Variant discovery in genes identified as differentially expressed genes between the abomasal lymph node transcriptome of resistant and susceptible adult sheep to teladorsagia circumcincta infection

Gastrointestinal nematode infections are one of the major health issues facing grazing sheep populations and it incurs on major economic losses for sheep breeders. The resistance/susceptibility trait appears to be a highly complex trait (Behnke et al. 2003; Dominik 2005). In sheep resistance to nematode infection shows a moderate level of heritability (range 0.3-0.6) (Stear et al. 2001). Several QTL mapping studies have tried to identify genomic regions and mutations that influence resistance to nematode infection (Atlija et al. 2016; Coltman et al. 2001; Gutiérrez-Gil et al. 2009; Sayers et al. 2005), although the detection of causal mutations for this trait is still a challenge for the research community. The recently available RNA-seq technology provides the opportunity to extract highthroughput transcriptome data from a specific tissue to perform gene quantification, differential gene expression and detection of variants (SNPs and indels), which could be assessed as potential causal mutations (Hudson, Dalrymple, and Reverter 2012). A previous study of our research group has identified a list of 106 differential expression genes (DEGs) based on RNA-Seq dataset obtained from the abomasal lymph nodes of 12 adult sheep, previously classified as resistant or susceptible to GIN infection based on an artificial infection with T. circumcincta larvae Chitneedi et al. (2018). In the present study we present a detailed study of the variants mapping within the list of DEGs previously reported in that study. Thus, the present study provides a list of functionally relevant variants that could underlie the genetic control of resistance/susceptibility to T. circumcincta in adult sheep. Financiado por la Junta de Castilla y León (Conserjería de Educación) y Fondo Social Europeo (Ref. LE248U14). Ejecución: Universidad de León. Dpto. Producción Animal. Investigador Principal: Dr. Beatriz Gutierrez Gi

Exploring the mechanisms of resistance to Teladorsagia circumcincta infection in sheep through transcriptome analysis of abomasal mucosa and abomasal lymph nodes

8 p.The present study exploited the RNA-seq technology to analyze the transcriptome of target tissues affected by the Teladorsagia circumcincta infection in two groups of adult ewes showing different statuses against gastrointestinal nematode (GIN) infection with the aim of identifying genes linked to GIN infection resistance in sheep. For this, based on the accumulated faecal egg count of 18 adult Churra ewes subjected to a first experimental infection with T. circumcincta, six ewes were classified as resistant and six others as susceptible to the infection. These 12 animals were dewormed and infected again. After humanitarian sacrifice of these 12 animals at day 7 post-infection, RNA samples were obtained from abomasal mucosa and lymph node tissues and RNA-Seq datasets were generated using an Illumina HiSeq 2000 sequencer. The distribution of the genes based on their expression level were very similar among the two different tissues and conditions. The differential expression analysis performed with two software (DESeq and EdgeR) only identified common differentially expressed genes (DEGs), a total of 106, in the lymph node samples which were considered as GIN-activated. The enrichment analysis performed for these GIN-activated genes identified some pathways related to cytokine-mediated immune response and the PPARG signaling pathway as well as disease terms related to inflammation and gastro-intestinal diseases as enriched. A systematic comparison with the results of previous studies confirmed the involvement of genes such as ITLN2, CLAC1 and galectins, in the immune mechanism activated against T. circumcincta in resistant sheep. Financiado por la Junta de Castilla y León (Conserjería de Educación) y Fondo Social Europeo (Ref. LE248U14). Ejecución: Universidad de León. Dpto. Producción Animal. Investigador Principal: Dr. Beatriz Gutierrez GilS

Estudio preliminar del transcriptoma de la mucosa abomasal de ovejas clasificadas como resistentes y susceptibles según la respuesta a una infección experimental con teladorsagia circumcincta

Este proyecto trata de estudiar el transcriptoma de los tejidos de mayor importancia durante la respuesta inmune de ovejas adultas ante la infección por nematodos gastrointestinales, la mucosa abomasal y los ganglios abomasales. El transcriptoma es el conjunto completo de todos los transcritos (regiones del DNA que pasan a RNA mensajero, o mRNA) de una célula, y su cuantificación en un momento fisiológico específico. La identificación de genes diferencialmente expresados en los tejidos afectados por la infección entre ovejas susceptibles y resistentes es un primer paso para la identificación de genes y rutas génicas involucradas en la resistencia/susceptibilidad a este tipo de infecciones. Esta comunicación es el resultado de la investigación dentro del Proyecto: “Análisis del transcriptoma de la mucosa y los ganglios abomasales para la identificación de genes involucrados en la resistencia a los nematodos gastrointestinales en ovejas adultas”. Financiado por la Junta de Castilla y León (Conserjería de Educación) y Fondo Social Europeo (Ref. LE248U14). Ejecución: Universidad de León. Dpto. Producción Animal. Investigador Principal: Dr. Beatriz Gutierrez Gi

Preliminary differential transcriptomic analysis of abomasal mucosa from resistant and susceptible sheep to gastrointestinal nematodes (GINs) after an experimental infection with T. circumcincta

Este proyecto trata de estudiar el transcriptoma de los tejidos de mayor importancia durante la respuesta inmune de ovejas adultas ante la infección por nematodos gastrointestinales, la mucosa abomasal y los ganglios abomasales. El transcriptoma es el conjunto completo de todos los transcritos (regiones del DNA que pasan a RNA mensajero, o mRNA) de una célula, y su cuantificación en un momento fisiológico específico. La identificación de genes diferencialmente expresados en los tejidos afectados por la infección entre ovejas susceptibles y resistentes es un primer paso para la identificación de genes y rutas génicas involucradas en la resistencia/susceptibilidad a este tipo de infecciones. Esta comunicación es el resultado de la investigación llevada a cabo en el marco del proyecto: “Análisis del transcriptoma de la mucosa y los ganglios abomasales para la identificación de genes involucrados en la resistencia a los nematodos gastrointestinales en ovejas adultas”. Financiado por la Junta de Castilla y León (Conserjería de Educación) y Fondo Social Europeo (Ref. LE248U14). Ejecución: Universidad de León. Dpto. Producción Animal. Investigador Principal: Dr. Beatriz Gutierrez Gi

Additional file 1 of Sequence-based GWAS meta-analyses for beef production traits

Additional file 1: Table S1. QTL detected in within-population GWAS and fixed-effects and z-score meta-analyses