Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso.

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for F ST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.

Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso.

In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.

Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso.

High-throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well-structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on-farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community-based breeding programs in the South-West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent-offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community-based breeding program will make use of genomic information about admixture levels.

Trypanosomosis: a priority disease in tsetse-challenged areas of Burkina Faso.

Trypanosomosis is an important disease affecting humans as well as animals. It remains a big constraint to livestock productions in tropical areas. The objective of this study was to assess the importance of trypanosomosis among cattle diseases in Burkina Faso, mainly in tsetse-challenged areas, and to capture information on how farmers apply available methods for controlling the disease. A survey has been carried out in 29 villages of Burkina Faso in three regions (north, southwest, and west regions). One hundred and thirty-four cattle breeders were interviewed individually with a questionnaire. The results indicate that among the 16 diseases mentioned by cattle breeders, trypanosomosis is the most important one in tsetse-challenged areas. Overall, 76.12 % of the breeders mentioned it as the most important disease, while 54.55 % of the farmers in the southwest region and 70.91 % of the farmers in the west region ranked it as a priority disease. Chemoprophylaxis/chemotherapy is widely used as a control method. Isometamidium chloride and diminazene aceturate were used by 53.49 and 46.52 % of the responders, respectively. Among farmers, 85.55 % ranked diminazene aceturate as the less efficient while 14.45 % ranked isometamidium chloride as the most efficient trypanocid. Trypanocidal drug quality and drug resistance were raised as a major concern by 30.77 and 50 % of the respondents, respectively. According to them, zebu cattle are more susceptible to trypanosomosis than taurine Baoule cattle and their crosses with zebu, emphasizing that crossing susceptible breeds with trypanotolerant ones, could be used as part of an integrated control strategy.

Effect of feeding some West African browse foliages on growth and carcass composition in sheep.

The effect of feeding foliage from Afzelia africana, Pterocarpus erinaceus or Khaya senegalensis on growth performance was evaluated using 32 West African Djallonké rams of about 8 months of age and with a mean initial body weight (BW) of 16.1 kg. The animals were randomly assigned to four groups of 8 animals and the experiment lasted for 13 weeks. All the animals received the same amount of hay from Andropogon gayanus and maize bran (200 g/day each) and dried foliage ad libitum. The control group was fed cottonseed cake in restricted amounts. The animals were able to consume higher amounts of A. africana than of P. erinaceus and K. senegalensis. There was no significant difference in growth rate between sheep offered A. africana or P. erinaceus, 62.9 and 58.8 g/d, respectively, but sheep offered K. senegalensis had a lower average daily gain, 48 g/day (P < 0.05) due to lower consumption of both energy and crude protein. Animals in the control group had the highest growth rate, 95.8 g/day. Sheep offered P. erinaceus and K. senegalensis had similar carcass characteristics and dressing percentage but lower fasted BW, empty BW, carcass weight and dressing percentage (P < 0.05) than sheep offered A. africana. These tree species can provide valuable feed during periods of feed shortage in the humid and sub-humid zones.

Intake and digestibility in sheep and chemical composition during different seasons of some West African browse species.

Foliage of Afzelia africana, Pterocarpus erinaceus and Khaya senegalensis, from 10 trees per species, was collected every two weeks during the late dry, rainy and cool season to determine the seasonal effects on chemical composition. Fifteen rams of the Djallonké breed, weighing on average 20.0 kg, were used to evaluate the voluntary intake and digestibility of hay of A. gayanus, foliage of A. africana (as a sole feed), and A. africana, P. erinaceus and K. senegalensis offered with 30% of the diet as A. gayanus hay. The crude protein (CP) content ofA. africana, and P. erinaceus decreased significantly from the late dry season to the cool season when that of K. senegalensis tended to increase. The mean CP of A. africana, P. erinaceus and K. senegalensis differed significantly (173 g, 139 g and 114 g/kg DM, respectively). The DM intake ofA. africana offered with hay (571 g/d) or as a sole feed (598 g/d) were not significantly different, but was higher than that of P. erinaceus (428 g/d) and K. senegalensis (298 g/d). The digestibility calculated by difference of DM and CP of A. africana (582 g/kg DM and 795 g/kg CP, respectively) did not differ significantly from A. africana as a sole feed, but were higher than for the other species. The nutritive value of A. africana seems to justify the high preference of herders for this species.