New DNA analysis techniques, which have developed rapidly in recent years, are starting to revolutionize livestock breeding, geneticist Dr. Patrick Charagu, with Hypor Inc, told delegates at the recent Saskatchewan Swine Symposium. These new technologies will speed up genetic progress dramatically and deliver huge benefits to producers, he says.
Over the last 20 years, the ability to make genetic progress has been primarily increased through the use of information technology, which has provided the ability to deal with massive amounts of data relating to performance traits. Previously it was only possible to select for traits with high heritability, such as growth rate, feed efficiency and carcass characteristics. The advent of BLUP (Best Linear Unbiased Prediction) in the early 90s enabled progress in the improvement of less-heritable traits, such as litter size.
“All contemporary genetic improvement programs are based on the BLUP-based selection index,” Charagu explains. “This entails assessing the breeding value of individual animals for as many different traits of economic importance as possible at the same time. In the index each trait is given a
Bernie Peet is president of Pork Chain Consulting Ltd. of Lacombe, Alberta, and editor of Western Hog Journal. weighting referred to as economic weight based on its influence on the final economic outcome.” The most important thing with this, Charagu says, is that the underlying genetic relationships, or correlations, between the different traits are taken into account.
“The BLUP model has been working well, as evidenced by the progress in such traits as litter size,” Charagu notes. “However, scientists have no idea which genes are responsible for a trait, which is why, as technology and knowledge advanced, they tried to discover genes for particular traits.”
Initially, single genes that code for specific traits were discovered. “It was this that led to the use of single-gene diagnostic tests, such as for the stress susceptibility (Halothane) gene, in the 1990s,” says Charagu. “Later, other single-gene tests were developed, among them the RN gene – related to pale soft and exudative (PSE) meat, and IGF2 gene – for muscle and fat deposition.”
Traits that are coded by single genes are of limited use in the improvement of most performance traits, because most traits are determined by very many genes. In recent years, the use of genetic markers, related to desirable traits, has dramatically improved the ability to measure breeding values.
“SNPs – an abbreviation for Single Nucleotide Polymorphisms – are genetic markers based on a mutation at a single point on the chromosome. The genome of the pig has millions of such SNP locations, so SNPs are a rich resource for use as genetic markers,” says Charagu. “Alternatively a SNP may merely be located close to, and inherited together with, another DNA sequence (gene) that is responsible for a difference in performance. In both cases the SNP variants reflect the differences in the performances we observe or measure in individual pigs.”
Since there are so many SNPs it is hoped that a very large proportion of all genetic variability may in one way or another be captured by the SNPs, he adds.
Over the past several years new technologies have been developed that are particularly suitable for testing large numbers of SNPs, so-called high-throughput genotyping technologies. “Thousands and indeed up to a million SNPs can be analyzed in a single DNA sample by a single lab procedure,” says Charagu. “And, what is even more important, the cost of high-throughput genotyping using so called DNA chips has come down to a fraction of a cent per SNP. Today it is possible to obtain the genotype of an animal for 60,000 SNPs at a cost of around $150.”
In theory, if there were sufficient genetic markers to cover all the pig’s DNA (its genome), it should be possible to describe all genetic variation for all measured traits. This concept is called Genome Wide Marker Assisted Selection (GWMAS) and is now a reality. GWMAS now provides a reasonably affordable tool to accurately estimate the breeding value of an animal for any trait at any age. “If the accuracy of such an SNP-based breeding value is higher than the accuracy of the BLUP breeding value that we have today at a given age of the candidate breeder, we can use this to increase genetic progress in swine breeding programs,” Charagu points out. “Such improvements may well be very significant for some traits, since the accuracy of the currently available BLUP breeding value at the time of selection is well under 50 per cent. If this can be increased to 70 per cent by using an SNP-based breeding value, genetic progress for such traits can be improved by 40 per cent.”
Such improvements in genetic progress have not been seen since the introduction of BLUP in the 1980s and 90s, he notes. Also, GWMAS offers the opportunity to much more easily select for traits that are now too costly or impractical to measure.
“Evidence suggests that the high hopes for the effectiveness of GWMAS are coming true,” says Charagu. “Indeed we have shown in poultry that we can estimate the breeding values of animals with as few as 20,000 SNPs to an accuracy of more than 80 per cent. Our results in Hypor pigs are convincing us that we can significantly increase genetic progress by the use of this novel technology. We expect to select our breeding candidates in the future using this new method.”