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Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment.

ABSTRACT: BACKGROUND:The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. RESULTS:Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. CONCLUSIONS:Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.

SUBMITTER: Yaro M

PROVIDER: S-EPMC6836352 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment.

Yaro M M Munyard K A KA Morgan E E Allcock R J N RJN Stear M J MJ Groth D M DM

BMC genomics 20191107 1

<h4>Background</h4>The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually.<h4>Results</h4>Here, we separately sequenced and then pooled according to breed the g ...[more]

PMID: 31699027

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Project description:BackgroundThe present study aimed at characterizing the Djallonké Sheep (DS), the only local sheep breed raised in Guinea-Bissau. A total of 200 animals were sampled from four regions (Bafatá, Gabú, Oio and Cacheu) and described using 7 visual criteria and 8 measurements. These parameters have been studied by principal components analysis. The genetic diversity and population structure of 92 unrelated animals were studied using 12 microsatellite markers.ResultsThe values of quantitative characters in the Bafatá region were significantly higher than those obtained in the other three regions. A phenotypic diversity of the DS population was observed and three genetic types distinguished: animals with "large traits" in the region of Bafatá, animals with "intermediate traits" in the regions of Gabú and Oio and animals with "small traits" in the Cacheu region. The hair coat colors are dominated by the white color, the shape of the facial head profile is mainly convex and the ears "erected horizontally". Most of the morphobiometric characteristics were significantly influenced by the "region" and "sex of animals". The average Polymorphism Information Content (PIC) of 0.65 ± 0.11 supports the use of markers in genetic characterization. Gabú subpopulation had the highest genetic diversity measures (He = 0.716 ± 0.089) while Cacheu DS subpopulation presented the smallest (He = 0.651 ± 0.157). Only Gabú and Bafatá subpopulations presented significant heterozygote deficiency across all loci indicating possible significant inbreeding. Mean values for FIT, FST, FIS and GST statistics across all loci were 0.09, 0.029, 0.063 and 0.043 respectively. The overall genetic differentiation observed between the four DS subpopulations studied was low. Bafatá and Gabú are the most closely related subpopulations (DS = 0.04, genetic identity = 0.96) while Bafatá and Cacheu were the most genetically distant subpopulations (DS = 0.14, genetic identity = 0.87). Using Bayesian approach, the number of K groups that best fit the data is detected between 2 and 3, which is consistent with the morphological analysis and the factorial analysis of correspondence.ConclusionsThe molecular results on DS population of Guinea-Bissau confirmed the ones obtained with morphological analysis. The three genetic types observed phenotypically might be due to a combination of the agro-ecological differences and the management of breeding rather than genetic factors.

Project description:A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76?% of the phenotypic variance for PCV, 21.24?% for lnFEC, and 34.38?% for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125?kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype-environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

Dataset Information

Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment.

Publications

Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment.

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