Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates

Abstract

BackgroundGenome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in cattle. However, the very small quantity of genomic DNA in biopsy material from early embryos poses daunting technical challenges. A reliable whole-genome amplification (WGA) procedure would greatly facilitate the procedure.ResultsSeveral PCR-based and non-PCR based WGA technologies, namely multiple displacement amplification, quasi-random primed library synthesis followed by PCR, ligation-mediated PCR, and single-primer isothermal amplification were tested in combination with different DNA extractions protocols for various quantities of genomic DNA inputs. The efficiency of each method was evaluated by comparing the genotypes obtained from 15 cultured cells (representative of an embryonic biopsy) to unamplified reference gDNA. The gDNA input, gDNA extraction method and amplification technology were all found to be critical for successful genome-wide genotyping. The selected WGA platform was then tested on embryo biopsies (n = 226), comparing their results to that of biopsies collected after birth. Although WGA inevitably leads to a random loss of information and to the introduction of erroneous genotypes, following genomic imputation the resulting genetic index of both sources of DNA were highly correlated (r = 0.99, P<0.001).ConclusionIt is possible to generate high-quality DNA in sufficient quantities for successful genome-wide genotyping starting from an early embryo biopsy. However, imputation from parental and population genotypes is a requirement for completing and correcting genotypic data. Judicious selection of the WGA platform, careful handling of the samples and genomic imputation together, make it possible to perform extremely reliable genomic evaluations for pre-transfer embryos.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-889) contains supplementary material, which is available to authorized users.

Potential of preimplantation genomic selection for carcass traits in Japanese Black cattle

“…Preimplantation genomic selection in cattle based on SNP genotypes is receiving increased attention as a means of accelerating genetic improvement by increasing selection pressure and avoiding the cost of producing genetically inferior animals [6, 19,20,21]. Although several groups have reported the potential of preimplantation genomic selection in dairy cattle [10, 11, 22,23,24], studies in Japanese Black cattle using this technique are limited. In the present study, we investigated the accuracy of GEBVs for carcass traits in preimplantation embryos derived from Japanese Black cattle.…”

“…[10] explored suitable WGA methodologies for SNP genotyping using biopsied embryonic cells (approximately 15 cells), and indicated that the illustra GenomiPhi V2 DNA amplification kit (GE Healthcare, MDA based method) produced the best results. Indeed, regarding the genetic value of the Lifetime Profit Index, their results showed an extremely high correlation (r = 0.99) between biopsied embryonic cells and the corresponding post-natal calves using the kit [10]. Correspondingly, we chose the illustra Single Cell GenomiPhi DNA Amplification Kit (GE Healthcare) for WGA in this study.…”

“…Therefore, whole-genome amplification (WGA) technology is necessary to amplify the input DNA prior to SNP genotyping. Several studies using dairy cattle have reported a high correlation between the genomic estimated breeding value (GEBV) of economic traits (such as Lifetime Profit Index and kilograms of milk protein) in biopsied embryonic cells processed for WGA and the corresponding factors in calves produced by ET [10, 11]. These findings demonstrated the effectiveness of WGA prior to SNP genotyping for accurate GEBV calculation and the possible application for a preimplantation genomic selection system in dairy cattle.…”

Production of calves by the transfer of cryopreserved bovine elongating conceptuses and possible application for preimplantation genomic selection

“…They also proposed in vitro culture of biopsied cells as a means of increasing the amount of DNA template and the reliability of genotyping. However, another researcher indicated that the cell culture approach is unacceptable from a commercial point of view because larger biopsies (20 to 30 cells) were required for successful cell proliferation in culture, leading to significant reduction in embryo viability [ 20 ]. The use of elongating conceptuses allows a large number of cells to be biopsied without any reduction in viability; therefore, we attempted to develop a genomic selection system by PGD combined with the elongating conceptus transfer technique.…”

Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

“…While it is possible to collect embryo biopsies for DNA genotyping without affecting the pregnancy rate of the embryos (Saadi et al, 2014), the IVP-ET efficiency is still relatively low and remains the bottleneck in this process. A possible way to increase the efficiency of IVP-ET procedures is identification and selection of high-quality oocyte donors and embryo recipients.…”