Potentials of single nucleotide polymorphisms and genetic diversity studies at HSP90AB1 gene in Nigerian White Fulani, Muturu, and N'Dama cattle breeds.

The study was aimed at genetic characterization of Nigerian breeds of Muturu, N'Dama, and White Fulani cattle breeds at heat shock protein 90AB1 locus. Also, the goal of the study was to detect the presence of single nucleotide polymorphisms (SNPs) at HSP90AB1 locus and consequently recommend them as bio-markers for thermo-tolerance potentials in Nigerian cattle breeds when exposed to assaults of thermal conditions/heat shock of tropical environment. Based on the previously published potentials of this candidate gene to lower assaults of thermal conditions/heat shock such as heat stress, the detected SNPs of HSP90AB1 within the population of the Nigerian cattle in this study will be recommended for population-based screening with a view to genetically improving those zebu cattle breeds that are more vulnerable to heat shock and assaults of thermal conditions. Total number of 200 blood samples were randomly collected from White Fulani (84 samples), Muturu (73 samples), and N'Dama (43 samples) breeds of cattle. Out of these, 20 DNA samples were randomly selected from each of the three cattle breeds and were used for DNA extraction and downstream analyses to further confirm findings of previous study, hence the goal of our study. DNA was extracted from the blood samples using the Zymo-bead DNA extraction kit and DNA sequencing of our samples was performed. A total number of 9 SNPs (within exons 5-6 coding regions) and 11 SNPs (within exons 12-13 coding regions) were detected at HSP90AB1 locus using the codon code aligner software. ARLEQUIN 2.0001 software was used to estimate the basic population genetic statistics while the DnaSP version 5.10.01 was used to estimate the genetic diversity indices. This study detected new SNPs (polymorphic sites) at HSP90AB1 locus within the DNAs of Nigerian White Fulani (WF), Muturu (MU), and N'Dama (ND) breeds of cattle. Within exons 5-6 coding regions, the N'Dama (ND) cattle breed had the highest for number of SNPs (5) and genetic diversity indices while White Fulani (WF) and Muturu (MU) had the least (2) number of SNPs each. Within exons 12-13 coding regions, WF had the highest numbers of SNPs (7) and genetic diversity indices while MU had the least number of SNPs (1) and genetic diversity indices. Some of the detected SNPs at HSP90AB1 locus were shared among the three breeds, suggesting that these three Nigerian cattle breeds showed shared ancestral alleles and lineage. Our study further revealed that HSP90AB1 is highly polymorphic/variable and diverse among the three Nigerian cattle breeds examined. Based on the previously documented thermo-tolerance potentials of members of HSP90 sub-family including the findings of our study, we hypothesize therefore that the presence of SNPs of HSP90AB1 within the DNAs of these three breeds of Nigerian cattle (WF, ND, and MU) may confer them thermo-tolerance potentials for thermal assault conditions and heat shock of the tropics at HSP90AB1 locus. Therefore, the detected SNPs can be recommended as bio-markers to improve the thermo-tolerance potentials of Nigerian breeds of zebu cattle raised under the challenges of heat shock for better adaptation and survival.

De Campos JS ，Onasanya GO ，Ubong A ，T Yusuff A ，Adenaike AS ，Mohammed AA ，Ikeobi CO ... -  《-》

SNP Diversity in CD14 Gene Promoter Suggests Adaptation Footprints in Trypanosome Tolerant N'Dama (Bos taurus) but not in Susceptible White Fulani (Bos indicus) Cattle.

Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the bovine gene promoter in trypanosome-tolerant (N'Dama) and susceptible (White Fulani) cattle, with genomic and computational approaches. Blood samples were collected from White Fulani and N'Dama cattle, genomic DNA extracted and the entire promoter region of the gene amplified by PCR. We sequenced this region and performed in silico computation to identify SNP variants, transcription factor binding sites, as well as micro RNAs in the region. promoter sequences were compared with the reference bovine genome from the Ensembl database to identify various SNPs. Furthermore, we validated three selected N'Dama specific SNPs using custom Taqman SNP genotyping assay for genetic diversity. In all, we identified a total of 54 and 41 SNPs at the promoter for N'Dama and White Fulani respectively, including 13 unique SNPs present in N'Dama only. The significantly higher SNP density at the gene promoter region in N'Dama may be responsible for disease tolerance, possibly an evolutionary adaptation. Our genotype analysis of the three loci selected for validation show that mutant alleles ( and ) were adaptation profiles within disease tolerant N'Dama. A similar observation was made for our haplotype analysis revealing that haplotypes H1 () and H2 () were significant combinations within the population. The SNP effect prediction revealed 101 and 89 new transcription factor binding sites in N'Dama and White Fulani, respectively. We conclude that disease tolerant N'Dama possessing higher SNP density at the gene promoter and the preponderance of mutant alleles potentially confirms the significance of this promoter in immune response, which is lacking in susceptible White Fulani. We, therefore, recommend further in vitro and in vivo study of this observation in infected animals, as the next step for understanding genetic diversity relating to varying disease phenotypes in both breeds.

Morenikeji OB ，Capria AL ，Ojurongbe O ，Thomas BN ... -  《Genes》

Production objectives, trait and breed preferences of farmers keeping N'Dama, Fulani Zebu and crossbred cattle and implications for breeding programs.

Many local livestock breeds in developing countries are being replaced by exotic breeds, leading to a loss of genetic resources. In southern Mali, for the past two decades, a trend towards increasing crossbreeding between the trypanotolerant N'Dama cattle and the trypano-susceptible Fulani Zebu cattle has been taking place. A survey with 160 farmers owning a cattle herd was carried out in southern Mali to investigate their production objectives, as well as trait and breed preferences and correlated socio-economic determinants in order to understand farmers' breeding decisions and to identify comparative advantages of three breed groups (N'Dama, Fulani Zebu and crossbreds) raised in the study area. Data were analyzed using an exploded logit model. The reasons for raising cattle, as well as trait and breed preferences reflected the multiple objectives of the farmers. Draught power and savings were the most important production objectives. Productive traits were ranked highest; farmers reported large body size as the most preferred trait, followed by fertility, draught ability and milk yield. Crossbreds were the favored breed group. Breed preferences were mainly explained by 'resistance to disease' for N'Dama cattle and 'high market price' for Fulani Zebu and crossbred cattle. Production objectives, trait and breed preferences were mainly influenced by farmer group (local farmers and settled transhumants). Local farmers put comparatively more emphasis on livestock functions linked to crop production such as draught power. They had a higher preference for traction ability as a selection trait and preferred N'Dama over Fulani Zebu cattle. Settled transhumants emphasized milk yield as a selection trait and preferred Fulani Zebu over N'Dama. The results indicate that the trend towards more crossbreeding will continue putting the N'Dama breed under high risk of genetic dilution in southern Mali. The N'Dama cattle remain a valuable breed due to their adaptive traits such as disease and drought tolerance and their good traction ability, fulfilling the diverse objectives of local farmers. Crossbreeding was found to be a promising breeding strategy, which might contribute to the maintenance of the local breed, provided that breeding schemes are thoroughly planned and organized.

Traoré SA ，Markemann A ，Reiber C ，Piepho HP ，Valle Zárate A ... -  《-》

Single nucleotide polymorphisms at heat shock protein 90 gene and their association with thermo-tolerance potential in selected indigenous Nigerian cattle.

Heat shock protein (HSP) 90 gene provides protection and adaptation to thermal assault and certain polymorphisms have been associated to heat tolerance in humans and animals. Single nucleotide polymorphisms (SNPs) of HSP 90 gene were used to evaluate the scientific basis of heat tolerance in four zebu breeds of Nigeria. The DNA was extracted from skin tissue of 90 adult bulls representing White Fulani (WF), Sokoto Gudali (SG), Red Bororo (RB), and Ambala (AM). The SNPs were determined in DNAs using PCR, sequencing, and visualization and bio-editing by chromatogram in SeqMan Ngen tool. Subsequently, respective genotypes were constructed and genotypic and allelic frequencies were computed. Also, body parameters related to heat stress (HS) including body temperature (BT), rectal temperature (RT), and respiratory rates (RR) were taken for each animal before biological sampling and heat tolerance coefficient (HTC) was calculated. We detected four SNPs distinct/specific for each breed as follows: change from thymine (T) to guanine (G) at position 116 (T116G) in RB, G to cytosine (C) at 220 (G220C) in SG, G to adenine (A) at two positions, 346 (G346A) and 390 (G390A) in AM and WF, respectively. Heterozygous SNPs showed significantly lower values (P < 0.0001) for BT, RT, RR, and HTC than homozygous genotypes at all positions. We hypothesize that animals with heterozygous SNPs in exon 3 of HSP 90 may be tolerant to HS. These SNPs can be used as bio-markers for screening large populations of cattle for tolerance to hot tropical conditions in Nigeria and other sub-humid places.

Onasanya GO ，Msalya GM ，Thiruvenkadan AK ，Sreekumar C ，Tirumurugaan GK ，Sanni TM ，Decampos JS ，Amusan SA ，Olowofeso O ，Fafiolu AO ，Okpeku M ，Yakubu A ，Ikeobi CO ... -  《-》

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.

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. 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 signatures 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. 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.

Paguem A ，Abanda B ，Achukwi MD ，Baskaran P ，Czemmel S ，Renz A ，Eisenbarth A ... -  《BMC GENETICS》