Genomic selection and use of molecular tools in breeding programs for indigenous and crossbred cattle in developing countries: current status and future prospects

Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion of genomically proven young bulls being used in breeding. This success has been undergirded by well-established conventional genetic evaluation systems. Here, the status of GS in terms of the structure of the reference and validation populations, response variables, genomic prediction models, validation methods, and imputation efficiency in breeding programs of developing countries, where smallholder systems predominate and the basic components for conventional breeding are mostly lacking is examined. Also, the application of genomic tools and identification of genome-wide signatures of selection is reviewed. The studies on genomic prediction in developing countries are mostly in dairy and beef cattle usually with small reference populations (500–3,000 animals) and are mostly cows. The input variables tended to be pre-corrected phenotypic records and the small reference populations has made implementation of various Bayesian methods feasible in addition to GBLUP. Multi-trait single-step has been used to incorporate genomic information from foreign bulls, thus GS in developing countries would benefit from collaborations with developed countries, as many dairy sires used are from developed countries where they may have been genotyped and phenotyped. Cross validation approaches have been implemented in most studies resulting in accuracies of 0.20–0.60. Genotyping animals with a mixture of HD and LD chips, followed by imputation to the HD have been implemented with imputation accuracies of 0.74–0.99 reported. This increases the prospects of reducing genotyping costs and hence the cost-effectiveness of GS. Next-generation sequencing and associated technologies have allowed the determination of breed composition, parent verification, genome diversity, and genome-wide selection sweeps. This information can be incorporated into breeding programs aiming to utilize GS. Cost-effective GS in beef cattle in developing countries may involve usage of reproductive technologies (AI and in-vitro fertilization) to efficiently propagate superior genetics from the genomics pipeline. For dairy cattle, sexed semen of genomically proven young bulls could substantially improve profitability thus increase prospects of small holder farmers buying-in into genomic breeding programs

Genetic evaluation of test day milk yields from smallholder dairy production systems in Kenya using genomic relationships: genetic evaluation in smallholder dairy cattle

Efforts to improve dairy production in smallholder farming systems of Eastern Africa over the past decade have had limited impact due to the lack of records on performance to guide targeted breeding programs. Estimates of genetic parameters in these systems are lacking. Using data generated through a project on “Germplasm for Dairy Development in East Africa” in Kenya, and a genomic relationship matrix from genotypic records, we examine the potential impact of different models handling contemporary groups or herd effects on estimates of genetic parameters using a fixed regression model (FRM) for test-day (TD) milk yields, and the covariance structure for TD milk yield at various stages of lactation for animals using a random regression model (RRM). Models where herd groups were defined using production levels derived from the data fitted the data better than those in which herds were either grouped depending on management practices or were random. Lactation curves obtained for animals under different production categories did not display a typical peak yield characteristic of improved dairy systems in developed countries. Heritability estimates for TD milk yields using FRM varied greatly with the definition of contemporary herd groups ranging from 0.05 ± 0.03 to 0.27 ± 0.05. The analysis using a RRM fitted the data better than the FRM. The heritability estimates for specific TD yields obtained by RRM were higher than those obtained by the FRM. Genetic correlations between TD yields were high and positive for measures within short consecutive intervals but decreased as the intervals between TDs increased beyond 60 days and became negative with intervals that were more than five months between TD. The magnitude of the genetic correlation estimates among TD records indicates that it would not be optimum to use TD milk records beyond a 60-day interval for genetic evaluation of animals on the smallholder farms as repeated measures of the same trait. Though each individual smallholder farmer retains only a few animals, using the genomic relationship between animals to link the large number of farmers operating under specified environments provide a sufficiently large “herd-group” for which a breeding program could potentially be developed

Survival and dispersal of a defined cohort of Irish cattle

An understanding of livestock movement is critical to effective disease prevention, control and prediction. However, livestock movement in Ireland has not yet been quantified. This study has sought to define the survival and dispersal of a defined cohort of cattle born in Co. Kerry during 2000. The cohort was observed for a maximum of four years, from January 1, 2000 to December 31, 2004. Beef and dairy animals moved an average 1.31 and 0.83 times, respectively. At study end, 18.8% of the beef animals remained alive on Irish farms, including 6.7% at the farm-of-birth, compared with 48.6% and 27.7% for dairy animals respectively. Beef animals werae dispersed to all Irish counties, but mainly to Cork, Limerick, Tipperary and Galway. Dairy animals mainly moved to Cork, Limerick, and Tipperary, with less animals going to Galway, Meath and Kilkenny. The four-year survival probability was 0.07 (male beef animals), 0.25 (male dairy), 0.38 (female beef), and 0.72 (female dairy). Although there was considerable dispersal, the number of moves per animal was less than expected

Farmer-preferred traits in smallholder dairy farming systems in Tanzania

Decisions of breeding schemes in many countries in sub-Saharan Africa tend to be either government or project driven, with a focus on upgrading local breeds. However, there is scant information on the individual animal traits that smallholder farmers prefer. The aim of this study was to examine farmers’ preferences of dairy cattle traits using a discrete choice experiment methodology. The study was conducted through visits to 555 randomly selected dairy farms in the sub-humid Eastern coast and temperate Southern highlands of Tanzania. Choices of animal traits were presented to farmers who were asked to evaluate choice alternatives based on attribute levels and finally select the alternative with the highest utility. The choice experiment data were analysed using a conditional logit model. Coefficients for milk yield, fertility, feed requirement, temperament and diseases resistance were overall statistically significant (p < 0.05). In order of perceived importance, farmers were willing to keep a cow with high milk yield (coefficient = 1.43 ± 0.059), good fertility (0.85 ± 0.050), easy temperament (0.76 ± 0.066), low feed requirement (− 0.56 ± 0.092) and enhanced tropical disease resistance (0.48 ± 0.048). The purchase price coefficient was negative (− 0.001 ± 0.0003), indicating that farmers would prefer improved dairy cattle at affordable prices. Farmers’ preferred traits were influenced by agro-ecological zone and type of production system (extensive vs intensive). The study provides an opportunity for breeding programme designers to take farmers’ preferred dairy traits into serious consideration

The productivity of holstein-friesian dairy cattle in different farming systems of Kenya

Information on performance of various breeds within different farming systems of Kenya would be useful in determining a breeding programme that would enable selection of appropriate animals for improved production. This study investigated the performance of Holstein-Friesian cows in small-scale farms (SSF), medium scale farms (MSF) and large-scale farms (LSF) and the factors which influenced performance in a range of milk production and fertility traits. Mean performance of animals for total lactation milk yield was 4540kg (LSF & MSF) and 2151kg (SSF). The age at first calving was lower on LSF and MSF (31.8 months)than on the SSF (45.0 months). Lactation lengths were lower on SSF (255 days) than on the MSF and LSF (301 days). Calving intervals in all systems were long, 404 days on MSF and LSF, and 429 days on SSF. Milk yield was highly influenced by seasonal effects, parity and lactation length, however lactation length, age at first calving and calving interval were only affected by seasonal effects on some of the LSF and MSF. Trends in performance over the years showed that between 1986 and 1996 there was little change in performance on SSF and MSF. On three LSF that altered the management of animals and introduced total-mixed-ration feeds, there was a marked increase in milk production. When comparing the performance of Holstein-Friesian cows on SSF with Ayrshire, Guernsey and Jersey, their level of performance was the lowest for total milk yield, calving interval and age at first calving. Further improvements and research on production systems are required in the country.International Journal of Agricultural and Rural Development Vol. 5 2004: 145-15