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Background: A back curvature defect similar to kyphosis in humans has been observed in swine herds. The defect ranges from mild to severe curvature of the thoracic vertebrate in split carcasses and has an estimated heritability of 0.3. The objective of this study was to identify genomic regions that affect this trait., Results: Single nucleotide polymorphism (SNP) associations performed with 198 SNPs and microsatellite markers in a Duroc-Landrace-Yorkshire resource population (U.S. Meat Animal Research Center, USMARC resource population) of swine provided regions of association with this trait on 15 chromosomes. Positional candidate genes, especially those involved in human skeletal development pathways, were selected for SNP identification. SNPs in 16 candidate genes were genotyped in an F2 population (n = 371) and the USMARC resource herd (n = 1,257) with kyphosis scores. SNPs in KCNN2 on SSC2, RYR1 and PLOD1 on SSC6 and MYST4 on SSC14 were significantly associated with kyphosis in the resource population of swine (P ≤ 0.05). SNPs in CER1 and CDH7 on SSC1, PSMA5 on SSC4, HOXC6 and HOXC8 on SSC5, ADAMTS18 on SSC6 and SOX9 on SSC12 were significantly associated with the kyphosis trait in the F2 population of swine (P ≤ 0.05)., Conclusions: These data suggest that this kyphosis trait may be affected by several loci and that these may differ by population. Carcass value could be improved by effectively removing this undesirable trait from pig populations.

Genetic parameters for scale activity score (AS) were estimated from generations 5, 6, and 7 of a randomly selected, composite population composed of Duroc, Large White, and 2 sources of Landrace (n = 2,186). At approximately 156 d of age, pigs were weighed (BW) and ultrasound backfat measurements (BF1, BF2, and BF3) were done. While pigs were in the scale, an AS was assigned, which ranged from 1 (calm) to 5 (highly excited), where 58.1, 28.5, 8.9, 4.0, and 0.5% were scored as 1, 2, 3, 4, and 5, respectively. Statistical model effects were year-week of measurement, sex, covariates of age for AS and BW or BW for BF1, BF2, and BF3, and an animal direct genetic effect. A 5-trait linear mixed model was used. Estimated heritabilities were 0.23, 0.54, 0.56, 0.52, and 0.48 for AS, BW, BF1, BF2, and BF3, respectively. Estimated genetic correlations between AS and BW, AS and BF1, AS and BF2, and AS and BF3 were -0.38, -0.11, -0.12, and -0.16 respectively. Results indicated AS had a heritable genetic component and was genetically correlated with performance traits. Estimated genetic correlations between AS and backfat measurements adjusted to a common BW were negative, as was the genetic correlation of AS with BW. Therefore, selection for more docile animals would be expected to result in fatter, faster growing pigs.

Genetic parameters for the splayleg (SL) condition were estimated from 37,673 records of pigs from six lines derived from a Large White-Land-race base population. Random selection for 22 generations was practiced in Lines C1 and C2. Line C2 was derived from C1 at Generation 8. Selection lines were as follows: 1) Line I, selected 11 generations for an index of ovulation rate and embryonic survival followed by 11 generations of selection for litter size; 2) Line IOL, derived from Line I at Generation 8 and which underwent eight generations of two-stage selection for ovulation rate and number of fully formed pigs per litter followed by four generations of litter size selection; 3) Line COL, derived from Line C1 at Generation 8 and selected eight generations in two stages for ovulation rate and number of fully formed pigs followed by four generations of litter size selection; and 4) Line T, selected 12 generations for increased testis size. From logistic models, it was found that boars were 224% more likely to have SL than gilts (P < 0.01). Decreases in birth weight, dam age at puberty, dam nipple number, and dam embryonic survival, and increases in dam litter size and inbreeding increased the odds of SL (P < 0.05). Direct and maternal heritabilities of SL were 0.07 and 0.16, respectively, and the correlation between direct and maternal effects was -0.24. Correlations between direct genetic effects for SL and number born alive, nipple number, birth weight, age at puberty, and embryonic survival were -0.19, -0.36, 0.23, -0.19, and -0.32, respectively. Except for the correlation of 0.32 between maternal effects for SL and direct effects for number of live pigs, correlations of SL maternal genetic effects with direct genetic effects of other traits were less than 0.11. Annual direct genetic trends (%) for SL in I, IOL, COL, T, C1, and C2 were -0.003 +/- 0.003, 0.121 +/- 0.012, -0.273 +/-0.009, 0.243 +/-0.014, -0.274 +/-0.004, and 0.086 +/-0.008, respectively; annual maternal genetic trends (%) were 0.106 +/-0.004, 0.508 +/-0.019, 0.383 +/-0.015, 0.527 +/-0.024, 0.188 +/-0.005, and 0.113 +/-0.012, respectively. Annual genetic maternal trend in Line I after Generation 12 was 0.339 +/-0.014. Maternal breeding value for SL is expected to increase as a correlated response to selection for increased litter size and increased size of testes.

Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P < 0.10) for reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models.

Our objective was to estimate responses in growth and carcass traits in the NE Index line (I) that was selected for 19 generations for increased litter size. Differences between Line I and the randomly selected control line (C) were estimated in pure line litters and in F1 and three-way cross litters produced by mating I and C females with males of unrelated lines. Contrasts of means were used to estimate the genetic difference between I and C and interactions of line differences with mating type. In Exp 1, 694 gilts that were retained for breeding, including 538 I and C and 156 F1 gilts from I and C dams mated with Danbred NA Landrace (L) sires, were evaluated. Direct genetic effects of I and C did not differ for backfat (BF) at 88.2 kg or days to 88.2 kg; however, I pigs had 1.58 cm2 smaller LM area than did C pigs (P < 0.05). Averaged over crosses, F1 gilts had 0.34 cm less BF, 4.29 cm2 greater LM area, and 31 d less to 88.2 kg than did pure line gilts (P < 0.05). In Exp 2, barrows and gilts were individually penned for feed intake recording from 27 to 113 kg and slaughtered. A total of 43 I and C pigs, 77 F1 pigs produced from pure line females mated with either L or Danbred NA 3/4 Duroc, 1/4 Hampshire boars (T), and 76 three-way cross pigs produced from F1 females mated with T boars were used. Direct genetic effects of I and C did not differ for ADFI, ADG, G:F, days to 113 kg, BF, LM area, ultimate pH of the LM, LM Minolta L* score, or percentage of carcass lean. Interactions of line effects with crossing system were significant only for days to 113 kg. Pure line I pigs took 4.58+/-4.00 d more to reach 113 kg than did C pigs, whereas I cross F1 pigs reached 113 kg in 6.70+/-3.95 d less than C cross F1 pigs. Three-way cross and F1 pigs did not differ significantly for most traits, but the average crossbred pig consumed more feed (0.23+/-0.04 kg/d), gained more BW per unit of feed consumed (0.052+/-0.005 kg/kg), grew faster (0.20+/-0.016 kg/d), had less BF (-0.89+/-0.089 cm), greater LM area (5.74+/-0.926 cm2), more lean (6.21+/-0.90%), and higher L* score (5.27+/-1.377) than the average pure line pig did (P < 0.05). Nineteen generations of selection for increased litter size produced few correlated responses in growth and carcass traits, indicating these traits are largely genetically independent of litter size, ovulation rate, and embryonic survival.

Direct selection for increased litter size was done for nine generations. The select line consisted of approximately 15 sires and 60 dams per generation, and selection was based on estimated breeding values for number of live pigs. A control line of approximately 10 sires and 30 dams was maintained with stabilizing selection. Heritabilities estimated in the select line using restricted maximal likelihood procedures, daughter-dam regression within sires, and half-sib analysis were 0.01, 0.04, and 0.00 for number of pigs born alive (NBA) and 0.02, 0.16, and 0.00 for total born per litter (TB). Corresponding estimates for the control line were 0.01, 0.06, and 0.23 and 0.02, 0.07, and 0.09 for NBA and TB, respectively. Realized heritabilities for NBA from multiple regression were 0.09 +/- 0.08 in the select line and 0.11 +/- 0.166 in the control line. Heritability estimated from regression of differences in response between lines on differences in cumulative selection differentials was 0.13 +/- 0.07. At Generation 9, litter sizes, estimated breeding values, and cumulative selection differentials were 0.86 (P < 0.05), 0.63 (P < 0.01), and 9.05 (P < 0.01) pigs larger for the select line than for the control line. Phenotypic differences between lines for TB, adjusted backfat (BF), and days to 104 kg (DAYS) were not significant. Genetic trends in the select line were 0.053 +/- 0.002 pigs/yr for NBA, 0.054 +/- 0.013 mm/yr for BF, and 0.398 +/- 0.110 d/yr for DAYS. Corresponding phenotypic trends were 0.145 +/- 0.051 pigs/yr, -0.012 +/- 0.089 mm per yr, and 0.307 +/- 0.278 d/yr, respectively. Genetic trends in the control line were -0.026 +/- 0.004 pigs/yr for NBA, 0.026 +/- 0.022 mm/yr for BF, and -0.532 +/- 0.182 d/yr for DAYS. Corresponding phenotypic trends were 0.001 +/- 0.085 pigs/yr, -0.043 +/- 0.147 mm/yr, and -0.519 +/- 0.462 d/yr, respectively. Litter size can be increased by direct selection using breeding values estimated from an animal model, in conjunction with rearing selected gilts in litters of 10 pigs or less.