Marker-assisted selection (MAS) is the process of using DNA markers to assist in the selection of individuals that would be parents of the next generation. This technology will not replace, but instead, complement conventional breeding and selection systems.

Published information from countries leading in swine production suggested that application of molecular marker-assisted selection offers the highest potential in improving reproductive efficiency and overall swine productivity.

MAS is advantageous for traits that are lowly heritable, sex-limited, expressed or measured only after sexual maturity, and traits that are difficult and expensive to measure. DNA markers allow identification of both males and females carrying beneficial alleles of genes early in life thereby improving accuracy, reducing generation interval and accelerating the genetic improvement of a trait.

Furthermore, MAS is good for traits that cannot be measured until the animal has contributed to the next generation (reproduction, longevity, carcass data) and traits that are genetically correlated with a characteristic that swine raisers do not want to increase (marbling with backfat thickness). In general, MAS improves the efficiency of selecting specific traits and the predictability of the outcome of selection. Thus, having DNA marker information available on individual animals enables selection on traits that would otherwise have been difficult to measure or not at all.

The use of genetic markers associated with economically important traits had been tried in other countries and has resulted in positive results to their industry. Under this assumption, a PCAARRD-supported R&D program titled “Private-Public Partnership in the Application of Animal Genomics to Increase Productivity and Improve Efficiency of the Philippine Swine Industry (Phase I)” was successfully implemented by PCC in 2012 in partnership with the Bureau of Animal Industry (BAI) and with the Accredited Swine Breeders Association of the Philippines (ASBAP).

The Phase I of the program has developed and initially promoted application of genetic markers in the breeding and selection of pigs in local breeder swine farms through the Swine Genetic Analytical Service Laboratory (SGASL). It has made significant accomplishment in establishing 17 gene marker protocols for genetic testing the includes gene markers that are associated with fertility traits, meat quality, genetic defects, and disease resistance of swine and the establishment of the SGASL that is operated by the ASBAP.

Some examples of these specific gene markers or protocols developed using this technology to assist the DNA evaluation includes Estrogen Receptor (ESR) gene, which is associated with fertility traits specifically with the number of piglets born alive per litter; Leukemia inhibitory factor (LIF) gene, which also contributes to the number of piglets born alive per litter and at the same time influences the early return to service post-weaning thus, supporting the productivity of the sow; Heart-type fatty acid binding protein (H-FABP), which is associated with intramuscular fat; and Leptin Receptor(LEPR), which is for backfat thickness. The genes coding for H-FABP (heart acid-binding protein) and LEPR (leptin receptor) are considered to be candidates for lipid metabolism and thus affect fat deposition in pigs. Both genes are strongly related to the development and function of fat tissue in pigs; and Halothane (HAL) gene for screening pigs which are carriers of the genetic defect Porcine Stress Syndrome (PSS).

The development of molecular methods of identifying genetic markers and the establishment of the swine genetic analytical service laboratory (SGASL) have provided opportunity for breeders and raisers to hasten the rate of genetic improvement and improve the prolificacy and production efficiency of local swine industry in conjunction with conventional method of culling and selection.

Such undertakings have paved  the way for the improvement of swine industry in the Philippines as it lags behind other pig-producing countries in terms of reproductive parameters. It has been noted that the productivity, production efficiency, and profitability of swine farms are highly dependent on sow reproductive performance, an area that the Philippine swine industry needs to improve on.

The slow progress in improving the reproductive aspect of swine performance could be attributed to inherent biological and management-related factors (i.e., low appreciation of good genetics by swine raisers and limited access to genetically superior breeder pigs). Another important factor is the lack of service providers that would facilitate identification and access of genetically superior breeder pigs to swine raisers.

Realizing the barriers and the need to enhance the productivity and efficiency of swine production in the country, adoption of updated and appropriate tools and techniques in breeding and selection to improve swine reproductive efficiency was considered. Thus, the PCC through its Animal Genomics and Breeding Section conducted a follow-up (Phase II) study titled “Utilization of DNA marker Selection in Breeder and Commercial Farm Units” engaging researchers namely Dr. Ester Flores, Sherwin Matias, and Jonathan Pablo.

Through the help of this technology, swine raisers or breeders can now have a guide to determine at an early stage the potential and quality of their piglets. They don’t have to wait for it to grow to determine its performance, thus, they would know which pig or piglet to invest on. 

For paying clienteles, the selection of genes to be tested per sample submitted in the laboratory were determined by the swine raiser but is limited to the list of abovementioned 17 tests being offered by the SGASL.

Meanwhile, for validation of marker effect, raisers that submitted samples for specific tests were approached if they could provide the phenotype (performance records) as well. The validation of marker effect was limited to selected genes that are associated with economically important positive phenotypes.

Once results are available, the client could request for a meeting to discuss the results and the implication of such. However, for results related to genetic defects, the SGASL will initiate the meeting.

The study further recommended that breeder animal be sourced out from farms that regularly conduct genetic tests to hasten the improvement in prolificacy and production in commercial swine population. Furthermore, breeder boars and imported semen should have been tested to be a non-carrier of genetic defect, most importantly, the HAL gene.