With the report from Dong et al.1 in this issue, the goat joins the pig, cow and chicken as major livestock species to have been sequenced. The authors assembled the genome de novo from short sequencing reads derived from a female Yunnan black goat.

A key limitation of genome sequencing using short reads is that the assembly usually consists of thousands of small fragments. Joining the fragments is a time-consuming, laborious process as it requires the generation of maps of markers throughout the genome. Dong et al.1 have simplified this step by taking advantage of a method known as optical mapping2. The goat genome represents the first application to a large, mammalian genome of a commercial optical mapping technology, which provides raw whole-genome mapping data in a matter of hours.

The instrument images single DNA molecules cleaved by restriction enzymes and generates maps of the distances between restriction sites. Optical mapping has been applied to assess, refine and/or assemble the genomes of many microorganisms and of rice3, maize4, mouse5 and human6 by the group of David Schwartz, which pioneered the technique, but the goat genome marks a milestone with respect to commercialization of the technology.

Dong et al.1 show that combining sequence data with optical mapping data yields 'super-scaffolds' that by a commonly used metric of genome assemblies (the N50 size) are >5 times longer than the scaffolds assembled from sequence data alone. These super-scaffolds represent a resource that should be valuable for gene mapping and marker-assisted breeding in goats. For example, the authors use their assembly to map RNA-seq data from hair follicle cells of cashmere goats, identifying candidate genes that may contribute to cashmere fiber production.

Credit: Dr. Bin Liu

The commercial breeding infrastructure for goats is tiny compared with that of cattle7. Over 90% of the world goat population is kept in small herds by farmers in developing countries, and there are few systematic phenotyping and breeding efforts. However, China's status as the world's top producer of goats and the Chinese government's investment in agricultural biotechnology8 could expedite practical applications of the goat genome sequence.