High variability of milk protein genes in Bos indicus cattle breeds of Cameroon and Nigeria and characterization of a new alphas1-casein promoter allele.

The study provides the first comprehensive information on the variability of milk protein genes of Bos indicus and Bos taurus cattle breeds in Cameroon and Nigeria. The investigations indicate a high diversity of milk protein genes for the zebu populations. Of the investigated alleles, 21 out of 29 were observed. The method of single strand conformation polymorphism (SSCP) was a particularly useful technique because it allowed discrimination of alleles, including zebu-specific alleles at the CSN2 (I) and CSN3 (A(I) and H) loci, not separated by protein electrophoretic techniques and also made possible the detection of a further CSN1S1 5' promoter allele (CSNIS1Prom5), which is also zebu-specific. Characterization of CSN1S1Prom5 showed that it was the most variable of all described CSN1S1 promoter alleles. A potential GATA consensus motif is created by mutations in CSN1S1Prom5. Intra-breed diversity measured as mean effective number of alleles was higher in the zebu populations than in the taurine breeds. Of the expected casein haplotypes, 96 out of 320 were present in the studied breeds. 2-C-A-A2-H (CSN1SIProm2-CSN1S1C-CSN1S2A-CSN2A2-CSN3H) and 5-C-A-A2-H were zebu-specific while 1-B-A-A2-B was specific to the taurines. Overall distribution of alleles and haplotypes clearly separated the zebu populations from the taurine breeds. Zebu influence on the taurine breed Namchi was detected through the occurrence of zebu alleles and haplotypes. High variability of milk proteins also means availability of resources for breed development, phylogenetic studies, and conservation and management decisions.

Ibeagha-Awemu EM ，Prinzenberg EM ，Erhardt G 《JOURNAL OF DAIRY RESEARCH》

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》

Genetic diversity, introgression and relationships among West/Central African cattle breeds.

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups--African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.

Ibeagha-Awemu EM ，Jann OC ，Weimann C ，Erhardt G ... -  《-》

Polymorphisms in blood proteins of Bos indicus and Bos taurus cattle breeds of Cameroon and Nigeria, and description of new albumin variants.

Polymorphisms in the five blood protein loci albumin (ALB), carbonic anhydrase (CA II), vitamin D binding protein (GC), haemoglobin (HBB), and transferrin (TF) were investigated in 520 individuals from 12 cattle populations (Bos indicus and Bos taurus) in Cameroon and Nigeria by isoelectric focusing with carrier ampholytes in ultrathin polyacrylamide gels (PAG-IEF) and by linear gradient polyacrylamide gel electrophoresis (PAGE). While all loci in nine populations were polymorphic with up to six alleles at the ALB and TF loci: the Namchi population showed monomorphism at the CA II locus and Muturu at the ALB, CA II, and HBB loci. There was a clear distinction between Bos indicus and Bos taurus breeds at the ALB locus with ALBB predominating in indicine and ALBA predominating in taurtine breeds. CA IIS, GCA, and HBBA were the most commonly occurring alleles in all populations. Two variants not described before were demonstrated by PAG-IEF at the ALB locus and named ALBJ and ALBK. Mean effective number of alleles as measure of intrabreed diversity was higher in zebu populations (2.040-2.288) as compared to taurine breeds (1.349-1.836). Significant deviations from Hardy-Weinberg equilibrium occurred in some populations at the HBB and TF loci. More haplotypes of ALB/GC occurred in the zebu than taurine breeds. ALBAGCA predominated in the taurine populations and ALBBGCA in the indicine populations. Influence of zebu genes on the Namchi and N'Dama taurine breeds was detected at the ALB, CA II, HBB, and TF loci, and estimated at 61.5% and 5.7%, respectively. The high resolution of PAG-IEF in screening for polymorphisms within diversity studies was demonstrated.

Ibeagha-Awemu EM ，Jäger S ，Erhardt G 《BIOCHEMICAL GENETICS》

Characterization of casein gene complex and genetic diversity analysis in Indian goats.

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Rout PK ，Kumar A ，Mandal A ，Laloe D ，Singh SK ，Roy R ... -  《-》