This study was conducted with the objectives of identifying genes which impact feed efficiency in pigs, quantifying those effects, and informing producers of how to utilize this information in selection programs. The purpose of this research was to identify markers that can be used in marker-assisted selection (MAS) to improve feed efficiency. Feed intake data are expensive to collect on individual pigs, so such trait data frequently are not included in a selection index despite the potential economic gains. By identifying genetic markers which can be used for selection, producers can have that benefit added to their bottom lines without the expense and hassle of collecting feed intake data.
About ten years ago, Iowa State University (ISU) started developing a randomly selected line and a line selected for decreased residual feed intake (RFI), a measure of the difference between what an animal actually consumes and the average amount of feed required for that animal’s levels of maintenance and growth. To establish the two lines, a single foundation population of Yorkshire pigs was divided by randomly splitting litters. For this gene marker association study, a total of 730 animals from the first seven generations of these lines were genotyped.
To improve the speed and reduce the cost of genotyping, a tool known as the PorcineSNP60 BeadChip (SNP chip) was developed with the assistance of the grant PI, Max Rothschild, and other researchers. The single nucleotide polymorphism (SNP) chip simultaneously genotypes 64,232 genetic markers in a single pig at a cost of approximately 0.3 cents per genotype. In conjunction with NPB grant #08-190, this SNP chip was used in this project to facilitate a more thorough analysis of the porcine genome and produce more significant results than would have been otherwise achieved by looking at individual candidate genes.
A computer program written by Drs. Dorian Garrick and Rohan Fernando at ISU was used to determine which of the 64,232 markers were associated with RFI. In addition, data on average daily feed intake (ADFI), average daily gain (ADG), and 10th-rib backfat (BF) were analyzed in this population to determine effects of the same 64,232 markers.
Results of this research look very promising for producers. The SNP chip works extremely well in many populations and produced an average call rate (useable genotypes) of 99.6% in this study. Statistical analyses showed that a genetic marker on chromosome 2 had the largest marker effect for RFI; markers on chromosomes 3, 10, and 15 also had significant effects on RFI, and many smaller effects were also identified throughout the genome. Markers with large effects on ADFI were found on chromosomes 1, 3, 4, 7, 9, and 16. Markers on chromosomes 1, 6, 7, 12, 14, and 15 had the largest effects on ADG. The gene MC4R, located near the significant markers on chromosome 1 for ADFI and ADG, was previously known to have large effects on both traits. A currently unmapped marker had the largest effect for BF, which accounted for over 3% of the genetic variance in the trait. The genetic markers with the largest effects on BF and known positions in the genome were on chromosomes 9, 12, 13, and 15. Additional research will be carried out on the genes near these markers to develop final markers for selection that maximize the effects for producers.
By selecting animals using genetic markers associated with residual feed intake, producers could reduce feed costs without the expense and difficulty of measuring feed intake and without reducing growth rates. Taken together, selection for the various markers identified in this study could save producers several dollars per pig in the near future.
For additional information, contact Dr. Rothschild at [email protected] or call (515) 294-6202.
