Abstract
Using genomic information, local ruminant populations can be better characterized and compared to selected ones. Genetic relationships between animals can be established even without systematic pedigree recording, provided a budget is available for genotyping. Genomic selection (GS) can rely on a subset of the total population and does not require a costly national infrastructure, e.g., based on progeny testing. Yet, the use of genomic tools for animal breeding in developing countries is still limited. We identify three main reasons for this: (i) the instruments for cheap recording of phenotypes and data management are still limiting. (ii) many developing countries are recurrently exposed to unfavorable conditions (heat, diseases, poor nutrition) requiring special attention to fitness traits, (iii) a high level of expertise in quantitative genetics, modeling, and data manipulation is needed to perform genomic analyses. Yet, the potential outcomes go much beyond genetic improvements and can improve the resilience of the whole farming system. They include a better management of genetic diversity of local populations, a more balanced genetic progress and the possibility to unravel the genetic basis of adaptation of local breeds through whole genome approaches. A GS program being developed by BAIF, a large Indian NGO, is analyzed as a pilot case. It relies on the creation of a female reference population of Bos indicus and crossbreds, recorded with modern technology (e.g., smartphones) to collect performances at low cost in tiny herds on production and fertility. Finally, recommendations for the implementation of GS in developing countries are proposed.
Highlights
The demand for animal products in developing countries is growing at an unprecedented rate due to a combination of factors, including steady population growth, diffuse urbanization and rising levels of family incomes (Steinfeld et al, 2006; Rothschild and Plastow, 2014)
The main drawback of setting up a reference population is the genotyping cost of a large number of animals: the amount of phenotypic information associated with each genotype and available for genomic evaluation is substantially smaller for cows than for progeny tested bulls (Goddard, 2009)
Genomic selection has the potential to overcome the difficulties encountered by developing countries to implement classical breeding programs where pedigree recording is a pre-requisite
Summary
The demand for animal products in developing countries is growing at an unprecedented rate due to a combination of factors, including steady population growth, diffuse urbanization and rising levels of family incomes (Steinfeld et al, 2006; Rothschild and Plastow, 2014). The possibility of using a whole-genome set of markers to improve the accuracy of breeding value prediction was first described by Meuwissen et al (2001) It consists in using a set of genotyped and phenotyped animals, called the reference population, to estimate markerphenotype association which makes possible to predict the breeding value of a calf without the need for progeny testing (PT), thereby reducing generation interval and cost of testing. Genotypes can replace pedigree recording and the set-up of a breeding program may start on a new basis, as compared to mandatory pedigree recording, often a limiting factor in developing countries Such a concept was tested on a real data set of 1,013 dairy cows in Kenya, which exhibited various degrees of crossbreeding with exotic breeds (Brown et al, 2016). Considering that pedigree recording was totally missing, this approach opens the way to the set-up of a breeding program but limitations were identified regarding the cost of genotyping and the collection of more phenotypic data
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