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Cutshaw R.L.,Purdue University | Schinckel A.P.,Purdue University | Schultz M.M.,Purdue University | Fix J.,National Swine Registry | And 2 more authors.
Livestock Science

The purpose of this study was to evaluate the relationships of litter weaning weight (LWW), number weaned (NW), mean pig weaning weight (PWT), litter birth weight (LBW), and survival percentage (%S) with number after transfer (NAT) and number born alive (NBA) on purebred and crossbred litters. Data consisted of purebred Duroc (29,297), Landrace (34,177), and Yorkshire litters (40,301) as well as Yorkshire×Landrace (8061) and Landrace×Yorkshire (4028) crossbred litters. The data were distributed into 4 time periods of 1980 through 1997, 1998 through 2002, 2003 through 2008, and 2009 through 2011. All variables were initially modeled with the fixed effects of litter breed, period, NAT, farm, parity-age class (P-AC) groupings and interactions, and random effects of sow and contemporary group. Non-significant variables and interactions (. P>0.05) were removed from final models. Periods 1 and 2 as well as 3 and 4 were combined based on non-significant main effects and interactions. The effect of NAT on LWW differed by time period (. P<0.01) such that heavier litters were achieved at larger litter sizes (NAT>11) in Landrace and Yorkshire litters (. P<0.05) in period 2. Mean PWT decreased as NAT increased with less effect on PWT during the second time period. Also %S decreased in a linear fashion from 6 to 12 NAT then decreased at an increasing rate for NAT>12, with a slight increase in %S over time for all breeds. Number weaned increased in a linear fashion up to NAT equal to 11 then increased at a decreasing rate to a maximum value depending on breed; above that value of NAT, NW decreased. There were no significant (. P>0.05) NBA by parity interactions for traits that were measured after processing and transfer. In every statistical analysis, farm was a significant and major source of variation. Also %S, and NW were greatly affected by NAT, and LBW was greatly affected by total number of pigs born (TNB). As litter size increases, greater emphasis should be placed on preweaning survival. The data indicate the effects of NAT on LWW, and PWT should be revaluated periodically. © 2014 Elsevier B.V. Source

Badke Y.M.,Michigan State University | Bates R.O.,Michigan State University | Ernst C.W.,Michigan State University | Schwab C.,The Maschhoffs | And 3 more authors.
BMC Genetics

Background: Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective of this study was to investigate variables affecting imputation accuracy from low density tagSNP (average distance between tagSNP from 100kb to 1Mb) sets in swine, selected using LD information, physical location, or accuracy for genotype imputation. We compared results of imputation accuracy based on several sets of low density tagSNP of varying densities and selected using three different methods. In addition, we assessed the effect of varying size and composition of the reference panel of haplotypes used for imputation.Results: TagSNP density of at least 1 tagSNP per 340kb (~7000 tagSNP) selected using pairwise LD information was necessary to achieve average imputation accuracy higher than 0.95. A commercial low density (9K) tagSNP set for swine was developed concurrent to this study and an average accuracy of imputation of 0.951 based on these tagSNP was estimated. Construction of a haplotype reference panel was most efficient when these haplotypes were obtained from randomly sampled individuals. Increasing the size of the original reference haplotype panel (128 haplotypes sampled from 32 sire/dam/offspring trios phased in a previous study) led to an overall increase in imputation accuracy (IA = 0.97 with 512 haplotypes), but was especially useful in increasing imputation accuracy of SNP with MAF below 0.1 and for SNP located in the chromosomal extremes (within 5% of chromosome end).Conclusion: The new commercially available 9K tagSNP set can be used to obtain imputed genotypes with high accuracy, even when imputation is based on a comparably small panel of reference haplotypes (128 haplotypes). Average imputation accuracy can be further increased by adding haplotypes to the reference panel. In addition, our results show that randomly sampling individuals to genotype for the construction of a reference haplotype panel is more cost efficient than specifically sampling older animals or trios with no observed loss in imputation accuracy. We expect that the use of imputed genotypes in swine breeding will yield highly accurate predictions of GEBV, based on the observed accuracy and reported results in dairy cattle, where genomic evaluation of some individuals is based on genotypes imputed with the same accuracy as our Yorkshire population. © 2013 Steibel et al.; licensee BioMed Central Ltd. Source

Yoder C.L.,Iowa State University | Schwab C.R.,The Maschhoffs | Fix J.S.,National Swine Registry | Duttlinger V.M.,Tempel Genetics | Baas T.J.,Iowa State University
Livestock Science

Daily feed intake during lactation was recorded on purebred Yorkshire (n=1587), Landrace (n=2197), and F1 Yorkshire x Landrace (n=6932) litters from day 1 to 22 of lactation. Lactation feed intake (LFI) curves were predicted using a mixed model which included fixed effects of breed, season, parity group (PG), day of lactation, interactions of day with breed and PG, and a covariate for litter size after cross-fostering. Random effects included litter, contemporary group (herd-year-month), dam, and sire nested within breed. Least squares means for each day were used to express LFI curves by breed through day 22 of lactation. Yorkshire and Landrace LFI curves were not different (P=0.09), though both differed from the LFI curve (P<0.05) of F1 sows. Due to a limited number of observations in late lactation, LFI data from days 19 to 22 were not included. Evaluation of the difference in feed intake between 2 consecutive days (DC) of lactation resulted in the following classifications: 3 periods for purebreds, day 1 to 6 (PB1), day 7 to 10 (PB2), and day 11 to 18 (PB3); 2 periods for F1 sows, day 1-5 (C1) and day 6-18 (C2). Average rate of change in intake (ARC), average daily intake (ADI), and variation from predicted LFI values (VAR) metrics were estimated for each period in purebred and F1 sows. Parity group 1 in both purebred and F1 sows had the lowest ARC and ADI metrics, but highest VAR (P<0.05) in each period of lactation. Similar differences were observed for seasonal effects (P<0.05) as LFI curves during summer months represented lower ARC and ADI and higher VAR values compared to all other seasons. For all breeds, increased ARC and ADI metrics resulted in higher 21-day litter weaning weights (P<0.05), while decreasing VAR metrics late in lactation (PB3 and C2) resulted in higher 21-day litter weaning weights and shorter wean-to-first service intervals (P<0.05). Average rate of change increased more quickly in early periods (PB1, PB2, C1) and was lower in late lactation (PB3, C2). An increase in average rate of change in intake, average daily intake, and decreased variation from predicted LFI values during a period of lactation resulted in improved measures of maternal performance. © 2012 Elsevier B.V. Source

Badke Y.M.,Michigan State University | Bates R.O.,Michigan State University | Ernst C.W.,Michigan State University | Schwab C.,National Swine Registry | Steibel J.P.,Michigan State University
BMC Genomics

Background: The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent and degree of LD is essential. The objective of this study is to estimate LD in four US breeds of pigs (Duroc, Hampshire, Landrace, and Yorkshire) and subsequently calculate persistence of phase among them using a 60 k SNP panel. In addition, we report LD when using only a fraction of the available markers, to estimate persistence of LD over distance.Results: Average r 2between adjacent SNP across all chromosomes was 0.36 for Landrace, 0.39 for Yorkshire, 0.44 for Hampshire and 0.46 for Duroc. For markers 1 Mb apart, r 2ranged from 0.15 for Landrace to 0.20 for Hampshire. Reducing the marker panel to 10% of its original density, average r 2ranged between 0.20 for Landrace to 0.25 for Duroc. We also estimated persistence of phase as a measure of prediction reliability of markers in one breed by those in another and found that markers less than 10 kb apart could be predicted with a maximal accuracy of 0.92 for Landrace with Yorkshire.Conclusions: Our estimates of LD, although in good agreement with previous reports, are more comprehensive and based on a larger panel of markers. Our estimates also confirmed earlier findings reporting higher LD in pigs than in American Holstein cattle, especially at increasing marker distances (> 1 Mb). High average LD (r 2> 0.4) between adjacent SNP found in this study is an important precursor for the implementation of marker assisted selection within a livestock species.Results of this study are relevant to the US purebred pig industry and critical for the design of programs of whole genome marker assisted evaluation and selection. In addition, results indicate that a more cost efficient implementation of marker assisted selection using low density panels with genotype imputation, would be feasible for these breeds. © 2012 Badke et al; licensee BioMed Central Ltd. Source

Cutshaw R.L.,Purdue University | Schinckel A.P.,Purdue University | Schultz M.M.,Purdue University | Fix J.S.,National Swine Registry | And 2 more authors.
Professional Animal Scientist

The purpose of this study was to evaluate the extent how performance traits in purebred pigs, including days to 113.4 kg (D113), ultrasound backfat depth (BF), and loin muscle area (LMA), are affected by variation in birth weight (BTW) and weaning weight (WW). Data consisted of BTW and WW records (Duroc, n = 26,260; Landrace, n = 31,209; Yorkshire, n = 53,037), and off-test records (Duroc, n = 10,103; Landrace, n = 9,478; Yorkshire, n = 18,647). Mean piglet BTW and WW decreased as total born and number weaned increased (P < 0.05). Models included significant effects of parity, sex, farm, and random effects of contemporary group and sow. Covariates of BTW, BTW2, WW, and WW2 were included to evaluate their effects. Mean D113 for pigs from parity 1 dams were 2 to 3 d greater than pigs from parity 2 and 3 dams (P < 0.05). However, when BTW and WW were included as covariates to the model, D113 was not different for pigs from parity 1 dams versus older sows. Birth weight (linear and quadratic) and WW (linear and quadratic) accounted for approximately 20% of the residual variance in D113 within each breed. Backfat depth and LMA were affected (P < 0.05) by BTW and WW. However, inclusion of BF and LMA as covariates in the models produced only small reductions in residual variances. Pigs with lighter BTW and WW, are more common in parity 1 litters and large litters and had poorer postweaning growth, BF, and LMA than heavier pigs at birth and weaning. © 2014 American Registry of Professional Animal Scientists. Source

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