Metastable monoclinic [110] layered perovskite Dy2Ti2O7 thin films for ferroelectric applications.

Using the Combinatorial Substrate Epitaxy (CSE) approach, we report the stabilization of Dy2Ti2O7 epitaxial monoclinic, layered-perovskite phase Dy2Ti2O7 thin films. To achieve this, the films are deposited on high density, polished La2Ti2O7 polycrystalline ceramic substrates, which are stable as monoclinic layered-perovskites, and were prepared by conventional sintering. Microstructural analysis using electron backscatter diffraction (EBSD), electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM) support this observation. Further, they reveal that the cubic pyrochlore phase is observed far from the interface as films are grown thicker (100 nm), confirming the importance of substrate-induced phase and space group selection. This works reinforces the vast potential of CSE to promote the stabilization of metastable phases, thus giving access to new functional oxide materials, across a range of novel material systems including ferroelectrics.

Porcine single nucleotide polymorphisms and their functional effect: an update.

OBJECTIVE: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. RESULTS: A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies.

A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome.

Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits. Whole-genome sequence was obtained from 72 of the founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace) and 48 Yorkshire-Landrace composite sows. Sequence reads were mapped to the Sscrofa10.2 genome build, resulting in a mean of 6.1 fold (×) coverage per genome. A total of 22 342 915 high confidence SNPs were identified from the sequenced genomes. These included 21 million previously reported SNPs and 79% of the 62 163 SNPs on the PorcineSNP60 BeadChip assay. Variation was detected in the coding sequence or untranslated regions (UTRs) of 87.8% of the genes in the porcine genome: loss-of-function variants were predicted in 504 genes, 10 202 genes contained nonsynonymous variants, 10 773 had variation in UTRs and 13 010 genes contained synonymous variants. Approximately 139 000 SNPs were classified as loss-of-function, nonsynonymous or regulatory, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of functional SNPs during future analyses.

Plasma concentrations of acyl-ghrelin are associated with average daily gain and feeding behavior in grow-finish pigs.

The objectives of this study were to determine the effect of sex, sire line, and litter size on concentrations of acyl-ghrelin and total ghrelin in plasma of grow-finish pigs and to understand the relationship of plasma concentrations of ghrelin with feeding behavior, average daily gain (ADG), and back fat in grow-finish swine. Yorkshire-Landrace crossbred dams were inseminated with semen from Yorkshire, Landrace, or Duroc sires. Within 24 h of birth, pigs were cross-fostered into litter sizes of normal (N; >12 pigs/litter) or small (S; ≤ 9 pigs/litter). At 8 wk of age, pigs (n = 240) were blocked by sire breed, sex, and litter size and assigned to pens (n = 6) containing commercial feeders modified with a system to monitor feeding behavior. Total time eating, number of daily meals, and duration of meals were recorded for each individual pig. Body weight was recorded every 4 wk. Back fat and loin eye area were recorded at the conclusion of the 12-wk feeding study. A blood sample was collected at week 7 of the study to quantify concentrations of acyl- and total ghrelin in plasma. Pigs from small litters weighed more (P < 0.05) and tended (P = 0.07) to be fatter than pigs from normal litters. Postnatal litter size did not affect ADG, feeding behavior, or concentrations of ghrelin in plasma during the grow-finish phase. Barrows spent more time eating (P < 0.001) than gilts, but the number of meals and concentrations of ghrelin did not differ with sex of the pig. Pigs from Duroc and Yorkshire sires had lesser (P < 0.0001) concentrations of acyl-ghrelin than pigs from Landrace sires, but plasma concentrations of total ghrelin were not affected by sire breed. Concentrations of acyl-ghrelin were positively correlated with the number of meals and negatively correlated with meal length and ADG (P < 0.05). A larger number of short-duration meals may indicate that pigs with greater concentrations of acyl-ghrelin consumed less total feed, which likely explains why they were leaner and grew more slowly. Acyl-ghrelin is involved in regulating feeding behavior in pigs, and measuring acyl-ghrelin is important when trying to understand the role of this hormone in swine physiology.

Litter-of-origin trait effects on gilt development.

The preweaning litter environment of gilts can affect subsequent development. In a recent experiment designed to test the effects of diet on gilt development, litter-of-origin traits including individual birth weights, immunocrits (a measure of colostrum intake), sow parity, number weaned, and individual weaning weights were collected for approximately 1,200 gilts that were progeny of approximately 300 sows. Subsequently, BW, LM area, and backfat were measured at 100 d of age and at 28-d intervals until slaughter (260 d of age). From 160 d of age to slaughter, gilts were observed daily for estrus. At slaughter, the reproductive tract and 1 mammary gland were recovered. The reproductive tract was classified as cyclic or prepubertal; the number of corpora lutea was counted. Uterine horn lengths and ovarian dimensions were measured. Uterus and ovary samples from every 10th gilt were prepared for histological evaluation of uterine gland development and follicle counts, respectively. Mammary gland tissue protein and fat were assayed. Day of the estrous cycle at slaughter was calculated using the first day of the most recent standing estrus (d 0) recorded previous to slaughter. Each gilt development trait was analyzed for association with each litter-of-origin trait, after adjusting for dietary treatment effects. Uterine length, ovarian dimensions, mammary gland protein and fat, and uterine gland development were also adjusted for day of the estrous cycle at slaughter. All litter-of-origin traits were associated ( < 0.05) with growth traits. Top-down (backward elimination) multiple regression analysis indicated that BW and LM accretion in gilts was positively associated with immunocrit ( < 0.01), birth weight ( < 0.01), preweaning growth rate ( < 0.01), and parity ( < 0.01). Backfat accretion was positively associated with preweaning growth rate ( < 0.01), number weaned ( < 0.05), and parity ( < 0.05). Age at puberty was associated with birth weight (positive; < 0.01) and preweaning growth rate (negative; < 0.01). Total uterine length was positively associated with only birth weights ( < 0.05). Mammary gland protein was negatively associated with preweaning growth ( < 0.01). Mammary gland fat was positively associated with birth weight and number of piglets weaned ( > 0.05). These results indicate that colostrum consumption, birth weights, preweaning growth rate, number weaned, and parity are associated with gilt development traits during later life.

Meta-analysis of genome-wide association from genomic prediction models.

Genome-wide association (GWA) studies based on GBLUP models are a common practice in animal breeding. However, effect sizes of GWA tests are small, requiring larger sample sizes to enhance power of detection of rare variants. Because of difficulties in increasing sample size in animal populations, one alternative is to implement a meta-analysis (MA), combining information and results from independent GWA studies. Although this methodology has been used widely in human genetics, implementation in animal breeding has been limited. Thus, we present methods to implement a MA of GWA, describing the proper approach to compute weights derived from multiple genomic evaluations based on animal-centric GBLUP models. Application to real datasets shows that MA increases power of detection of associations in comparison with population-level GWA, allowing for population structure and heterogeneity of variance components across populations to be accounted for. Another advantage of MA is that it does not require access to genotype data that is required for a joint analysis. Scripts related to the implementation of this approach, which consider the strength of association as well as the sign, are distributed and thus account for heterogeneity in association phase between QTL and SNPs. Thus, MA of GWA is an attractive alternative to summarizing results from multiple genomic studies, avoiding restrictions with genotype data sharing, definition of fixed effects and different scales of measurement of evaluated traits.

Implementing meta-analysis from genome-wide association studies for pork quality traits.

Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.

Age at puberty, ovulation rate, and uterine length of developing gilts fed two lysine and three metabolizable energy concentrations from 100 to 260 d of age.

The objective of this study was to determine the effect of ad libitum feeding diets differing in standard ileal digestible (SID) lysine and ME concentrations that bracket those fed to developing gilts in U.S. commercial settings. Average SID lysine and ME concentrations in diets currently fed to developing gilts were obtained from a poll of the U.S. commercial swine industry. Crossbred Large White × Landrace gilts (n = 1,221), housed in groups, were randomly allotted to 6 corn-soybean diets in a 2 × 3 factorial arrangement formulated to provided 2 SID lysine and 3 ME concentrations. Gilts received grower diets formulated to provide 1.02% (control = survey average) or 0.86% (control minus 15%) SID lysine and 2.94, 3.25, or 3.57 (survey average ME ± 10%) Mcal of ME/kg from 100 d of age until approximately 90 kg BW. Then, gilts were fed finisher diet containing 0.85% (control = survey average) or 0.73% (control minus 15%) SID lysine and 2.94, 3.26, or 3.59 (control ± 10%) Mcal of ME/kg until 260 d of age. Gilts were weighed, and backfat thickness and loin muscle area were recorded at the beginning of the trial and then every 28 d. Starting at 160 d of age, gilts were exposed daily to vasectomized boars and observed for behavioral estrus. At approximately 260 d of age, gilts were slaughtered and their reproductive tract was collected. Each reproductive tract was examined to determine whether the gilt was cyclic, the stage of estrus cycle, ovulation rate, and uterine length. Data were evaluated for normality and analyzed using mixed model methods. Average age at puberty was 193 d of age with a range from 160 to 265 d. When all gilts on trial at 160 d of age were included in the analysis, 91.0% reached puberty as determine by observation of standing estrus. Differences between dietary treatments on age at puberty or measurements of the reproductive tract were not detected. Growth rates to 160 d were not limiting for attainment of puberty in response to daily boar stimulation from 160 d.

Genomewide association analysis for average birth interval and stillbirth in swine.

Reproductive efficiency has a great impact on the economic success of pork production. Stillborn pigs and average birth interval contribute to the number of pigs born alive in a litter. To better understand the underlying genetics of these traits, a genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 798 females farrowing over a 4-yr period (all first parity). Birth intervals and piglet birth status (stillborn or alive) were determined by videotaping each farrowing event. A total of 41,148 SNP were tested using the Bayes C option of GenSel (version 4.61) and 1-Mb windows. These 1-Mb windows explained proportions of 0.017, 0.002, 0.032, 0.029, and 0.030 of the total variation, respectively, for litter average birth interval after deletion of the last piglet born, last birth interval in the litter, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet. Significant 1-Mb nonoverlapping SNP windows were identified by using a conservative approach requiring 1-Mb windows to have a genetic variance ≥1.0% of genomic variance and these were considered to be QTL. Quantitative trait loci were located for number of stillborn piglets ignoring the last piglet born (1 QTL), number of stillborns in the last birth position (1 QTL), and percent stillborn ignoring the last piglet (3 QTL). In addition, 2, 13, 3, and 6 suggestive 1-Mb nonoverlapping SNP windows were identified for litter average birth interval after deletion of the last piglet born, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet, respectively. Possible candidate genes affecting both birth interval and stillbirth included () and (). Possible genes affecting only birth interval included (), and (), and those affecting only stillbirth included (), LOC100518697 (a nostrin-like gene), and (). The QTL and the suggestive 1-Mb nonoverlapping SNP windows may lead to genetic markers for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.

Genomewide association and identification of candidate genes for ovulation rate in swine.

Reproductive efficiency has a great impact on the economic success of pork production. Ovulation rate is an early component of reproduction efficiency and contributes to the number of pigs born in a litter. To better understand the underlying genetics of ovulation rate, a genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 1,180 females with ovulation measurements ranging from never farrowed to measurements taken after parity 2. A total of 41,848 SNP were tested using the Bayes C option of GenSel. After the Bayes C analysis, SNP were assigned to sliding windows of 5 consecutive SNP by chromosome-position order beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on SSCX. The 5-SNP windows were analyzed using the Predict option of GenSel. From the Predict analysis, putative QTL were selected having no overlap with other 5-SNP window groups, no overlap across chromosomes, and the highest genetic variation. These putative QTL were submitted to statistical testing using the bootstrap option of GenSel. Of the putative QTL tested, 80 were found to be statistically significant (P < 0.01). Ten QTL were found on SSC1, 12 on SSC2, 4 on SSC3, 8 on SSC4, 3 on SSC5, 3 on SSC6, 3 on SSC7, 4 on SSC8, 2 on SSC9, 4 on SSC10, 1 on SSC12, 4 on SSC13, 2 on SSC14, 4 on SSC15, 4 on SSC16, 6 on SSC17, 4 on SSC18, and 1 on SSCX. Sixteen QTL were found to be statistically significant at the P < 0.001 level. Six additional QTL were significant at the P = 0.001 level. These 22 QTL accounted for 71.10% of the total genetic variance. The most compelling candidate genes in these regions include Estrogen receptor 1, growth differentiation factor 9, and inhibin ßA. These QTL, when combined with information on genes found in the same regions, should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.

Identifying genetic loci controlling neonatal passive transfer of immunity using a hybrid genotyping strategy.

Colostrum intake is critical to a piglet's survival and can be measured by precipitating out the γ-immunoglobulins from serum with ammonium sulfate (immunocrit). Genetic analysis of immunocrits on 5312 piglets indicated that the heritabilities (se) for direct and maternal effects were 0.13 (0.06) and 0.53 (0.08) respectively. To identify QTL for direct genetic effects, piglets with the highest and lowest immunocrits from 470 litters were selected. Six sets of DNA pools were created based on sire of the litter. These 12 DNA pools were applied to Illumina Porcine SNP60 BeadChips. Normalized X and Y values were analyzed. Three different SNP selection methods were used: deviation of the mean from high vs. low pools, the deviation adjusted for variance based on binomial theory and ANOVA. The 25 highest ranking SNPs were selected from each evaluation for further study along with 12 regions selected based on a five-SNP window approach. Selected SNPs were individually genotyped in the 988 piglets included in pools as well as in 524 piglets that had intermediate immunocrits. Association analyses were conducted fitting an animal model using the estimated genetic parameters. Nineteen SNPs were nominally associated (P < 0.01) with immunocrit values, of which nine remained significant (P < 0.05) after Bonferroni correction, located in 16 genomic regions on 13 chromosomes. In conclusion, the pooling strategy reduced the cost to scan the genome by more than 80% and identified genomic regions associated with a piglet's ability to acquire γ-immunoglobulin from colostrum. Each method to rank SNPs from the pooled analyses contributed unique validated markers, suggesting that multiple analyses will reveal more QTL than a single analysis.

Impact of genetic drift on access and benefit sharing under the Nagoya Protocol: the case of the Meishan pig.

Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berkshire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confirmed divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational.

Genome-wide association with delayed puberty in swine.

An improvement in the proportion of gilts entering the herd that farrow a litter would increase overall herd performance and profitability. A significant proportion (10-30%) of gilts that enter the herd never farrow a litter; reproductive reasons account for approximately a third of gilt removals, with anestrous and failure to conceive the most common reasons for culling. Tools to select gilts for reproductive longevity through genomics or alternative phenotypes would be of great benefit to the producer. Ninety-one gilts that failed to display behavioral estrus by 240 days (cases) and 127 pubertal littermates (controls) were genotyped with the Illumina Porcine SNP60 Beadchip. One hundred and seventy-four SNPs with the most significant associations were genotyped in an additional 86 cases and 103 controls. Twelve of these associations were significant in the final analysis. The most significant (P < 1.5 × 10(-14) ) region associated with failure to attain puberty was on chromosome 4 surrounding the NHLH2 gene. Delayed pubertal development and age at first estrus have been associated with NHLH2 in mice. Because attainment of puberty is a complex trait, identifying genes that affect pubertal age would greatly contribute to our knowledge of reproductive development as well as overall fertility.

Genome-wide association of meat quality traits and tenderness in swine.

Pork quality has a large impact on consumer preference and perception of eating quality. A genome-wide association was performed for pork quality traits [intramuscular fat (IMF)], slice shear force (SSF), color attributes, purge, cooking loss, and pH] from 531 to 1,237 records on barrows and gilts of a Landrace-Duroc-Yorkshire population using the Illumina PorcineSNP60 BeadChip. Associations were detected using MTDFREML for all traits. Intramuscular fat had the greatest number of SNP associations, followed by pH, purge, cooking loss, shear force, and color. Two regions contained associations for multiple traits; one on SSC1 at 255 Mb near calcineurin subunit B (PPP3R2) was associated with SSF, moisture loss, and pH, and one on SSC6 from 28 to 29.5 Mb for purge and IMF containing the candidate genes glucose-6-phosphate isomerase (GPI) and KCTD15. Some of the other compelling candidate genes in regions associated with meat quality include CEBPA, SNAI1, and FAM132A for IMF, CAPN1 for SSF, GLUL for pH, and PRKAG3 and ITGB1 with cooking loss.

Grain boundary character distribution of nanocrystalline Cu thin films using stereological analysis of transmission electron microscope orientation maps.

Stereological analysis has been coupled with transmission electron microscope (TEM) orientation mapping to investigate the grain boundary character distribution in nanocrystalline copper thin films. The use of the nanosized (<5 nm) beam in the TEM for collecting spot diffraction patterns renders an order of magnitude improvement in spatial resolution compared to the analysis of electron backscatter diffraction patterns in the scanning electron microscope. Electron beam precession is used to reduce dynamical effects and increase the reliability of orientation solutions. The misorientation distribution function shows a strong misorientation texture with a peak at 60°/[111], corresponding to the Σ3 misorientation. The grain boundary plane distribution shows {111} as the most frequently occurring plane, indicating a significant population of coherent twin boundaries. This study demonstrates the use of nanoscale orientation mapping in the TEM to quantify the five-parameter grain boundary distribution in nanocrystalline materials.

Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs.

Numerous reports have described genetic markers or genomic regions (QTL) associated with pork quality and/or palatability but few validation studies have been reported. Therefore, 156 SNP markers from 45 candidate genes and eight QTL regions were analyzed for association with pork quality and palatability traits from 888 pork loins. Loins were collected at three slaughter facilities and selected to represent a wide range of pork color, pH and marbling. Phenotypic data recorded included objective and subjective measures of color and marbling, purge loss, shear force, and cooking loss. Data were analyzed with SAS PROC MIXED where loin was fit as a random effect. Results indicated some of the markers tested should be useful in industry, while others are not segregating in all populations or linkage disequilibrium between markers and causative genetic variation fluctuates among populations limiting their universal utility. Genes with the largest effects on pork quality were MC4R, IGF2, CAST and PRKAG3.

Genome-wide association study of swine farrowing traits. Part I: genetic and genomic parameter estimates.

The primary objective of this study was to determine genetic and genomic parameters among swine (Sus scrofa) farrowing traits. Genetic parameters were obtained using MTDFREML. Genomic parameters were obtained using GENSEL. Genetic and residual variances obtained from MTDFREML were used as priors for the Bayes C analysis of GENSEL. Farrowing traits included total number born (TNB), number born alive (NBA), number born dead (NBD), number stillborn (NSB), number of mummies (MUM), litter birth weight (LBW), and average piglet birth weight (ABW). Statistically significant heritabilities included TNB (0.09, P = 0.048), NBA (0.09, P = 0.041), LBW (0.20, P = 0.002), and ABW (0.26, P < 0.0001). Statistically significant genetic correlations included TNB-NBA (0.97, P < 0.0001), TNB-LBW (0.74, P < 0.0001), NBA-LBW (0.56, P < 0.0017), NSB-LBW (0.87, P < 0.0395), and LBW-ABW (0.63, P < 0.0002). Genetic parameters are similar to others found in the literature. The proportion of phenotypic variance explained by genomic markers (GP) generated by GENSEL was TNB (0.04), NBA (0.06), NBD (0.00), NSB (0.01), MUM (0.00), LBW (0.11), and ABW (0.31). Limited information is available in the literature about genomic parameters. Only the GP estimate for NSB is significantly lower than what has been published. The GP estimate for ABW is greater than the estimate for heritability found in this study. Other traits with significant heritability had GP estimates half the value of heritability. This research indicates that significant genetic markers will be found for TNB, NBA, LBW, and ABW that will have either immediate use in industry or provide a roadmap to further research with fine mapping or sequencing of areas of significance. Furthermore, these results indicate that genomic selection implemented at an early age would have similar annual progress as traditional selection, and could be incorporated along with traditional selection procedures to improve genetic progress of litter traits.

Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data.

Reproductive efficiency has a great impact on the economic success of pork (sus scrofa) production. Number born alive (NBA) and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of birth traits, a genome-wide association study (GWAS) was undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip from 1,152 first parity gilts. Traits included total number born (TNB), NBA, number born dead (NBD), number stillborn (NSB), number of mummies (MUM), total litter birth weight (LBW), and ABW. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. From that analysis, 5-SNP groups were selected having no overlap with another 5-SNP groups and no overlap across chromosomes. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. Eleven QTL were found for TNB, 3 on SSC1, 3 on SSC4, 1 on SSC13, 1 on SSC14, 2 on SSC15, and 1 on SSC17. Statistical testing for NBA identified 14 QTL, 4 on SSC1, 1 on SSC4, 1 on SSC6, 1 on SSC10, 1on SSC13, 3 on SSC15, and 3 on SSC17. A single NBD QTL was found on SSC11. No QTL were identified for NSB or MUM. Thirty-three QTL were found for LBW, 3 on SSC1, 1 on SSC2, 1 on SSC3, 5 on SSC4, 2 on SSC5, 5 on SSC6, 3 on SSC7, 2 on SSC9, 1 on SSC10, 2 on SSC14, 6 on SSC15, and 2 on SSC17. A total of 65 QTL were found for ABW, 9 on SSC1, 3 on SSC2, 9 on SSC5, 5 on SSC6, 1 on SSC7, 2 on SSC8, 2 on SSC9, 3 on SSC10, 1 on SSC11, 3 on SSC12, 2 on SSC13, 8 on SSC14, 8 on SSC15, 1 on SSC17, and 8 on SSC18. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. These QTL when combined with information on genes found in the same regions should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.

Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace × Chinese-European crossbred population.

Several quantitative trait loci (QTL) for different meat quality traits have been localized on the q arm of porcine chromosome 2 at position 55-78 cM. Association analyses were performed in a commercial Landrace × Chinese-European (LCE) crossbred population (n = 446) slaughtered at approximately 127 kg and an average age of 198 days with records for performance (growth, fat and meat accretion) and meat quality [intramuscular fat (IMF), Minolta L*, Minolta a*, Minolta b* and pH at 45 m]. Polymorphisms within positional candidate genes cloned from homologous regions on human chromosome 19, ubiquitin-like 5 (UBL5- AM950288:g.566G>A), resistin (RETN- AM157180:g.1473A>G causing substitution p.Ala36Thr), insulin receptor (INSR- AM950289:g.589T>C) and complement factor D (adipsin) (CFD- AM950287:g. 306C>T) were located at positions 62.1, 64.0, 68.0 and 70.7 cM respectively on the current USDA USMARC map of porcine chromosome 2 and had the following allele frequencies in the LCE: UBL5 566G - 0.57; RETN 1473G - 0.84; INSR 589C - 0.70; and CFD 306C - 0.73. The effects of alleles within the candidate genes on the recorded traits were estimated using an animal model. Significant effects (P < 0.05) were found for pH(45) in m. semimembranosus (m. sm.) (UBL5), IMF (RETN) and Minolta L* (RETN, CFD). Differences between phenotypic means of homozygotes at UBL5, RETN and either RETN or CFD explained 0.34 SD for pH(45) in m. sm., 0.47 SD for IMF and 0.68 SD for Minolta L* respectively. Suggestive effects (P < 0.10) on IMF (UBL5, CFD), Minolta a* (INSR, CFD) and Minolta b* (INSR) were also observed. Our results support the localization of further QTL for meat quality traits in this region and suggest that there are several genes affecting different meat quality traits.