Widespread co-endemicity of Trypanosoma species infecting cattle in the Sudano-Sahelian and Guinea Savannah zones of Cameroon

Paguem, Archile; Abanda, Babette; Ndjonka, Dieudonné; Weber, Judith Sophie; Ngomtcho, Sen Claudine Henriette; Kingsley, Manchang Tanyi; Adoulmoumini, Mamoudou; Eisenbarth, Albert; Renz, Alfons; Kelm, Sørge; Achukwi, Mbunkah Daniel

doi:10.1186/s12917-019-2111-6

Cited by 19 publications

(28 citation statements)

References 36 publications

(78 reference statements)

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“…cosmopolitan blood parasites of ruminants which are known to in ict diseases were detected in Namchi, but only supported by a very low number of Blastn alignments [Additional le 1 Table S1]. Still, the presence of such organisms in our samples is in line with a recent epizootiological survey in the same indigenous Cameroonian cattle breeds that revealed nearly 90% of animals carried tickborne bacterial, piroplasmid and protozoan pathogens [18,19].…”

Section: Resultssupporting

confidence: 72%

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Paguem

Abanda

Achukwi³

et al. 2020

Preprint

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Background: West African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi , an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.Results: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~100 million (M) SNPs were identified and 7.7 M of those were breed-specific. An approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic traits and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome. Conclusions: The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

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Section: Resultssupporting

confidence: 72%

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Paguem

Abanda

Achukwi³

et al. 2020

Preprint

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“…At even lower rates also Babesia spp., a blood-borne parasite known to cause Texas fever in cattle and Theileria spp., a cosmopolitan blood parasite of cattle and blood-invading bacteria of the Anaplasma genus were also detected in Namchi (Doayo) [see Supplement file 5 Table Supplemental S1]. Although these finding are only supported by a very low number of alignments of assembled contigs to the blastn database, this data is still in line with a recent epizootiological survey in the same indigenous Cameroonian cattle breeds which revealed that nearly 90% of animals were 8 infected with tick-borne bacterial, piroplasmid and protozoan pathogens [24,25].…”

Section: De Novo Assembly and Analysis Of Unmapped Genomic Sequence Rsupporting

confidence: 72%

“…The data used for this paper was obtained from the project "Pathogen detection in African cattle Breeds" Abanda et al, [24] and Paguem et al, [25].…”

Section: Sampling Library Construction and Sequencingmentioning

confidence: 99%

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Paguem

Abanda

Achukwi³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous trypanosusceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Giga bases of raw sequencing data were generated and mapped to the cattle reference genome UMD3.1. The coverage was 22 to 30-fold. The single nucleotide polymorphisms (SNPs) were compared with reference genomes of European Bos taurus Holstein and of Asian Bos indicus Brahman and the African trypanotolerant N’Dama breeds.Of a total of 50 million SNPs identified, 3.43 million were breed-specific ranging from 0.37 to 0.47 million SNPs in the domestic Cameroonian breeds and approximately 0.58 million constituted of small insertions and deletions. We identified breed specific-non-synonymous variants as genetic traits that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi (Doayo) breed, heat tolerance in the Kapsiki breed, and growth, metabolism and meat quality in the Gudali breeds. Phylogenetic comparison grouped Namchi (Doayo) to the African Zebu clade indicating a hybrid status of the selected animal with a Zebu breed, albeit it showed the Namchi breed’s phenotype.ConclusionsThe findings provide the first comprehensive set of full genome variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

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“…cosmopolitan blood parasites of ruminants which are known to inflict diseases were detected in Namchi, but only supported by a very low number of Blastn alignments [Additional file 1 Table S1]. Still, the presence of such organisms in our samples is in line with a recent epizootiological survey in the same indigenous Cameroonian cattle breeds that revealed nearly 90% of animals carried tick-borne bacterial, piroplasmid and protozoan pathogens [18,19].…”

Section: Whole Genome Sequencing Analysissupporting

confidence: 70%

“…The data used for this paper was obtained from the project "Pathogen detection in African cattle Breeds" Abanda et al [18] and Paguem et al [19].…”

Section: Sampling Library Construction and Sequencingmentioning

confidence: 99%

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs, husbandry practices, limited feed resources, disease burden and lack of sustained breeding for trait improvement. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi, an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.

show abstract

Widespread co-endemicity of Trypanosoma species infecting cattle in the Sudano-Sahelian and Guinea Savannah zones of Cameroon

Cited by 19 publications

References 36 publications

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

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