Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed

Cecchi, Francesca; Russo, Cláudia; Iamartino, Daniela; Galiero, Alessia; Turchi, Barbara; Fratini, Filippo; Degl’Innocenti, Sara; Mazza, Raffaele; Biffani, Stefano; Preziuso, Giovanna; Cantile, Carlo

doi:10.1007/s11250-017-1306-8

Cited by 20 publications

(16 citation statements)

References 31 publications

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“…For instance, ruminants differ in their response to a wide range of economically important pathogens. Variation in the expression of NRAMP1 ( SLC11A1 ) is involved in the response of sheep and goat to Johne’s disease (Cecchi et al, 2017). Similarly, resistance to Haemonchus contortus infections in sheep and goats is associated with a stronger Th2-type transcriptional immune response (Gill et al, 2000; Alba-Hurtado and Munoz-Guzman, 2013).…”

Section: Resultsmentioning

confidence: 99%

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

et al. 2019

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Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

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Section: Resultsmentioning

confidence: 99%

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

et al. 2019

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“…Blood samples of forty eight female GRF goats were collected and animals were genotyped with the Illumina GoatSNP50 BeadChip (Illumina Inc., San Diego, CA) containing 53,347 Single Nucleotide Polymorpishms (SNPs) [12]. Genomic data of nine Italian autochthonous goat breeds, namely Argentata dell’Etna (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS) were downloaded from the online repository (https://datadryad.org/stash/dataset/doi:10.5061/dryad.v8g21pt10.5061/dryad.v8g21pt) of the ADAPTmap project [3,13].…”

Section: Methodsmentioning

confidence: 99%

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

Dadousis

Cecchi

Ablondi

et al. 2020

Preprint

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The objective of this study was to investigate the genomic background of the Garfagnina (GRF) goat breed that faces the risk of extinction. In total, 48 goats genotyped with the Illumina CaprineSNP50 BeadChip were analyzed together with 214 goats belonging to 9 Italian breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. We estimated i) runs of homozygosity (ROH), ii) admixture ancestries and iii) traceability success via discriminant analysis on principal components (DAPC) based on cross-validation. For GRF, an excess of frequent ROH (more than 45% in the GRF samples analyzed) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), spanned between the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area was also present in DIT, while the broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis depicted the uniqueness of the GRF breed, with a small part of common ancestry shared with BIO, VSS, ARG and CCG breeds. The DAPC model resulted in a 100% assignment success. We hope this work will contribute to the efforts of preventing the GRF from extinction and to add value to all the socio-agro-economic factors related with the farming of the GRF breed.

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“…Twenty-one serologically negative goats were considered as the control group. Diagnosis was also achieved by post-mortem examination of affected animals (Cecchi et al 2017b).…”

Section: Diagnostic Assessment and Selection Of Animals For Genotypingmentioning

confidence: 99%

“…In a previous paper (Cecchi et al 2017b), a genome-wide scan was performed on the individual marker genotypes on the same goats' population and nine significant markers located within, or nearby to annotated genes, were highlighted. Two genes found encoded or are linked to protein kinases that are among the most important enzymes involved in the immune response to Johne's disease and four genes are involved in the functions of the Golgi complex.…”

Section: Introductionmentioning

confidence: 99%

Preliminary association analysis of microsatellites and Mycobacterium avium subspecies paratuberculosis infection in the native Garfagnina goats

Cecchi

Russo

Fratini

et al. 2017

Journal of Applied Animal Research

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Paratuberculosis disease occurs with high frequency in many places of the world and it is a chronic infection of ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to investigate the association between MAP-resistant or MAP-susceptible goats and short tandem repeats (STR) markers. Blood samples were collected from 48 adult goats (27 positive and 21 negative) of the Italian native Garfagnina goat breed from a single flock that had experienced annual mortalities due to MAP infection. Diagnosis was achieved by serological tests and by postmortem examination of affected animals. To investigate possible genetic influences on susceptibility or resistance of goats to MAP disease, 12 STR markers were used. For each marker, allele and genotypes frequencies between MAP-positive and MAP-negative groups of animals were compared using the chisquare test and Fisher's exact tests. In this study, two microsatellite loci SRCRSP05 and ETH10 were associated with the disease playing an interesting role in the susceptibility or resistance to the disease. Although the present study should be considered preliminary, our results reveal for the first time that two microsatellite loci were associated with the development of lesions due to MAP in the Garfagnina goat breed.

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Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed

Cited by 20 publications

References 31 publications

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

Preliminary association analysis of microsatellites and Mycobacterium avium subspecies paratuberculosis infection in the native Garfagnina goats

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