Location: Livestock Bio-SystemsTitle: Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side
Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2016
Publication Date: 1/4/2017
Publication URL: http://handle.nal.usda.gov/10113/5726051
Citation: Rohrer, G.A., Nonneman, D.J. 2017. Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side. Genetics Selection Evolution. 49:4. doi:10.1186/s12711-016-0282-1.
Interpretive Summary: Number of functional teats is an important trait in commercial swine production. As litter size continues to increase, the number of teats must also increase to supply nutrition to all piglets. The pig displays considerable variation for number of teats; therefore, a study was conducted to identify genomic regions that affect this trait in a commercial swine population. In addition, genetic parameters were estimate for number of teats on the right side and number of teats on the left side to determine if selection for total teat number could be enhanced with this information. Nearly 3,000 pigs were genotyped to identify genomic regions and then these regions were validated by including an additional 2,500 pigs. Eight genetic markers were found to have an effect of more than 0.1 teats per pig in the validation project and may be suitable for marker assisted selection. Heritability was greatest for total teat number (estimates ranged from 0.37 to 0.49) indicating that adding other traits to a selection index would have minimal effects on selection progress. Sex of the pig and percentage of males in a litter did not have a significant effect on teat number. These results indicate that number of teats can be increased in pigs through selection on total teat number and would be enhanced with genetic marker data.
Technical Abstract: Background: Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded. From this information, the following traits were derived: number of teats on the left (LTN) and right side (RTN), maximum number of teats on a side (MAX), difference between LTN and RTN (L - R) and absolute value of L - R (DIF). Bayes C option of GENSEL (version 4.61) and 1-Mb windows were implemented. Identified regions that explained more than 1.5% of the genomic variation were tested in a larger group of animals (n = 5453) to estimate additive genetic effects. Results: Marker heritabilities were highest for TTN (0.233), intermediate for individual side counts (0.088 to 0.115) and virtually nil for difference traits (0.002 for L - R and 0.006 for DIF). Each copy of the VRTN mutant allele increased teat count by 0.35 (TTN), 0.16 (LTN and RTN) and 0.19 (MAX). 15, 18, 13 and 18 one-Mb windows were detected that explained more than 1.0% of the genomic variation for TTN, LTN, RTN, and MAX, respectively. These regions cumulatively accounted for over 50% of the genomic variation of LTN, RTN and MAX, but only 30% of that of TTN. Sus scrofa chromosome SSC10:52 Mb was associated with all four count traits, while SSC10:60 and SSC14:54 Mb were associated with three count traits. Thirty-three SNPs accounted for nearly 39% of the additive genetic variation in the validation dataset. No effect of piglet sex or percentage of males in litter was detected, but birth weight was positively correlated with TTN. Conclusions: Teat number is a heritable trait and use of genetic markers would expedite selection progress. Exploiting genetic variation associated with teat counts on each side would enhance selection focused on total teat counts. These results confirm QTL on SSC4, seven and ten and identify a novel QTL on SSC14.