Dataset Information

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats.

ABSTRACT: Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.

SUBMITTER: Serranito B

PROVIDER: S-EPMC8369930 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats.

Serranito Bruno B Serranito Bruno B Taurisson-Mouret Dominique D Harkat Sahraoui S Laoun Abbas A Ouchene-Khelifi Nadjet-Amina NA Pompanon François F Benjelloun Badr B Cecchi Giuliano G Thevenon Sophie S Lenstra Johannes A JA Da Silva Anne A

Frontiers in genetics 20210803

Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selecti ...[more]

PMID: 34413881

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Project description:BackgroundAfrican animal trypanosomosis (AAT) is a major constraint to sustainable development of cattle farming in sub-Saharan Africa. The habitat of the tsetse fly vector is increasingly fragmented owing to demographic pressure and shifts in climate, which leads to heterogeneous risk of cyclical transmission both in space and time. In Burkina Faso and Ghana, the most important vectors are riverine species, namely Glossina palpalis gambiensis and G. tachinoides, which are more resilient to human-induced changes than the savannah and forest species. Although many authors studied the distribution of AAT risk both in space and time, spatio-temporal models allowing predictions of it are lacking.Methodology/principal findingsWe used datasets generated by various projects, including two baseline surveys conducted in Burkina Faso and Ghana within PATTEC (Pan African Tsetse and Trypanosomosis Eradication Campaign) national initiatives. We computed the entomological inoculation rate (EIR) or tsetse challenge using a range of environmental data. The tsetse apparent density and their infection rate were separately estimated and subsequently combined to derive the EIR using a "one layer-one model" approach. The estimated EIR was then projected into suitable habitat. This risk index was finally validated against data on bovine trypanosomosis. It allowed a good prediction of the parasitological status (r2 = 67%), showed a positive correlation but less predictive power with serological status (r2 = 22%) aggregated at the village level but was not related to the illness status (r2 = 2%).Conclusions/significanceThe presented spatio-temporal model provides a fine-scale picture of the dynamics of AAT risk in sub-humid areas of West Africa. The estimated EIR was high in the proximity of rivers during the dry season and more widespread during the rainy season. The present analysis is a first step in a broader framework for an efficient risk management of climate-sensitive vector-borne diseases.

Project description:Abstract The search for selection signatures in wild boars was meant to assist in identifying genomic regions associated with adaptation to environmental conditions. The aim of our study was to seek selection signatures in European wild boars of Russia. We studied 66 wild boars from 20 different regions in four different climatic zones. DNA samples were genotyped using Porcine SNP60 BeadChips and GeneSeek SNP-chips (Illumina, San Diego, USA). Quality control procedures were carried out resorting to PLINK v1.9; briefly, individuals with genotype call rates of < 0.8 and SNPs with call rates of < 0.3 or minor allele frequencies less than 0.99 were excluded. Also, we resorted to “–LD” to make prune filtering in Plink. In total 37065 markers from full subset of SNPs were used for subsequent analysis. We removed close relatives with enabling option --rel-cutoff 0.75. After filtering 11271 SNPs remained and total genotyping rate of obtained dataset was 98.4%. We subsequently identified SNPs, which had cross within log-likelihood ratio scores (LLRS) values > 2, in addition to integrated Haplotype Score (iHS) values > 2. After comparing 2 methods we detected 6 common elements in “IHS” and “LLRS” - ASGA0101898 – intergenic variant; H3GA0020102 – intergenic variant; ASGA0093835 - intron variant, RBFOX1 (RNA binding fox-1 homolog 1) is a Protein Coding gene, RNA-binding protein that regulates alternative splicing events by binding to 5’-UGCAUGU-3’ elements, regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis; ASGA0098807 - DSG3 (Desmoglein 3) is a Protein Coding gene, component of intercellular desmosome junctions, involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion; MARC0064247 – non coding transcript exon variant ENSSSCG00000035431, ASGA0020755 – intron variant, ARHGAP30 Rho GTPase activating protein 30). The result of the research will assist in revealing genetic regions associated with adaptation of the Russian wild boars. This research was supported by the Russian Scientific Foundation (RSF) within Project No. 19-16-00109.

Dataset Information

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats.

Publications

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats.

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