The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

We have forgotten to thank our collaborators who provided the Creole samples. The Acknowledgements section should read:

The demand and consumption of dairy products are expected to increase exponentially in developing countries, particularly in tropical regions. However, the intensification of dairy production to meet this increasing demand has its challenges. The challenges ranged from feed costs, resources, and their utilization, as well as the heat stress associated with rearing temperate–tropical crossbred cattle in the tropics. This article focused on key nutritional and environmental factors that should be considered when temperate–tropical crossbred cattle are used in the tropics. The article also describes measures to enhance the utilization of regional feed resources and efforts to overcome the impacts of heat stress. Heat stress is a major challenge in tropical dairy farming, as it leads to poor production, despite the genetic gains made through crossbreeding of high production temperate cattle with hardy tropical animals. The dependence on imported feed and animal-man competition for the same feed resources has escalated feed cost and food security concerns. The utilization of agricultural by-products and production of stable tropical crossbreds will be an asset to tropical countries in the future, more so when scarcity of feed resources and global warming becomes a closer reality. This initiative has far-reaching impacts in the tropics and increasingly warmer areas of traditional dairying regions in the future.

No abstract

Genetic improvement of breeding depends on selective breeding of superior phenotypes. In order to increase accuracy of breeding and selection for efficient production systems, current trend is towards applying molecular markers. The purpose of the study was to identify markers associated with birth weight in Boer goats using 50k single nucleotide polymorphism (SNP) chip. A total of 657 Boer goats were selected based on the availability of birth weight data from a commercial farm. Individuals were genotyped using 50k SNP chip from Illumina using Illumina Genome Analyzer IIx. A genome wide association analysis using a mixed model was carried out and resulted in 32 detected markers for birth weight. In previous genotyping study done on the same population of goat using 20k custom-designed SNP chip resulted in 14 markers for birth weight. However, markers identified should be verified in an independent population before being applied in a Marker Assisted Selection (MAS) program. Further consideration should be on socioeconomic factors as well as their sustainability in biodiverse environments.