Estimation of inbreeding and effective population size of full-blood Wagyu cattle registered with the American Wagyu Cattle Association

The objective of this research was to examine the population structure of full-blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full-blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST ) and the effective population size (Ne ) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full-blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH ) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH ) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full-blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.

Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform

Advances in high-throughput genotyping technologies have afforded researchers the opportunity to study ever-increasing numbers of SNP in animal genomes. However, many studies encounter difficulties in obtaining sufficient quantities of high-quality DNA for such analyses, particularly when the source biological material is limited or degraded. The recent development of in vitro whole-genome amplification approaches has permitted researchers to circumvent these challenges by increasing the amount of usable DNA in normally small-quantity samples. Here, we assess the performance of whole-genome amplification products generated from ovine genomic DNA using a high-throughput SNP genotyping platform, the newly developed Illumina ovineSNP50 BeadChip. Our results demonstrate a high genotype call rate for conventional genomic DNA and whole-genome amplified genomic DNA. The data also reveal an exceptionally high concordance rate ( > or = 99%) between the genotypes generated from whole-genome amplified products and their conventional genomic DNA counterparts. This study supports the use of whole-genome amplification as a viable solution for the analysis of high-density SNP genotypic data using compromised or limited starting material.

48 PREGNANCY AND FETAL CHARACTERISTICS AFTER TRANSFER OF VITRIFIED IN VIVO AND CLONED BOVINE EMBRYOS

This study was conducted to examine pregnancy progression and fetal characteristics following transfer of vitrified bovine nuclear transfer (NT) vs. in vivo-derived (Vivo) embryos. Nuclear transfer was conducted using skin fibroblast cells derived from cultured ear explants taken from an elite Holstein-Friesian dairy cow. Expanding and hatching blastocysts on Day 7 were vitrified using liquid nitrogen surface vitrification (Shen et al. 2004 Reprod. Fertil. Dev. 16, 158). Day 7 in vivo embryos, produced using standard superovulation procedures applied to Holstein-Friesian heifers (n = 6), were vitrified in the same way. Following warming, embryos were transferred to synchronized recipients (2 per recipient; NT: n = 81 recipients; Vivo: n = 20 recipients). Pregnancies were monitored by ultrasound scanning on Days 25, 45, and 75, and a sample of animals was slaughtered at each time point to recover the fetus/placenta for further analyses. On Day 25, the entire conceptus was weighed together; on Day 45, the fetus and placenta were weighed separately; on Day 75, the fetus was dissected and the major organs were weighed. Significantly more animals remained pregnant after transfer of in vivo-derived embryos than NT embryos at all time points: Day 25 (95.0 vs. 61.7%, P < 0.01), Day 45 (93.3 vs. 39.7%, P < 0.001), and Day 75 (90.9 vs. 19.8%, P < 0.001). There was no significant difference (P = 0.10) in the weight of the conceptus on Day 25 from NT transfers (1.14 ± 0.23 g, n = 8) vs. Vivo transfers (0.75 ± 0.19 g, n = 8). On Day 45, there was no significant difference in the weight of either fetus (P = 0.393) or membranes (P = 0.167) between NT embryos (fetus: 2.76 ± 0.40 g, n = 12; membranes 59.0 ± 10.0 g, n = 11) or in vivo-derived embryos (fetus: 2.60 ± 0.15 g, n = 6; membranes 41.8 ± 5.2 g, n = 4). However, on Day 75, the weights of the fetus and several of the major organs were heavier from NT embryos (Table 1). These data suggest that the large calf syndrome is manifested after Day 45. Table 1. Fetal characteristics on Day 75 of gestation following transfer of vitrified in vivo-derived vs. NT blastocysts This work was supported by the U.S. Department of Agriculture.