scholarly journals Whole-Genome comparative analysis reveals genetic mechanisms of disease resistance and heat tolerance of tropical Bos indicus cattle breeds

Genome ◽  
2021 ◽  
Author(s):  
Periyasamy Vijayakumar ◽  
Arunasalam Singaravadivelan ◽  
Anamika Mishra ◽  
Krishnan Jagadeesan ◽  
Sanniyasi Bakyaraj ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Comparative Analysis ◽  
Stress Response ◽  
Functional Annotation ◽  
Indian Subcontinent ◽  
Bos Indicus ◽  
Whole Genome ◽  
Immune Genes ◽  
Cattle Breeds ◽  
Genetic Mechanisms

The Bos indicus cattle breeds have been naturally selected over thousands of years for disease resistance and thermo-tolerance. However, a genetic mechanism of these specific inherited characteristics needs to be discovered. Hence, in this study, the whole-genome comparative analysis of Bos indicus cattle breeds of Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. The genetic variants identification analysis revealed a total of 15,58,51,012 SNPs and 1,00,62,805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17,252 genes that comprised both, SNPs and InDels, of high functional impact on proteins, has been carried out. The functional annotation results revealed the pathways that were involved in the innate immune response including toll-like receptors, a retinoic acid-inducible gene I like receptors, NOD-like receptors, Jak-STAT signaling pathways, and the non-synonymous variants in the candidate immune genes. Further, we also identified several pathways involved in heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and the non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes were directly or indirectly contributing to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.

scholarly journals 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

2020 ◽  
Author(s):  
Archile Eric paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Zebu Cattle ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle

Abstract 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.

scholarly journals 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

2020 ◽  
Author(s):  
Archile Eric Paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle ◽  
Reference Genomes

Abstract 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. 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.

scholarly journals Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences

2012 ◽  
Vol 5 (1) ◽  
Author(s):  
Jérôme Grimplet ◽  
John Van Hemert ◽  
Pablo Carbonell-Bejerano ◽  
José Díaz-Riquelme ◽  
Julie Dickerson ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Functional Annotation ◽  
Whole Genome ◽  
Gene Sequences

scholarly journals 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

2020 ◽  
Author(s):  
Archile Eric Paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle ◽  
Reference Genomes

Abstract 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.

scholarly journals Comparative analysis of multiple disease resistance in ryegrass and cereal crops

2008 ◽  
Vol 117 (4) ◽  
pp. 531-543 ◽  
Author(s):  
Young-Ki Jo ◽  
Reed Barker ◽  
William Pfender ◽  
Scott Warnke ◽  
Sung-Chur Sim ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Comparative Analysis ◽  
Cereal Crops ◽  
Multiple Disease Resistance

scholarly journals Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guilherme B. Neumann ◽  
Paula Korkuć ◽  
Danny Arends ◽  
Manuel J. Wolf ◽  
Katharina May ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Studies ◽  
Bos Indicus ◽  
Diversity Management ◽  
Whole Genome Sequencing Data ◽  
General Interest ◽  
Whole Genome ◽  
Sequencing Data ◽  
Snp Chip ◽  
Selection Of

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

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