incurs substantial sequencing costs. In contrast, RNA-seq data, which are more accessible and less expensive, can simultaneously yield gene expressions and SNPs. Thus, eQTL analysis based on RNA-seq offers significant potential applications. Two primary strategies were employed for eQTL in this study. The first involved analyzing expression levels in relation to variant sites detected between populations from RNA-seq data. The second approach utilized kmers, which are sequences of length k derived from RNA-seq reads, to represent variant sites and associated these kmer genotypes with gene expression. We discovered 87 significant association signals involving eGene on the basis of the SNP-based eQTL analysis. These genes include DYNLT1, NMNAT1, and MRLC2, which are closely related to neurological functions such as motor coordination and homeostasis, play a role in cellular energy metabolism, and function in regulating calcium-dependent signaling in muscle contraction, respectively. This study compared the results obtained from eQTL mapping using RNA-seq identified SNPs and gene expression with those derived from kmers. We found that the vast majority (23/30) of the association signals overlapping the two methods could be verified by haplotype block analysis. This comparison elucidates the strengths and limitations of each method, providing insights into their relative efficacy for eQTL identification.

show abstract

Study on the Association between LRRC8B Gene InDel and Sheep Body Conformation Traits

Cited by 3 publications

References 44 publications

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

Multi-omics elucidated parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

SNP-Based and Kmer-Based eQTL Analysis Using Transcriptome Data

Contact Info

Product

Resources

About