Estimating backfat depth, loin depth, and intramuscular fat percentage from ultrasound images in swine.

Fast, accurate, and reliable estimates of backfat depth, loin depth, and intramuscular fat percentage in swine breeding stock are used to increase genetic improvement and farm profitability. The objective of this study was to develop an equation-based model for the estimation of swine backfat depth, loin depth, and intramuscular fat percentage estimates obtained from longitudinal ultrasound images. Images were collected from purebred Duroc (n = 230), purebred Large White (n = 154), and commercial (n = 190) pigs born in January 2021 at three farms located in North Carolina. An Exapad ultrasound machine captured longitudinal images across the 10th to 13th ribs at 182 (±12.8 SD) days of pig age. The total number of images processed for Duroc, Large White, and commercial pigs was 1 385, 928, and 1 168 images, respectively. To establish a standard measurement for model comparison, trained personnel following standard company procedures using the BioSoft Toolbox (v4.0.1.2; Biotronics Inc., Ames, IA) obtained backfat and loin depth measurements from the images. Longissimus muscle intramuscular fat percentage was predicted using near-infrared spectroscopy at approximately 22 h postmortem. Backfat and loin depth estimation were conducted only for commercial pigs (n = 190) while intramuscular fat estimation was conducted on all pigs (n = 574). Average backfat depth, loin depth, and intramuscular fat percentage were 14.6 (±2.6 SD) mm, 63.7 (±5.5 SD) mm, and 2.21 (±0.82 SD) %. Image analysis and estimation model development were conducted in MATLAB R2021a. Edge detection via the image gradient was applied to segment ultrasound images into backfat, loin, and rib regions. Segmented images were used to estimate backfat depth, loin depth, and loin intramuscular fat percentage. After image quality control and filtering, the image inclusion rate for each breed-trait combination ranged from 76 to 97%. All Duroc and commercial pigs and 97% of Large White pigs were represented by at least one image for trait estimation. Coefficient of determination of models for the estimation of backfat depth, loin depth, and intramuscular fat percentage were 0.58, 0.57, and 0.56, respectively. Root mean square error of backfat depth, loin depth, and intramuscular fat estimation were 1.65 mm, 3.58 mm, and 0.54%, respectively. Results demonstrate the feasibility of using ultrasound image gradient and an equation-based approach to estimate swine backfat and loin depth, and intramuscular fat percentage. This equation-based approach to estimate carcass traits in live swine can enhance genetic improvement.

A comparison of accuracy validation methods for genomic and pedigree-based predictions of swine litter size traits using Large White and simulated data.

The objective of this study was to compare and determine the optimal validation method when comparing accuracy from single-step GBLUP (ssGBLUP) to traditional pedigree-based BLUP. Field data included six litter size traits. Simulated data included ten replicates designed to mimic the field data in order to determine the method that was closest to the true accuracy. Data were split into training and validation sets. The methods used were as follows: (i) theoretical accuracy derived from the prediction error variance (PEV) of the direct inverse (iLHS), (ii) approximated accuracies from the accf90(GS) program in the BLUPF90 family of programs (Approx), (iii) correlation between predictions and the single-step GEBVs from the full data set (GEBVFull ), (iv) correlation between predictions and the corrected phenotypes of females from the full data set (Yc ), (v) correlation from method iv divided by the square root of the heritability (Ych ) and (vi) correlation between sire predictions and the average of their daughters' corrected phenotypes (Ycs ). Accuracies from iLHS increased from 0.27 to 0.37 (37%) in the Large White. Approximation accuracies were very consistent and close in absolute value (0.41 to 0.43). Both iLHS and Approx were much less variable than the corrected phenotype methods (ranging from 0.04 to 0.27). On average, simulated data showed an increase in accuracy from 0.34 to 0.44 (29%) using ssGBLUP. Both iLHS and Ych approximated the increase well, 0.30 to 0.46 and 0.36 to 0.45, respectively. GEBVFull performed poorly in both data sets and is not recommended. Results suggest that for within-breed selection, theoretical accuracy using PEV was consistent and accurate. When direct inversion is infeasible to get the PEV, correlating predictions to the corrected phenotypes divided by the square root of heritability is adequate given a large enough validation data set.

Variance component estimates for alternative litter size traits in swine.

Litter size at d 5 (LS5) has been shown to be an effective trait to increase total number born (TNB) while simultaneously decreasing preweaning mortality. The objective of this study was to determine the optimal litter size day for selection (i.e., other than d 5). Traits included TNB, number born alive (NBA), litter size at d 2, 5, 10, 30 (LS2, LS5, LS10, LS30, respectively), litter size at weaning (LSW), number weaned (NW), piglet mortality at d 30 (MortD30), and average piglet birth weight (BirthWt). Litter size traits were assigned to biological litters and treated as a trait of the sow. In contrast, NW was the number of piglets weaned by the nurse dam. Bivariate animal models included farm, year-season, and parity as fixed effects. Number born alive was fit as a covariate for BirthWt. Random effects included additive genetics and the permanent environment of the sow. Variance components were plotted for TNB, NBA, and LS2 to LS30 using univariate animal models to determine how variances changed over time. Additive genetic variance was minimized at d 7 in Large White and at d 14 in Landrace pigs. Total phenotypic variance for litter size traits decreased over the first 10 d and then stabilized. Heritability estimates increased between TNB and LS30. Genetic correlations between TNB, NBA, and LS2 to LS29 with LS30 plateaued within the first 10 d. A genetic correlation with LS30 of 0.95 was reached at d 4 for Large White and at d 8 for Landrace pigs. Heritability estimates ranged from 0.07 to 0.13 for litter size traits and MortD30. Birth weight had an h of 0.24 and 0.26 for Large White and Landrace pigs, respectively. Genetic correlations among LS30, LSW, and NW ranged from 0.97 to 1.00. In the Large White breed, genetic correlations between MortD30 with TNB and LS30 were 0.23 and -0.64, respectively. These correlations were 0.10 and -0.61 in the Landrace breed. A high genetic correlation of 0.98 and 0.97 was observed between LS10 and NW for Large White and Landrace breeds, respectively. This would indicate that NW could possibly be used as an effective maternal trait, given a low level of cross-fostering, to avoid back calculating litter size traits from piglet records. Litter size at d 10 would be a compromise between gain in litter size at weaning and minimizing the potentially negative effects of the nurse dam and direct additive genetics of the piglets, as they are expected to increase throughout lactation.

Phenotypic and genetic correlations between gilt estrus, puberty, growth, composition, and structural conformation traits with first-litter reproductive measures.

The objective was to estimate correlations of gilt estrus, puberty, growth, composition, and structural conformation traits with first-litter reproductive measures. Four groups of gilts (n = 1,225; Genetic Improvement Services of NC, Newton Grove, NC) entered the NC Swine Evaluation Station (Clayton, NC) averaging 162 d of age and were observed daily for symptoms of estrus. Once symptoms of first estrus were observed in 70% of gilts, recording of symptoms of estrus in all gilts occurred every 12 h for 30 d, utilizing fence-line boar contact. Subjective estrous traits were maximum and total strength of standing reflex, as observed with and without the presence of a boar, and strength of vulva reddening and swelling. Objective estrous traits consisted of vulva redness, vulva width, length of estrus, and age at puberty. Growth and composition traits included BW at puberty, days to 114 kg, and 10th rib backfat and LM area at 114 kg and at puberty. Subjective structural conformation traits were muscle mass, rib width, front leg side view, rear leg side view, front legs front view, rear legs rear view, and locomotion. First-litter sow traits included if gilt farrowed (Stay), age at first farrowing (AFF), total number of piglets born (TNB), and weaning to conception interval (WCI). Variance components were estimated using an animal model with AIREMLF90 for linear traits and THRGIBBS1F90 for categorical traits. Heritability estimates for Stay, AFF, and TNB were 0.14, 0.22, and 0.02, respectively. Genetic correlations between length of estrus, the standing reflex traits, and age at puberty with Stay were 0.34, 0.34 to 0.74, and -0.27, respectively, and with AFF were -0.11, -0.04 to -0.41, and 0.76, respectively. Days to 114 kg had genetic associations with Stay, AFF, and TNB of 0.52, -0.25, and -0.08, respectively. Backfat at 114 kg had genetic correlations with Stay, AFF, and TNB of -0.29, 0.14, and 0.47, respectively. Vulva redness and TNB were negatively correlated phenotypically (r = -0.14) and genetically (r = -0.53). Associations between structural conformation traits with Stay, AFF, TNB, and WCI were generally low to moderate and favorable. Selection for longer length of estrus, stronger standing reflex, or younger age at puberty would increase the proportion of gilts that farrow and reduce age at first farrowing.

Estimates of variance components for genetic correlations among swine estrus traits.

Variance components and genetic correlations were estimated among estrus, puberty, growth, and composition traits in Landrace-Large White gilts (n = 1,225; Genetic Improvement Services, Newton Grove, NC) from 59 sires and 330 dams. Four groups of gilts entered the North Carolina Swine Evaluation Station in Clayton at an average age of 162 d and were checked daily for estrus. Once 70% of gilts had reached puberty, recording of estrus symptoms occurred every 12 h for 30 d, using fence-line boar contact. Subjective estrus traits were maximum strength of standing reflex with or without a boar present, total strength of standing reflex with or without a boar present, and strength of vulva reddening and swelling. Objective estrus traits consisted of vulva redness, vulva width, length of estrus in consecutive days based on 12-h observations, and age at puberty (AGEPUB). Growth and composition traits included puberty weight, days to 114 kg (DYS), 10th-rib backfat, and 10th-rib LM area at 114 kg (BF, LMA) and puberty. Variance components were estimated using AIREMLF90 with an animal model. All models included gilt development diet class and breed composition as fixed effects, entry age as a covariate (except DYS, BF, and LMA), a random common litter effect, and a random animal genetic effect. Heritability estimates for length of estrus, maximum strength of the standing reflex with a boar, total strength of the standing reflex with a boar, maximum strength of the standing reflex without a boar, total strength of the standing reflex without a boar, vulva redness, strength of vulva reddening and swelling, and vulva width were 0.21, 0.13, 0.26, 0.42, 0.42, 0.26, 0.45, and 0.58, respectively. Heritability estimates for AGEPUB, puberty weight, 10th-rib backfat at puberty, 10th-rib LM area at puberty, DYS, BF, and LMA were 0.29, 0.39, 0.41, 0.38, 0.24, 0.47, and 0.39, respectfully. Common litter effect estimates ranged from 0.01 to 0.09. The estimated genetic correlation between length of estrus and maximum strength of standing reflex with a boar was 0.99. Genetic correlations between AGEPUB and length of estrus, maximum strength of standing reflex with a boar, and vulva redness were -0.23, -0.32, and 0.20, respectively. Length of estrus had positive genetic associations with DYS and BF (0.30 and 0.29, respectively). It was concluded that past selection for lean BW gain may have weakened the strength of the standing reflex and that sufficient genetic variation exists to make selection for improved swine estrus traits effective.