PIC implements imputation of selection candidates

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PIC has continued acceleration of genetic improvement by successfully developing and routinely implementing imputation of 60K SNP genotypes for nucleus selection candidates.

The leading-edge technology is driven by the combination of 60K SNP genotypes of parents with the individual candidate’s genotypes for 300-400 markers, according to a company news release.

The result is extremely high accuracy for estimated breeding values for each pig within a litter at a very early age. Previously, 60K genotypes of the parents were only able to give an average genomic EBV to the litter. “As an example of this dramatic transformation, genomic selection for total number born based on parental 60k genotypes improved accuracy by 11 percent; adding imputed selection candidate 60k genotypes resulted in a 68 percent increase in accuracy” says Dr. Selma Forni, Genus Quantitative Research Geneticist.

This significant advancement in swine breeding was made possible through an active research partnership with the University of New England (UNE) in Australia. Scientists from the university and Genus developed the methodology and software necessary to implement imputation into PIC’s industry leading genomic selection platform.

“This has been a two and half year project that began with funding research with UNE,” says Dr. Matthew Cleveland, Genus quantitative research scientist. “A key element to the successful implementation of the imputation process was PIC’s extensive genomic database of over 20,000 animals genotyped on the 60K chip test - the largest genomic database in the industry - that allowed us to ‘train’ the software. PIC then developed the proprietary test for the candidates, verified the imputation result, developed the software system for automated production of breeding values and finally invested in a substantial upgrade in computing power to routinely handle over 1 billion genotypes."

“PIC is leading the global livestock industry in the practical implementation of genomic imputation into routine genetic evaluations,” says Dr. Matt Culbertson, PIC director of global product development. “While all the leading pig breeding companies are trying to begin to apply genomic selection, PIC is leading in the depth and scale of that implementation and the resulting increases in rates of genetic improvement will bring higher productivity and profitability to our customers.”



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