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Publication Contribution of cattle breeds to household livelihoods and food security in southern Mali(2017) Traoré, Sékou Amadou; Valle Zárate, AnneIn recent decades, there has been a rapid shift in livestock breeds used in developing countries. Local breeds are increasingly being replaced by exotic breeds, leading to a loss of genetic resources. The introduction of more productive but less adapted exotic livestock breeds might offer opportunities. However, it may also pose threats to the livelihoods of poor farmers. In southern Mali, where cattle play an important role in the livelihoods of rural households, the endemic trypanotolerant N’Dama cattle, are increasingly replaced and crossbred with the larger and more milk yielding trypano-susceptible Fulani Zebu. Thus, the N’Dama cattle face serious threats of genetic erosion, despite their adaptive attributes. A systematic comparison of the endemic N’Dama cattle, Fulani Zebu cattle and their crosses under the same farming conditions is required to reveal whether farmers benefit from the introduction of Fulani Zebu cattle or are negatively affected by the replacement of N’Dama purebreds. The overall objective of the study was, therefore, to evaluate and compare N’Dama cattle with Fulani Zebu and their crossbreds based on their performance and contribution to household economic benefits and food security, taking into account the production environment and farmer breeding strategies. Specific objectives were (i) to investigate the production objectives and trait and breed preferences of cattle keepers; (ii) to evaluate and compare the productive and economic performances of N’Dama cattle, Fulani Zebu cattle and their crossbreds in order to assess the comparative advantages of these breed groups for farmers; and (iii) to examine households’ food security and coping strategies, with a particular emphasis on the contribution of different cattle breeds. The study was carried out in the communes of Sibirila and Garalo, which are located in the Sikasso region of southern Mali. A stratified random sampling based on cattle and breed ownership was applied for the selection of 258 households. The 160 households with a herd were grouped into four herd categories based on breed composition. Forty-five households with only oxen and 53 without cattle represented two additional herd categories. Data collection methods encompassed household interviews, herd surveys and focus group discussions. The herd surveys were carried out for 120 households to assess individual cows’ (n=770) performances using a cow progeny history survey and body condition scoring (BCS). Food security was assessed using a household dietary diversity score (HDDS), food consumption score (FCS), and modified household food insecurity access scale (mHFIAS). Gross margin, net benefit and cost benefit ratio were calculated for the assessment of economic performance and efficiency. Besides descriptive statistics, data were analysed using an exploded logit model, mixed linear models and non-parametric tests using the Statistical Analysis System (SAS). Draught power and savings were the most important production objectives. Farmers reported a large body size as the most preferred trait, followed by fertility, draught ability and milk yield. N’Dama was valued for disease and drought tolerance and their good traction ability. Crossbreds were the favored breed group and were appreciated for milk yield and body size, similar to Fulani Zebu. 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 farmers ethnicity and cultural background. Results on cow individual performances showed a higher body condition for N’Dama compared to crossbred and Fulani Zebu cattle. Gross margin and the benefit-cost ratio were highest in Fulani Zebu herds, followed by crossbred herds due to higher revenue generated from cattle and milk sale from these herds. The higher cash revenue for the sale of cattle in crossbred and Fulani Zebu herds was explained by the higher offtake rate in these two herd categories and a 25 and 60% higher selling price for crossbred and Fulani Zebu, respectively, than for N’Dama cattle. When non-market benefits were included, economic performances between the herd categories were similar as shown by the similar net benefit per cattle. Cattle ownership and breed group were important determinants of all household food security indicators. Households keeping Fulani Zebu and mixed herds had the highest FCS, which was mainly explained by their more frequent milk consumption compared to the other breed groups. HDDS and FCS were positively correlated with diversity of food crops cultivated on farm and household wealth and negatively correlated with cotton cultivation. Generally cattle herd ownership was strongly associated with improved household diet diversity and reduced vulnerability to food insecurity. The results of the present study showed that the ongoing replacement of native N’Dama cattle by Fulani Zebu cattle and their crosses is contributing to an improved household economic situation and food security. Fulani Zebu and crossbred cattle are the most suitable options for market-oriented local and settled transhumant farmers, given their higher price and increased profitability. The N’Dama cattle remain a valuable breed for subsistence-oriented local farmers for whom non-market benefits from cattle such as saving play a considerable role. Further research is required to investigate possible ways of optimizing and organizing the ongoing process of crossbreeding between the N’Dama and Fulani Zebu cattle, with a more systematic crossbreeding and selection program in line with the farmers’ interest.Publication Genomic methods for rotational crossbreeding in local dairy cattle breeds(2022) Stock, Joana; Bennewitz, JörnLocal dairy breeds, such as German Angler, usually have small population sizes and thus a reduced genetic gain, compared to high-yielding breeds. Especially since genomic selection is widely used in the latter, the performance gap between local breeds and high-yielding breeds increased further, as it requires large reference populations in order to achieve accurate estimated breeding values. As a result, many farmers switched to high-yielding breeds. On the other hand, to increase the performance of local breeds the introgression of high-yielding breeds was a common strategy in the past, which resulted in high amounts of foreign genetic material in many of them. Much of the original genetic background got lost, however, they do not achieve the same performance level as high-yielding breeds. Local breeds are therefore faced with the risk of two types of extinction, i.e. a numerical extinction due to the small and decreasing numbers of breeding animals, and a genetic extinction due to massive introgression from high-yielding breeds. To promote local dairy breeds, the implementation of a genomic rotational crossbreeding scheme can be a promising strategy. Local breeds can benefit from a genomic rotational crossbreeding scheme with a high-yielding breed due to 1) an enlarged reference population including both the local breed and crossbred animals, and 2) the increased performance level of crossbred animals. On the other hand, crossbreeding is particularly known to improve functional traits by the exploitation of heterosis. Thus, it appears to be an appealling option for high-yielding breeds, as well, as they tend to struggle with fitness related problems. This thesis aimed to develop genomic methods for numerically small local dairy breeds in crossbreeding schemes in order to improve their genetic gain, genetic uniqueness, and their ability to compete with high-yielding breeds. In Chapter 2 a review study conducted a comparison of different genomic models which are suitable for crossbred data. Different additive models (such as the parental model, a model with breed-specific allele effects, and a single step model) and dominance models, which were either line-dependent, line-independent or included imprinting were discussed. It was concluded that the model choice needs to be made based on desired accuracies, computational possibilities, and data availability. In general, dominance models showed to result in higher accuracies compared to additive models. A breed of origin of alleles model approach was introduced in Chapter 3, which assumes different SNP effects for different origins of haplotypes. This model is suitable for the multi-breed genomic prediction of breeding values of numerically small breeds (i.e. German Angler) that have experienced introgression from high-yielding breeds in the past. The breed of origin of alleles model approach tended to be advantageous for Angler over multi-breed and within-breed genomic predictions with GBLUP. Chapter 4 contains a simulation study about the implementation of a rotational crossbreeding scheme including German Angler x German Holstein, while introducing genomic selection in Angler. Different sizes and structures of growing reference populations and selection goals of Angler were examined. The results showed that crossbred animals had a small overall superiority to both Holstein and Angler populations. In addition, a reference population containing both Angler and crossbred animals, in combination with a selection based on the purebred performance of Angler, gave the highest response to selection in the purebred Angler population and in the crossbred population. The difference between selection methods for Angler individuals could only be observed in the long term, as the purebred-crossbred correlations decreased. In Chapter 5 a simulation study on rotational crossbreeding was performed including different Optimum Contribution Selection methods, in order to realize genetic gain while regaining the original genetic background of Angler. Different constraints regarding mean kinships, native kinships, and migrant contributions from Holstein were applied to investigate their effects on Angler, crossbred, and Holstein populations. Constraining the amount of migrant contribution in Angler increased their genetic uniqueness. However, it led to a notable reduction of genetic gain and thus a reduced superiority of the crossbred animals. The slowed rate of genetic gain and thus the large difference of the performance between the parental breeds could not be compensated by heterosis effects. In Chapter 6 the thesis ends with a general discussion about further genomic models for crossbreeding, and the practical relevance of crossbreeding in dairy cattle.Publication Phenotypic and genetic analysis of meat production traits in German Merinoland purebred and crossbred lambs(2016) Schiller, Katja; Bennewitz, JörnThe overall aims of the present thesis were to investigate various meat quality (MQ) traits including branched chain fatty acids and their correlation to sensory traits and to perform DNA-based and quantitative genetic analysis for growth, carcass and MQ traits using the data set with about 1600 phenotyped lambs. The lambs were Merinoland (ML) lambs and lambs of five crossbreds of meat type sire breeds and Merinoland ewes. The crosses were CH (Charollais × ML), IF (Ile de France × ML), SK (German black-headed mutton sheep (BHM) × ML), SU (Suffolk × ML) and TX (Texel × ML). In chapter one, growth curves, daily gain and feed conversion of ML sheep and the five ML crosses were investigated via mixed linear models. Linear and Gompertz models were fitted and the quality of fit was assessed. Differences in the model parameters were detected between crosses, genders and birth types. According to the parameters, coefficient of determination and mean square error, the Gompertz provided a better fit compared to the linear model. Additionally feed conversion rate and daily gain were observed, with only the crosses IF and TX showing significant superiority in these traits compared to purebred ML. For practical reasons, however, the common trait daily gain can be recommended to use for breeding purpose, despite if altering the shape of a growth curve is attractive because of e.g. possible lower maintenance costs for a flock. In chapter two, lamb meat and fat of the crosses and ML was investigated for concentration of three branched chain fatty acids (4-Me8:0, 4-ET8:0 and 4-Me9:0) and its correlation to sensory abnormality. Differences between crosses and between sexes were determined, but no significant correlations to sensory traits were found. In chapters three to five, genetic background and genetic parameters were investigated and a chromosome-wide association study imputing SNP panels was undertaken. Furthermore, the possibilities of implementation of this data to improve breeding programs were discussed. Chapter three focuses on genetic parameters of growth, carcass and MQ traits in purebred ML and crossbred lambs. A series of analyses for twelve traits were performed and heritabilities and genetic correlations were estimated using general linear mixed models. Several significant correlations and low to moderate heritabilities were found, indicating that selection on these traits is possible. In chapter four, a targeted association mapping was undertaken with about 330 SNPs using two different statistical models, one with estimation of SNP effects across all crosses and the other with SNP effects per cross. The investigated traits were growth, carcass and MQ traits. In this connection, several weak significant SNPs were revealed. In chapter five, F1 lambs were genotyped on selected chromosomes with a very low SNP panel and imputed via Illumina Ovine 50k SNP BeadChip genotypes from the sires and purebred ML. These were included in a haplotype bibliography before. Furthermore, chromosome-wise association analyses using single marker mixed linear models were performed for MQ, carcass, and growth traits. This was done using the imputed genotypes and the trait phenotypes. Several significant associations were detected, e.g. for the traits shoulder width and cutlet area, and these were discussed with regard to other literature reports as well as their use for practical breeding purpose. The thesis ends with a general discussion.Publication Untersuchungen zu Einfachgebrauchskreuzungen beim Merinolandschaf(2013) Henseler, Stefanie; Bennewitz, JörnThe present study examined the meat and carcase quality of lambs slaughtered in the German federal state of Baden-Württemberg in order to determine the sire breeds most suitable for the Merinolandschaf, a Merino land race. For this purpose, rams of the meat breeds Charollais, Ile de France, Blackheaded sheep, Suffolk and Texel were bred to the widespread Merinolandschaf in order to produce cross bred lambs. In addition, rams of the Merinolandschaf were used to produce purebred lambs. The lambs were raised on seven farms, then fattened at one farm and slaughtered. 1600 lambs were used to evaluate meat quality, fattening performance and yield at slaughter. 105 animals were chosen from a total of 1600 lambs used in the study. These were tasted by a panel consisting of 21 persons. Results of this sensory analysis were combined with results in regard to fattening performance, yield at slaughter and quality of meat in a joint index. The net gain from fattening of the Texel sheep surpassed all other crossbreeds. In regard to yield from slaughter, crossbreeds with Charollais, Ile de France and Texel showed improvement in development of haunches and classification. Texel crossbreed ranked highest in respect to meat area of the chops. The parameters determining the quality of the meat – drip loss and loss by cooking – were lowest for pure Merinolandschaf. High shear force was necessary for meat of Suffolk and Texel crossbreeds, whereas Charollais crossbreed showed the lowest value for this parameter. The sensory analysis showed that crossbreeds with Charollais, Blackhead sheep and Suffolk as well as the pure breed Merinolandschaf are well suited to production of high-quality lamb‘s meat. In addition, it was shown that lamb’s meat from the German federal state of Baden-Württemberg differs significantly from lamb’s meat from New Zealand. There is a significant negative correlation between shear force according to Warner-Bratzler and the perceived tenderness of meat. The joint index consists of 10 economically relevant parameters, relatively weighted according to economic factors. The first rank was achieved by the crossbreed with Ile de France, followed by Texel, Suffolk and Blackhead sheep. To choose the optimal rams, i.e. the optimal sire breed, under practical circumstances, it is vital to take the conditions of the individual farm – such as marketing strategies – into consideration. With different weighting of single traits ranking of breeds can differ.