Sequences are available from GenBank with the Bioproject accession number PRJNA312138. The regions with P values less than 0.005 (0.5%) were considered significant signals in the breed group of interest. A summary of the total number of SNPs identified is provided in Additional file 1: Table S3. On a practical note, these results provide new genomic evidence and options for designing and implementing genetic intervention strategies for improved cattle productivity and resilience in sub-Saharan Africa. Google Scholar. Brahman cattle come from India, and are the most common cattle breed in the world. Box 5689, Addis Ababa, Ethiopia, International Livestock Research Institute (ILRI), Box 30709 -00100, Nairobi, Kenya, Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, 13314, Khartoum North, Sudan, National Coordinateur RGA, Ministère Elevage – Productions Animales, B.P.
Fst is calculated between B. indicus and commercial samples.
a Estimated effective population size of each African cattle breed and the combined commercial (Hanwoo + Jersey + Holstein + Angus). 2009;463:311–7. Last, but not least, we thank the Directors of Veterinary Services and the cattle keepers from Ethiopia Guinea, Kenya, Uganda, and Sudan for their assistance and permission to sample the animals.
J Hered. Earl DA. Article Li R, Fan W, Tian G, Zhu H, He L, Cai J, et al.
b Nucleotide genome diversity. FGF18 is required for early chondrocyte proliferation, hypertrophy and vascular invasion of the growth plate.
Canavez FC, Luche DD, Stothard P, Leite KR, Sousa-Canavez JM, Plastow G, et al. Moreover, unraveling their genome diversity may provide new insights into the genetic mechanisms underlying their adaptation to various agro-ecosystems [14].
In the Ankole versus all other African cattle comparisons, we identified 187 genes within the outlier genome windows (Table 1, Additional files 2 and 3).
While the studied breeds represent only a small subset of the 150 recognized on the African continent [86], they illustrate the extraordinary diversity present within and across African cattle breeds.
We were able to highlight and map at the genome level some unique African adaptations, which may represent responses to climatic challenges (e.g. 2012;7:e38601. PLoS Genet.
Among a few “trypanotolerant” indigenous African cattle breeds, the West African N’Dama is the best characterized, while the “newcomer” B. indicus are generally highly susceptible to trypanosomosis [39].
Am J Hum Genet.
A total of ~37 million SNPs were finally retained and breed-specific SNPs were identified using SnpSift [18] (Fig. Notably, we found a fixed SLC40A1 haplotype in N’Dama, with frequency of 24% and 58% in other African cattle and commercial breeds, respectively, strongly supporting selection at the gene (Fig.
Stewart GW.
These results together suggest that the PRLH mutation may confer a selective advantage in regulating prolactin expression which might be linked to the thermotolerance in African cattle, especially in B. indicus.
These West African cattle populations have been subjected in recent times to new environmental pressures imposing strong adaptive constraints (e.g. There is also a large variety of farmers, ranging from subsistence to large commercial producers and breeders. They can produce more milk for their weight than any other breed, and their milk yields up to a quart of cream per gallon. Article
Several filtering steps to minimize the number of false-positive calls were applied before using candidate SNPs in further analyses. London, New York: Longman; 1978.
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, et al. Genome Res. Limousin cattle may be as old as Europe itself; cattle in 20,000-year-old cave paintings in France are strikingly similar in appearance to today's breed. We also found putative candidate selected regions that might have shaped the massive horn in Ankole. To consider the variation in SNP density, we binned genomic windows according to their numbers of SNPs in increments of 500 SNPs (combining all windows ≥ 1000 SNPs into one bin). statement and Parasite Immunol.
PANTHER (version 11.0) [92] was used to determine if there was any significant over-representation of genes with particular functional categories (GO-slim Biological Process and PANTHER pathways), that is, functional enrichment, among positive selected genes in each African breed. Using the “REMOVE_DUPLICATES = true” option in “MarkDuplicates” command-line tool of Picard (http://broadinstitute.github.io/picard), potential PCR duplicates were filtered. Bulls in Germany must undergo extensive tests to become A.I. 2014;10:e1004254.
2007;449:913–8. In SnpSift, several statistical tests are implemented such as Fisher’s exact test and Cochran–Armitage trends test for analyzing genotype count data composed with two factors. The major histocompatibility complex and disease resistance in cattle.
Numerous studies indicate that polymorphism within hypocretin genes are associated with alterations in feeding and drinking behaviors [41, 42].