RESUMO
A structural variant (SV) in the agouti signaling protein gene (ASIP), namely ASIP-SV1, has been found to strongly correlate with the darkness of hair coat in specific regions of the body of bulls from the zebu (Bos indicus) Nellore breed. Here we visually analyzed the whole-genome sequence of zebu and taurine (Bos taurus) cattle to elucidate the extent of spread of ASIP-SV1 in different cattle populations. Of 216 sequences analyzed, 63 zebu (45.9%) and five taurine (6.3%) animals had at least one copy of ASIP-SV1. Four of the taurine animals presenting the SV were Romagnola cattle, a breed with history of zebu introgression. The remaining taurine animal was a Simmental, a breed frequently used in crossbreeding. These data provide evidence that ASIP-SV1 is commonly found in zebu populations, in addition to taurine animals with zebu admixture.
Assuntos
Cabelo , Hibridização Genética , Bovinos/genética , Masculino , Animais , Escuridão , AlelosRESUMO
BACKGROUND: CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. RESULTS: Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. CONCLUSION: For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.
Assuntos
Variações do Número de Cópias de DNA , Genoma , Animais , Bovinos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The study was conducted to characterize the morphological features of Mursi cattle breed and to identify the species of trypanosome infecting the cattle and its prevalence in these traditionally managed cattle in the Bodi and Mursi pastoral communities. Cattle body description and measurements were made on 201 matured animals. Blood samples were collected from 409 animals into heparin-treated capillary tubes and were centrifuged to 12,000 rpm for 5 min to identify trypanosome species from the wet smeared buffy coat and to estimate the degree of anemia (PCV). Tsetse flies were collected using phenol-treated biconical trap and the caught flies identified to species level. The breed possesses variable coat color pattern, coat color type, and have small to medium hump size on the thoracic vertebrae. Body measurement of Mursi cattle in the two locations did not show significant differences except chest girth, rump width, and horn length. Trypanosome prevalence in the Mursi cattle breed was 6.1%. The highest trypanosome infection was caused by Trypanosoma congolense (56%) followed by Trypanosoma vivax (40%) and Trypanosoma brucei (4%). Trypanosome prevalence significantly varies between dry (2.0%) and late rainy (10.1%) seasons (P < 0.001) and between lean (11.9%) and medium (2.4%) body condition score (P < 0.01). The PCV value was 22.1 ± 0.5%, which is significantly varied with season (P < 0.01) and parasitism (P < 0.001). Parasitaemic cattle show the lowest PCV value (20.4 ± 1%) than aparasitaemic (23.7 ± 0.3%) cattle and cattle with lean BCS showed the lowest (P < 0.0001) PCV value (20.4 ± 0.6%). Tsetse fly species identified in the study area were Glossina pallidipes, Glossina morsitans submorsitans, and Glossina fuscipes. The number of flies captured in late rainy season was higher than in dry season (P < 0.01). Despite the existence of trypanosome and high tsetse fly infestation in the areas, large proportion of the Mursi cattle shows medium BCS, low trypanosome prevalence, and higher PCV value.
Assuntos
Tripanossomíase Bovina/epidemiologia , Animais , Constituição Corporal , Bovinos , Etiópia/epidemiologia , Feminino , Humanos , Insetos Vetores , Masculino , Fenótipo , Prevalência , Estações do Ano , Inquéritos e Questionários , Trypanosoma brucei brucei/isolamento & purificação , Trypanosoma congolense/isolamento & purificação , Trypanosoma vivax/isolamento & purificação , Tripanossomíase Bovina/parasitologia , Moscas Tsé-TséRESUMO
The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.
Assuntos
Genoma , Bovinos/genética , Animais , Genômica , África , Cruzamento , Variação GenéticaRESUMO
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.
Assuntos
Evolução Biológica , Ecossistema , Animais , Bovinos , Alelos , Variação Genética , Sequenciamento Completo do Genoma , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.