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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #413906
Research Project: Multi-Dimension Phenotyping to Enhance Prediction of Performance in Swine

Location: Genetics and Animal Breeding

Title: Genomic regions associated with electronic measures indicative of structural soundness in pigs

Author
item Rohrer, Gary
item OSTRAND, LEXI - University Of Nebraska
item Rempel, Lea
item Keel-Mercer, Brittney
item SCHMIDT, TY - University Of Nebraska
item MOTE, BENNY - University Of Nebraska

Submitted to: American Society of Animal Science Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/30/2024
Publication Date: 9/13/2024
Citation: Rohrer, G.A., Ostrand, L., Rempel, L.A., Keel-Mercer, B.N., Schmidt, T.B., Mote, B.E. 2024. Genomic regions associated with electronic measures indicative of structural soundness in pigs [abstract]. American Society of Animal Science Annual Meeting. 102(3):24-25. https://doi.org/10.1093/jas/skae234.027.
DOI: https://doi.org/10.1093/jas/skae234.027

Interpretive Summary:

Technical Abstract: The objective was to determine the genetic factors influencing mobility traits recorded from five-month-old gilts. Mobility was measured using a pressure-sensing mat (GAIT4) and 7 days of video recorded activity (NUtrack). Gilts (n=3659) were evaluated for the study, but only 2172 gilts had data for both systems. GAIT4 system creates a series of measurements for each foot related to pressure, duration and step length of each foot generating a lameness score for each foot. Traits studied summarized values for all 4 feet: average stride length, average stance time, standard deviation of stance time, lameness score and total scaled pressure. NUtrack measurements were rotations, velocity, and distance walked as well as determines the time spent eating, sitting, standing, lying sternal and lying lateral. All NUtrack traits were standardized to a mean of zero and standard deviation of 1.0 based on each pen-day subgroup. Mixed model analyses were conducted in R fitting animal as a random effect and fixed effects of breed of sire and contemporary group, with day included for NUtrack data. ssGBLUP analyses were conducted in WOMBAT using animal effects from R models as phenotypes. Three generations of pedigree were included and genotypic data from the NeoGen Porcine 50K beadchip on 3186 animals representing 60% of gilts with NUtrack data, 67% of gilts with GAIT4 data and most parents (>99%). Single trait analyses were conducted for all traits, gEBVs estimated and then SNP effects estimated by back-solving equations. Significance values were determined by 5,000 permutations and a Bonferroni adjustment factor applied. Estimates of heritability ranged from 0.08 to 0.41 and traits from the NUtrack system tended to have greater heritability than GAIT4 traits. There were 343 significant SNP effects in 39 unique chromosomal regions. There were 133 significant SNP associations located on chromosome 14 between 45-47 Mb associated with rotations, distance and times standing and lying. Pathway analysis identified proteoglycan and apelin pathways to be over-represented based on associations with SNP located at 2:45, 2:51, 13:79 and 14:40 (SSC:Mb). Proteoglycans are a subunit of cartilage and apelins affect blood flow and angiogenesis which make them candidates for the development of osteochondrosis, a leading cause of lameness in pigs. These results will facilitate selection of more robust animals capable of withstanding commercial production environments and group sow housing. USDA is an equal opportunity employer.