Predictive markers in calpastatin for tenderness in commercial pig populations

The identification of predictive DNA markers for pork quality would allow US pork producers and breeders to select genetically superior animals more quickly and efficiently for the production of consistent, high-quality meat. Genome scans have identified QTL for tenderness on SSC 2, which have been fine-mapped to the calpastatin locus. The objectives of this study were to identify the sequence variation in calpastatin that likely affects tenderness in commercial-level pig populations and to develop definitive DNA markers that are predictive of pork tenderness for use in marker-assisted selection programs. We resequenced the calpastatin regulatory and transcribed regions in pigs with divergently extreme shear force values to identify possible mutations that could affect tenderness. A total of 194 SNP were identified in this sequence, and 31 SNP were found in predicted transcription factor binding sites. We tested 131 polymorphisms in our research population and a subset (40) of these in samples of industry pigs for their association with objective measures of tenderness. We identified 4 SNP that were consistently associated with pork tenderness in all the populations studied, representing 2,826 pigs from 4 distinct populations. Gel shift assays were designed for these SNP and 12 other polymorphic sites. Six sites demonstrated a gel shift when probes were incubated with nuclear extract from muscle, heart, or testis. Four of these sites, a specificity protein 1 (Sp1) site around nucleotides 12978 and 12979, a potential thyrotroph embryonic factor (Tef) site at nucleotide 25587, an unknown site at nucleotide 48699, and myocyte enhancer factor-2 (Mef-2)/TATA sites with SNP at positions 49223 and 49228 were allele specific in binding nuclear proteins. The allele frequencies for the tender alleles were similar (0.11 to 0.36) in the 4 different commercial populations. These 4 SNP were not in complete linkage disequilibrium with each other and may independently affect calpastatin expression, tenderness, or both. These markers should be predictive of pork tenderness in industry populations.

Fine-mapping quantitative trait loci for twinning rate on Bos taurus chromosome 14 in North American Holsteins

A previous genome-wide search with a moderate-density 10,000-SNP set identified many marker associations with twinning rate on BTA14 through either single-marker analysis or combined linkage-linkage disequilibrium (LLD; haplotype) analysis. The objective of the current study was to fine-map putative QTL using a more densely populated marker map and both a larger and an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half-sib families were genotyped for 129 SNP markers that included both original and additionally selected markers for increasing marker density in the targeted 34 megabase region. Twinning rate predicted transmitting abilities were calculated using calving records from 1994 to 1998 (data I) and 1999 to 2006 (data II), and the underlying liability scores from threshold model analysis were used as the trait in marker association analyses. The previous analysis used 201 bulls with daughter records in data I. In the current analysis, this was increased to 434, providing a revised estimate of effect and significance. Bulls with daughter records in data II totaled 851, and analysis of these data provided an opportunity for an independent analysis separate from data I. Single-marker association and LLD analyses were performed. Fifteen significant single-marker associations were found (minimally exceeding P < 8.74 x 10(-3)) to concur between data sets. Three and 12 regions in data I and data II, respectively, showed positive results for the presence of QTL from LLD analysis (P < 0.001) within the respective data sets. After combining results from single-marker association, LLD analysis, and model-building strategies, 3 QTL were identified on BTA14. Based on single-marker results from data II, BTA14 harbors QTL responsible for approximately 24% of the variation in twinning rate predicted transmitting ability.

Validation of whole genome linkage-linkage disequilibrium and association results, and identification of markers to predict genetic merit for twinning

A previous genome-wide search with a moderate density 10K marker set identified many marker associations with twinning rate, either through single-marker analysis or combined linkage-linkage disequilibrium (LLD; haplotype) analysis. The objective of the current study was to validate putative marker associations using an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half-sib families were genotyped. Twinning rate predicted transmitting abilities were calculated using calving records from 1994 to 1998 (Data I) and 1999 to 2006 (Data II), and the underlying liability scores from threshold model analysis were used as the trait in marker association analyses. The previous analysis used 201 bulls with daughter records in Data I. In the current analysis, this was increased to 434, providing a revised estimate of effect and significance. Bulls with daughter records in Data II totaled 851, and analysis of this data provided the validation of results from analysis of Data I. Single nucleotide polymorphisms (SNPs) were selected to validate previously significant single-marker associations and LLD results. Bulls were genotyped for a total of 306 markers. Nine of 13 LLD regions located on chromosomes 1, 2, 3, 6, 9, 22, 23(2) and 26 were validated, showing significant results for both Data I and II. Association analysis revealed 55 of 174 markers validated, equating to a single-marker validation rate of 31%. Stepwise backward elimination and cross-validation analyses identified 18 SNPs for use in a final reduced marker panel explaining 34% of the genetic variation, and to allow prediction of genetic merit for twinning rate.

146 RELOCATION OF SWINE GENETICS USING EMBRYO TRANSFER

Swine production requires a stable health status that can be compromised by introduction of live animals for genetic change. Our objective was to use embryo transfer to avoid disease transmission during genetic relocation. Forty genotype-specific (GS) donor females were scheduled for 3 sessions of embryo recovery at 6-week intervals using Altrenogest (Matrix®, Intervet, Millsboro, DE), 1250 IU of equine chorionic gonadotropin (eCG/PMSG; Sigma, St. Louis, MO) and 750 IU of human chorionic gonadotropin (hCG; Chorulon®, Intervet). Single-sire GS matings were made 34 h after Chorulon® injection. To accomplish single-sire transfers, color specific (CS) supplemental embryos were used to assist in maintenance of recipient pregnancy. The CS embryo donors and GS embryo recipients were synchronized with Matrix®, P.G. 600® (200 IU hCG, 400 IU PMSG, Intervet) and Chorulon®. Embryos from GS donors were surgically recovered on Day 5 post-insemination, washed per IETS recommendations using a zwitterion-buffered culture medium (PorcPro E-Blast, Minitube of America, Verona, WI) and transported in a portable incubator (Minitube of America) 2.5 h to the recipient herd. Embryos were surgically transferred into –24-h asynchronous recipients within 6 to 14 h after recovery. A total of 620 embryos were recovered from 65.2% (60/92) of GS matings, and 587 (59.4%) GS and 402 (40.6%) CS embryos were transferred into 63 recipients. On average, 9.3 GS and 6.4 CS embryos were transferred per recipient (15.7). A total of 33 GS embryos were discarded before transfer. To achieve a target of 17 embryos per transfer, 59 embryo transfers required CS embryos and 4 embryo transfers were only GS embryos. Fifty-three (84.1%) recipients were confirmed pregnant by ultrasound at 35 days of gestation. Of the 40 GS donors, one was culled for genetic reasons, 6 did not give transferable embryos, and 1 gave transferable embryos but the corresponding recipient returned to estrus for a total genetic transfer rate of 80% (32/40). After 3 sessions of embryo transfer, 32/33 (97%) GS donors that produced embryos for transfer were represented by a minimum of 1 pregnant recipient at 35 days of gestation; 17/32 GS donors were represented by a single pregnancy and 15/32 by multiple pregnancies. Sera from GS donors were evaluated for porcine reproductive and respiratory syndrome (PRRSV) and porcine circovirus type 2 (PCV2) before each embryo recovery session. Serology results were negative for PRRS (0/98)) and positive for PCV2 in 27.5% (27/98) of GS donors. Embryo wash media from the last 2 washes from PCV2 positive GS donors producing embryos for transfer were pooled and evaluated for PCV2 after transfer; all samples (0/18) were negative for PCV2. In summary, zona pellucida-intact embryos were successfully used to relocate swine genetics from a donor herd into a recipient herd with no apparent health status change in the recipient herd.