Genetics and Breeding

Inbreeding is the mating of closely related animals to increase homozygosity within a population. Common alleles become more concentrated — the gene frequency increases in other words — and animals become more and more closely related with each generation. The reliability of high performing animals producing more high performing animals becomes very predictable. It sounds like the only breeding approach you’ll ever need, but there can be consequences. Outbreeding on the other hand increases heterozygosity by mating unrelated animals. New alleles are introduced and the gene pool widens. From this and the Hardy-Weinberg Equilibrium, it would appear that a breeding programme would go nowhere fast were it to rely solely on outbreeding. Yet there can be benefits. more »

Once animals have been selected for breeding, the next step is to decide which are mated to which via a mating system. Some examples of mating systems, each with different intentions, were briefly covered here. Last week we saw how selecting for a particular allelic expression (ie selecting for ‘best’ phenotype) can change the gene frequency significantly in a population. Genotypic frequencies change indirectly as a result — they ‘tag along’. Mating systems do however change genotypic frequencies directly, with gene frequencies less affected. These systems fall into two general categories: inbreeding systems and outbreeding systems. Inbreeding is a mating system which increases homozygosity. Outbreeding is a mating system which increases heterozygosity. more »

Genome research has progressed rapidly in recent years and DNA-based selection tools are now available in a number of domesticated species. To date, advanced genomics technologies have not been developed in alpacas (Vicugna pacos). Therefore, breeders select for traits of economic importance (fleece phenotypes) using traditional techniques such as line breeding. Alpacas have experienced a history of population bottlenecks including the mass destruction of alpacas and llamas during the 16th Century, therefore traditional breeding may exacerbate an already depleted gene pool. Alpaca veterinarians report a prevalence of congenital defects much higher than any other livestock species. This study investigated levels of genetic diversity at genome-wide markers in Australian alpacas. Samples have been collected from unrelated individuals with normal and defective phenotypes including choanal atresia, polydactyly, cyclopia, syndactyly, vulval atresia and anal atresia. Multi-locus heterozygosity and inbreeding coefficients were estimated using microsatellite data from 53 or 22 loci. In addition, pedigrees were examined in order to detect pedigree inbreeding. Inbreeding coefficients estimated from genomic data reveal that individuals with congenital defects do not have significantly higher molecular inbreeding levels than healthy individuals. These results suggest that high levels of inbreeding cannot explain the high prevalence of congenital abnormalities in alpacas. This study is the first to report on the genetic variability of Australian alpacas and represents an important first step in the use of genomics to inform alpaca breeding practices. more »