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Meat and milk production needs to increase ~ 70–80% relative to its current levels for satisfying the human needs in 2050. However, it is impossible to achieve such genetic gain by conventional animal breeding systems. Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells, herein we propose a novel embryo-stem cell breeding system. Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals, the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish. In comparison to the conventional dairy breeding scheme, this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity. However, several major obstacles must be overcome before we can fully use this system in livestock breeding, which include derivation and mantaince of pluripotent stem cells in domestic animals, as well as in vitro induction of primordial germ cells, and subsequent haploid gametes. Thus, we also discuss the potential efforts needed in solving the obstacles for application this novel system, and elaborate on their groundbreaking potential in livestock breeding. This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans. Keywords: Animal breeding, Embryos, Genomic selection, In vitro germ cell induction, Pluripotent stem cells Introduction production efficiency is the only way to provide enough pro- As the main dietary protein sources, meat and milk produc- tein sources for human needs in future. Genetic selection is tion requires approximately 70–80% increase relative to one of the most important means for improving livestock current levels [1, 2] in order to meet the demand of the production . However, genetic improvement in feed con- predicted 9.6 billion human population in 2050 [3, 4]. How- version efficiency by conventional breeding is very slow dur- ever, it is difficult to increase meat and milk production by ing the past decades in farm animals including swine, cattle, raising more livestock as the global yield of major crops will sheep, and goats. Annual genetic improvement in feed con- peak in thenearfuture[5, 6]. In addition, large expansion of verion efficiency is estimated to be only 0.7% in swine  livestock head would create an environmental threat be- and this number is even lower in cattle and sheep . Gen- cause the greenhouse gas emission by livestock accounts for etic improvement in other important economic traits, e.g., approximately 14.5% of human-induced global emissions disease resistance and fertility , are also slow or even . Hence, because of the upper limit of major crop yields stagnant. Further, more traits are expected to be included as and total head of livestock, improving animal feed and important considerations in future breeding schemes. Thus, the global demand for milk and meat production requires more efficient and sustainable animal breeding systems for * Correspondence: email@example.com Zhuocheng Hou and Lei An contributed equally to this work. accelerating genetic improvement [8, 11]. Key Laboratory of Animal Genetics, Breeding and Reproduction of the During the past decades, researchers have made en- Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, couraging progresses in improving animal breeding effi- College of Animal Science and Technology, China Agricultural University, Beijing, China ciency and have realized many proposed concepts. From Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 2 of 11 1990’s, several landmark studies [12, 13] concluded that of generations, thereby reconstituting an entire mamma- marker-assisted selection (MAS) can improve the animal lian life cycle in vitro (Fig. 1b). This rapidly renewed life breeding efficiency. As most economic traits are con- cycle can be used to constitute a recurrent animal trolled by multiple genes/alleles, single MAS cannot be breeding cycle by selecting and mating embryos directly, effectively applied in animal breeding, that is why gen- i.e., IVF using PSC-derived gametes. Thus, we propose omic selection methods are needed for improving selec- a novel animal breeding system termed animal tion accuracy. After long-term MAS theoretic studies, embryo-stem cell breeding system that can revolutionize genomic selection (GS) was first coined in 1998 , the design and implementation of current breeding pro- and later genomic selection theoretic framework was grams in livestock. Here we describe the workflow of the proposed in 2001 . With the help of quick progresses breeding system in view of relevant technologies involved in high-density chip and high-throughput sequencing, and discuss the challenges and its promising implications. genomic selection was first used in dairy breeding after 10 years of proposing genomic selection concept . Animal embryo-stem cell breeding system Until now, GS has been widely implemented in swine, The animal embryo-stem cell breeding system completes beef cattle, and chicken breeding. Threrefore, it takes a livestock breeding scheme in a dish by integrating in more than 20 years from the conceiving MAS concept vitro germ cell induction, IVF, genome sequencing, and to large-scale industrial application of GS. In addition, genomic selection. Based on the in vitro reconstituted the combination of embryonic technologies and MAS life cycles, an animal breeding cycle can be renewed by was also proposed to improve animal breeding efficiency directly selecting and mating embryos rather than adult . As early as 1980–1990s, it has been recognized that individuals, thereby achieving rapid genetic improve- embryonic technoloies such as oocyte pick-up (OPU), in ment of important economic traits. vitro fertilization (IVF), and preimplantation genetic diagnosis (PGD) could be potentially applied to intensify breeding process. Due to the continuous improvement Major procedures of efficiency in these molecular and embryonic technolo- Step 1: Form a breeding plan and establish a nuclear gies, many of these conceptions have been achieved or breeding population even industrially applied in animal breeding. Similar to the conventional breeding system, the stem Recent advances in stem cell biology offer an unprece- cell-embryo breeding system also needs to first create a dented opportunity for revolutionizing the animal breed- breeding scheme based on market demand and genetic ing system. Using pluripotent stem cells (PSCs), resources of the breeding herd and then establish a plat- including both embryonic stem cells (ESCs) and induced form for genomic selection or use an established plat- pluripotent stem cells (iPSCs), germ cells can be induced form. The breeding value of each individual should be in vitro to complete the entire gametogenesis processes evaluated and elite candidates will be selected to estab- and form functional spermatids or oocytes [17, 18]. In lish a base breeding population (Fig. 2, Part A). natural conditions, in vivo gametogenesis need to go through both fetal and postnatal gonadal development, Step 2: Establish the base and nuclear breeding population which usually take several months to over 1 year in large of elite embryos farm animals. However, using mouse as model, in vitro Using the sperms and oocytes from individuals with the induction of germ cells can reconstitute gametogenesis best breeding values in the breeding population, IVF will in a much shorter time (e.g. 6 weeks in mice). Moreover, be performed to generate male and female base embryos embryos can be obtained from in vitro generated sper- according to the breeding scheme. Genomic estimated matids and oocytes, and then the blastocysts can be fur- breeding values (GEBV) will be evaluated for all base ther used to derive ESCs, which is designated as embryos. Embryos with the top GEBV will be used as regenerated ESCs (rESCs). The rESCs can subsequently parental embryos to establish a nuclear breeding popula- undergo complete gametogenesis via a new round of in tion of elite embryos (Fig. 2, Part B). vitro germline induction . This renewed in vitro life cycle perpetuates the direct cross-generational transmission of genetic information Step 3: Transgenerational breeding cycle from parental from parental embryos to offspring embryos (E-to-E), embryos to offspring embryos (E-to-E) distinct from the natural cross-generational transmission This step includes three essential breeding compo- from parental individuals to offspring individuals (I-to-I) nents similar to the conventional breeding system: se- (Fig. 1a). In vitro germline induction, together with sub- lective breeding of parental embryos; controlled sequent in vitro fertilization (IVF) and ESC derivation, mating of parental embryos; and multigenerational has successfully created new individuals and alternation breeding of embryos. Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 3 of 11 Fig. 1 Mammalian generation transmission by parental individuals to offspring individuals (I-to-I) and parental embryos to offspring embryos (E- to-E). a I-to-I transmission: gametogenesis is a long-term process highly associated with individual development and growth. PGCs, from which both oocytes and sperm originate, are established by the post-implantation stage. The subsequent oogenesis and spermatogenesis necessarily depend on fetal development and postnatal gonadal growth from birth until puberty. Gametogenesis ensures the creation of new individuals of the next generation of mammals, where genetic information is transmitted to next generation. b E-to-E transmission: gametogenesis is induced in vitro in ESCs to form functional oocytes and sperm. The entire process depends on in vivo fetal development and prepubertal growth. The induced oocytes and sperm develop into normal offspring embryos following IVF. The IVF offspring embryos are further used to derive ESCs, which can in turn undergo complete gametogenesis via a new round of in vitro germline induction Fig. 2 A schematic workflow of the animal embryo-stem cell breeding system. The novel system comprises the following modules: Part A:Form a breeding plan and establish a nuclear breeding population; Part B:Establish the base and nuclear breeding population of elite embryos; Part C:Transgenerational breeding cycle from parental embryos to offspring embryos; Part D:Reference population construction and updating Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 4 of 11 (a) Selective breeding of parental embryos: Single cells postnatal growth. Aside from the classic major factors of a (blastomeres or trophectoderm cells) will be conventional breeding system, this system is characterized isolated from parental preimplantation embryos and by direct selection and mating of candidate embryos, they will be genotyped by whole-genome sequen- followed by an E-to-E breeding cycle, entirely distinct from cing. The genotyping results will be used to predict individual-based conventional breeding selection. A detailed the embryo genomic estimated breeding value comparison between the embryo-stem cell breeding system (eGEBV) by which elite parental embryos will be se- and conventional breeding system is summarized in Table 1. lected as candidates for controlled mating. During the transgenerational breeding of embryos, the (b) Controlled mating of parental embryos: Selected reference population can be updated as frequently as parental embryos will be used to derive ESCs, which needed. In general, individual production performance will be subsequently induced in vitro to form sperm and genome-wide single-nucleotide polymorphisms or oocytes. Based on the eGEBV-based breeding (SNPs) are required to construct original reference popu- scheme, in vitro derived gametes will undergo IVF to lation under the breeding plan guidelines as discussed in generate offspring embryos to complete the con- detail previously . The progeny of the elite breeders trolled mating of parental embryos. among the breeding embryo nucleus can be transferred (c) Transgenerational breeding of embryos: Following directly to the commercial production population or per- selective breeding and controlled mating of the formance testing population. The original reference popu- parental embryos, the offspring embryos will lation will be updated by new phenotypic data obtained undergo a new round of selective breeding and from the performance testing population (Fig. 2, Part D). controlled mating, which in turn starts a new selection cycle (Fig. 2, Part C). By repeating this Advantages of the animal embryo-stem cell breeding process, the embryo-stem cell breeding system can system achieve rapid transgenerational breeding. It should ihrσ Key factors affecting genetic gain (R= ) include be noted that live birth is not a prerequisite for standard deviation of breeding value (σ ), selection in- achieving the breeding cycles from parental em- tensity (i), selection accuracy (r), and the generation bryos to offspring embryos. interval (L). Genomic selection plays an important role in these key factors for accelerating genetic gain . The generation interval of the embryo-stem breeding sys- Compared to the conventional breeding method or gen- tem spans from parental embryos to offspring embryos, in- omic selection alone, our proposed system has signifi- volving ESC derivation, in vitro germ cell induction, and cant advantages in the following aspects. IVF. It should be mentioned that ESCs are more preferred for constructing transgenerational breeding cycles. In con- trast, the use of iPSCs, or germline-potential stem cells, will Shorter generation interval prolong the breeding cycle because differentiated fetal or The generation interval is about 5–7 years for sire(s) or adult somatic cells are needed. The entire breeding cycle is dam(s) of bulls in the conventional dairy breeding scheme. independent of the lengthy processes of pregnancy and This can be drastically reduced to approximately 2.5 years Table 1 Comparisons of major elements among different breeding systems Major breeding Conventional breeding Genomic selection Embryo-stem cell breeding elements Breeding scheme Yes Yes Yes Pedigree record Yes Yes, can also reconstruct pedigree from Yes, can also reconstruct pedigree from genotyping data genotyping data Performance testing Breeding animals Only for reference population Only for reference population Reference population No Yes Yes Candidate breeding Individual Individual, embryo Embryo animal Generation transfer Individual to individual Individual to individual Embryo to embryo Breeding value EBV GEBV eGEBV Gametogenesis In vivo gametogenesis In vivo gametogenesis In vitro induced gametogenesis Fertilization /Embryo In vivo fertilization and In vivo fertilization and development; In vitro fertilization and culture development; In vitro fertilization and culture In vitro fertilization and culture Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 5 of 11 by applying genomic selection . However, our pro- selection. Recently, functional haploid male and female posed E-to-E breeding system will require only approxi- gametes have been successfully induced in vitro in mice. mately 2 months for a complete one generation of These works provide a robust paradigm for achieving in selection. The annual genetic gain will increase about vitro germ line induction in farm animals, and could E−E 2:512 make the proposed breeding system technically feasible, 10-fold or even more ( ¼ ¼ 15 times)when com- R 2 GS although a series of obstacles need be overcome. A re- pared to the standard dairy genomic selection system if cent study reported that stable bovine ESCs can be effi- other selection factors are the same. Taking breeding dairy ciently derived from bovine blastocysts, which offers a cows as an example, ideally, our envisioned system is ex- technical basis for further establishment of in vitro germ ð5−7Þ12 E−E pected to be 30–40 times ( ¼ ¼ 30−40 ) R 2 conventiaon cell induction in farm animals . Here, we summarize more efficient in comparison to the conventional system, the current state and recent advances as well as the chal- meaning that 1-year genetic gain of in vitro breeding can lenges in supporting this novel breeding system. be the same as that of 30–40 years of conventional breed- ing. However, as the selection limitation and accuracy of In vitro germ cell induction in mammals genomic selection might decrease over several genera- Until now, using mouse PSCs, the entire germline cycle can tions, more theoretical studies are needed. be reconstituted in vitro to form functional gametes, al- though the efficiency remains limited [17, 18]. The gener- Higher selection intensity ation of primordial germ cells (PGCs), which can initiate IVF makes it possible to produce 100,000 or 1,000,000 meiosis, is of prime importance for generating haploid gam- embryos at the same time, which is equivalent to that of etes . Using ESCs bearing the PGC markers PR/SET do- 100,000 or 1,000,000 of selected individuals. We can de- main 1 (Prdm1, also known as Blimp1)and developmental sign the best sequencing strategy for genomic selection pluripotency–associated 3 (Dppa3, also known Stella), Haya- to achieve the best selection progresses in considering shi et al reported that the combination of bone morpho- the breeding cost and genetic improvement. genetic protein 4, leukemia inhibitory factor (LIF, interleukin 6 family cytokine) and stem cell factor are highly competent Better breeding scheme for monotocous animals for inducing PGC marker expression in epiblast-like cells Monotocous animals, such as cows and ewes, naturally (EpiLCs); these cells in turn become PGC-like cells produce only a few offspring in its lifetime. The elite fe- (PGCLCs) to facilitate in vitro induction of PGCs (Fig. 3a). males cannot produce enough offspring as needed, even if This work provides a robust paradigm for the first step for some IVF technologies can assist females to have more in vitro gametogenesis. Upon transplantation into an envir- offspring. If we overcome the obstacles in stem cell biol- onment of appropriate somatic cells in vivo, the induced ogy of farm animals and apply them in this system, mono- PGCLCs undergo meiosis and produce functional sperma- tocous females will make much more genetic contribution tids and oocytes, which can be subsequently used for gener- than conventional breeding program. Thus, the breeding ating normal offspring following IVF [24, 25]. system will introduce more genetic variations to the More recently, in vitro germ cell induction systems breeding population, especially for monotocous animals. have been further optimized to make meiotic differenti- ation no longer depend on in vivo gonadal niches. Easier integration of new biotechnologies Through aggregation with fetal or neonatal gonadal The breeding system provides easy access to the latest tech- somatic cells under in vitro conditions, in vitro derived nologies for further improvement of the in vitro breeding PGCLCs are successfully converted into primary sper- system because it relies on manipulation of embryos and matocytes/oocytes, respectively, which can be further in- ESCs that can be performed in a dish. For example, more duced into functional haploid spermatids and oocytes sophisticated genome editing can be integrated into the sys- (Fig. 3a). The functionality of these in vitro derived hap- tem. Harmful mutations within the population can be elim- loid gametes has been confirmed by the production of inated via whole-genome sequencing and genome editing. viable and fertile offspring via intracytoplasmic sperm Promotion of alleles by genome editing (PAGE) combined injection (ICSI) or IVF [17, 18]. It should be noted that with genomic selection can be 1.08–4.8 times more efficient blastocysts derived from the in vitro generated gametes than genomic selection itself . can be further used to derive rESCs, which can undergo a new round of in vitro germline induction. Therefore, Technical basis and challenges by integrating in vitro germ cell induction, IVF, and ESC The proposed novel embryo-stem cell breeding system derivation in mouse models, these studies have success- is mainly based on the recently developed technologies fully reconstituted a recurrent life cycle from parental for in vitro germ cell induction and the established rou- embryos to offspring embryos, without producing off- tines including IVF, genome sequencing, and genomic spring animals . Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 6 of 11 Fig. 3 A schematic of ESC derivation and in vitro induced gametogenesis. a In vitro induction of functional gametes from ESCs. EpiLCs and PGCLCs are sequentially induced using well-established female or male ESCs. Next, via aggregation with fetal or neonatal gonadal somatic cells under in vitro conditions, in vitro–derived PGCLCs are successfully converted into primary spermatocytes/oocytes respectively, which are further induced into functional haploid sperm and oocytes. b Derivation and establishment of pluripotent ESC lines from inner cellular mass (ICM) frim in vitro cultured blastocysts The most prominent challenge for establishing in vitro researches, on one hand, have drawn attention to the im- germ cell induction system in farm mammals may be the portance of formulating culture conditions that are con- pluripotent status of PSCs. Pluripotent ESCs are sistent with the apparent requirement of factors essential well-established in mice, rhesus monkeys, and humans for maintining pluripotency of domestic ESCs. In addition, (Fig. 3b). However, despite the lengthy history of efforts to these data indicates that significant modifications of cul- establish truly undifferentiated ESCs in farm animals, au- ture conditions may be needed even for those that had thentic ESC lines that can be proven by stringent germline previously proved so successful for mouse and human, chimera assay have not been established conclusively in since the mechanism for capturing pluripotency may be any of these species. Even using the conditions for gener- considerably different between rodent and domestic spe- ating mouse ESCs, such as LIF, BMP4, inhibitors of GSK3 cies. More recently, Bogliotti et al. reported successful der- and ERK (2i), derivation of such cell lines has been shown ivation of stable primed pluripotent ESCs from bovine to be chanllenging in nonrodents, especially in domesti- blastocysts by using fibroblast growth factor 2 (FGF2) and cated species . Up to date, the majority of the morpho- an inhibitor of the canonical Wnt–β-catenin signaling logically resembling ESC lines derived from bovine and pathway (IWR1) to optimize culture condition . This porcine embryos/fetus, inlcuding those recovered from work is a breakthrough as it overcomes the challenge of natural conception, IVF or somatic cell nuclear transfer, establishing high-quality pluripotent livestock ESCs. Until fail to contribute to chimeras and exhibite only limited now, precise mechanisms of how signaling pathways con- differentiation potential [27, 28]. It should be mentioned trol the pluripotent state and early embryo development here that the putative porcine ESC lines maintained on a remains largely elusive in farm animals, and it appears that basal medium supplemented with FBS plus three growth the essential pathways are considerably distinct from those factors, namely FGF2, LIF, and KITLG, are more capable of rodent species. Bogliotti’s study, shows that combin- of forming teratomas . Thus, it is promising that a ation of FGF supplementation and WNT signaling inhib- combination of growth factors may considerably benefit ition, both of which are critical for capturing bovine the system for deriving and maintaining dometic ECS pluripotency and important for normal preimplantation lines, as revealed by the fact that the self-renewal capcity embryo development in bovines [32, 33], is critical for of porcine ES-like cells are both LIF-dependent and capturing bovine pluripotency. This fact highlights that FGF2-dependent . Similarly, combined use of LIF exploring the mechanism underlying pluripotency of do- and FGF2 is also beneficial for maintaining the bovine mestic embryos, will help identify major obstacles that ES-like cells in an undifferentiated state [30, 31]. These hamper the establishment of true ESC lines in domestic Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 7 of 11 animals. However, even high-quality ESC lines are estab- germ cell biology in porcine and bovine, provide more sub- lished in farm animals, the efficient PGC specification stantial basis for eventually achieving in vitro germ cell in- pathway and subsequent aggregation with gonadal som- ductionindomesticanimals. atic cells remains challenging. From the feasibility perspective, a relative low-frequent Except the promising studies in ESCs, iPSCs also provide but noticeable de novo generation of single-nucleotide a practical alternative for successful in vitro germ cell in- variants (SNVs) can be elicited in the proposed breeding duction. By continuous formulation and optimization of re- system, along with the derivation culture and passage of programming factors and medium conditions, primed- or ESCs, especially by the induced reprogramming of iPSCs naive-type iPSCs have been successfully derived from por- [50, 51]. For example, dozens to several hundred de cine and bovine embryonic fibroblast cells or other cell novo SNVs can be detected between generations in ESCs types [34–37]. Using porcine iPSCs as progenitor cells, our or somatic cells and the mutation rate (approximately − 9 − 8 group has successfully induced porcine iPSCs to the 10 to 10 at global genome level) is more frequent PGCLCs. Further, xenotransplantation of the PGCLCs into than that from in vivo germline differentiation (approxi- − 10 − 9 seminiferous tubules of infertile immunodeficient mice can mately 10 to 10 at global genome level which varies result in immunohistochemically identifiable germ cells largely based on species, cell types, and culture or induc- . Moreover, with the extensive studies over the past de- tion methods). Although de novo mutations induced by cades that investigate the origins and mechanisms under- the manipulation of pluripotent cells have minimal con- lying PGC and germ line specification/differentiation in tributions to the reference sites of genome selection, the domestic animal, a series of key growth factors (e.g. SCF, biological significance and potential application as well LIF, FGF2, BMP4) [39–42] and signaling pathways (Acti- as the risk of de novo mutations should be re-evaluated vin/Nodal signaling, redox/apoptotic signaling) [42, 43] based on offspring phenotypes. have been identified to be implicated in maintaining the survival and self-renewal of domestic PGCs. All these find- In vitro fertilization in domestic mammals ings will benefit the high-efficient system of domestic PGC IVF is the process of creating embryos from oocytes by fer- induction. Interestinly, a more recent study, using in vitro tilizing them with sperm cells in a dish. A broader defin- model of germ cell induction, showed conserved principles ition of IVF in cattle industry often involves oocytes of epiblast development for PGC fate among porcine and retrieval from the ovaries, including recovery and in vitro model animals, although the mechanisms underlying maturation of oocytes, and in vitro fertilization and culture pluripotency networks and early post-implantation devel- of embryos. The high-efficient IVF methodology is an im- opment are thought to be divergent among species . In portant component of embryo-stem cell breeding system to addition, studies highlighting the origins of domestic support large-scale production of highly competent em- germline-potential stem cells, provide alternate source of bryos for ESCs derivation. According to data from Inter- domestic PGSs. Aside for those from developing fetal national Embryo Transfer Society (IETS), global production gonad, stem cells derived from adult bovine and porcine and transfer of IVF bovine embryos increased over 10-fold ovaries [45, 46] or fetal porcine skin [47, 48] also exhibit during the past decade. In 2015, over 60,000 embryos were the intrinsic ability to differentiate into PGCLCs or even produced in vitro and approximately 40,000 were trans- oocyte-like cells (OLCs). However, these germline-potential ferred globally, contributing to ~ 50% of total transferred stem cells are not preferred in our proposed breeding sys- embryos . Large international breeding corporations, tem, because developmentally advanced stem cells will pro- such as ABS Global, Inc., Semex, and Alta Genetics Inc., as long the breeding cycle since differentiated fetal or adult well as specialized suppliers of IVF services, such as Trans- somatic cells are needed. Considering the big challenge of Ova Genetics and L’Alliance Boviteq, have significantly ac- establishing high-quality ESC lines in domestic animals, celerated the commercial usage of IVF in driving genetic iPSCs or germline-potential stem cells, may be feasible al- improvement in herds . In South America, the exten- ternates for connecting transgenerational breeding cycles. sive application of IVF embryos in the breeding scheme of Furthermore, Hayashi’s work also offers a valuable refer- beef cattle plays a determinant role in rapidly accelerating ence for formatting and purifying PGCLCs from ESCs genetic improvement in herds [52, 54]. without relevant transgenic markers from domestic ani- Compared with in vivo conceived embryos, the IVF em- mals. Specifially, they identified SSEA1 (stage-specific em- bryos often have compromised developmental potential, par- bryonic antigen) and Integrin β3 as essential surface ticularly in certain domestic species. By using standard or markers for achieving PGCLC isolation and purification chemically defined culture conditions in combination with . A more recent study further indicated that epithelial different growth factors during oocyte maturation or embryo cell adhesion molecule (EpCAM) and integrin α6 are effi- culture, e.g., colony-stimulating factor, bone morphogenetic cient in distinguishing PGCLC following human iPS induc- protein 15, LIF, natriuretic peptide type C, and/or biologic- tion . These advances, together with the studies of ally active small molecules, e.g., 3-isobutylmethylxanthine, Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 8 of 11 5-aza-2′-deoxycytidine, the efficiency in producing IVF em- However, the accuracy of genomic selection might bryos and their developmental potential have been substan- decrease as multiple generation selection using the tially improved [55–59]. Thus, further understanding of same referene population. At first several generations, oocyte and embryo physiology will assist the development of our proposed breeding system can still achieve high safer and more efficient IVF systems for producing compe- accuracy of selection as the large reference population tent embryos to support the proposed in vitro breeding and whole genome variations will be used. For later system. generations, we can add production population phe- notypes in the reference population to maintain the Genome-wide sequencing accuracy of GS (Fig. 2d). During this selection mating Single-cell genomic DNA amplification technology has stage, we need to carefully design the mating between been fully established and can sequence the genome of male and female embryos to avoid the increase of in- various species [60–62]. Thus, genome-wide variations breeding in the population. of each candidate embryo can be obtained by As the significant shorter generation interval for genome-wide sequencing of one or more cells from the this E-to-E breeding system, it is possible that some embryo to estimate GEBV. Amplification bias and het- detrimental mutations would accumulate in the em- erogeneity/uniformity of several commonly used bryo breeding populations before more phenotypes single-cell whole genome amplification kits may have an show up. This should be carefully considered when impact on subsequent SNV calling and copy number executing the breeding program. Efforts should be variations (CNVs) . However, newly developed direct taken to reduce the potential damages of harmful library construction has addressed these technical limita- mutations by considering all known mutations, and tions . The rapid development of automated and also develop more powerful prediction for these new process-based whole-genome sequencing library con- mutations. Ineed, several algorithms such as SIFT, struction programs have also helped achieve large-scale PolyPhen-2, and CADD, and EVmutation are available embryo genetic screening and characterization . to estimate the mutation effects (refs: NBT,2017, Mu- Moreover, the well-established protocols for preimplan- tation effects predicted from sequence co-variation). tation genetic screening (PGS) or sex determination util- More bioinformatic analysis may need to be included izing blastomere or trophectoderm biopsies have been in the GS pipeline for novel mutations. used successfully in large-scale commercial dairy cow Compared to whole-genome sequencing, chip-based breeding and propagation without evident adverse ef- genotyping techniques are limited in detecting insertions/ fects on subsequent fetal development and postnatal deletions (indels) and CNVs. Therefore, whole-genome se- growth. Thus, the well-controlled biopsy of preimplanta- quencing data can yield more informative genetic varia- tion embryos will be a safe and valid approach to obtain tions and can further improve the accuracy of genomic genomic information from a preimplantation embryo selection . Except yield and growth rate, traits such as without sacrificing the quality of the tested embryos. quality and disease resistance will gain more attention; the need for SNPs will also increase substantially. In addition, Genomic selection developing genome-wide markers is of great significance Genomic selection is a milestone in animal breeding. for maximizing future use of reference populations and Compare to conventional animal genetic selection pro- data from different reference populations [10, 66]. As the grams that use individual GEBV, an important feature of cost of sequencing is drastically reduced, a whole-genome our proposed system is to use embryonic GEBV instead. sequencing–based genotyping approach will be an import- Numerous theoretical breeding studies and applications ant new development for future genomic selection. have confirmed that the GEBV can replace the conven- As the number of traits, SNPs, and candidate tional pedigree-based estimated breeding value entirely breeding animals and size of reference population will as long as the reference population, number of markers, continue to increase and simultaneous whole-genome and prediction equation meet the basic requirements [8, sequencing of thousands or more individuals produces 65, 66]. Genomic selection has been widely used in the massive data, it is possible that computation time will commercial breeding of animals such as dairy [16, 67] be an important limitation in commercial breeding and beef cattle , pigs [69, 70], chickens [71–73], and programs. Continuous optimization will be required sheep . Following the introduction of genomic selec- for reducing computation expenditure for genomic se- tion, the annual genetic improvement of yield traits in lection analysis–related processes, such as analysis of American dairy cows has increased by about 50–100% massive sequencing data, haplotyping, imputation, and compared to the conventional breeding systems; the pro- model selection. A robust and scalable data handling gress of some low heritability traits has increased by and analysis pipeline will be desired for these sequen- about 3–4 times . cing data and phenotypic data. Hou et al. Journal of Animal Science and Biotechnology (2018) 9:90 Page 9 of 11 Conclusions and outlooks propagation of bovine ESCs, and this provides us an The embryo-stem cell breeding system has significant unshakeable confidence for constituting the proposed advantages compared to the conventional breeding sys- breeding system. However, huge effort remains to be tem, especially in shortening generation interval, in- required since high-quality ESCs have not been proven creasing the number of female monotocous offspring, in pigs or other domestic species. As well, even using and selection intensity. Taking breeding dairy cows as an the recently-reported pluripotent ESCs, the in vitro example, ideally, our envisioned system is expected to be germ line induction in bovines will be a great challenge. 30–40 times more efficient in comparison to the con- In addition, the improvement and optimization of IVF ventional system, meaning that 1-year genetic gain of in and genomic selection technologies, highlighting their vitro breeding can be the same as that of 30–40 years of integration in the embryo-stem cell breeding system, conventional breeding. are also needed. The establishment of in vitro germ cell induction, as Farm animal populations harbor numerous genetic well as the generation of subsquent embryos and off- variations with phenotypic effects and thus serve as a spring in farm animals, remain the most fundamental unique model for understanding the genetic basis of challenges for creating an embryo-stem cell breeding phenotypic diversity. The breeding practice of our sys- system. High-quality and stable ESC lines are pre- tem will extend the understanding of genetic basis, e.g. requisite for achieving in vitro germ cell induction. genetic transmission, recombination, and variance During the preparation of our manuscript, a recent under in vitro-reconstituted E-to-E life cycle. Based on study reported the efficient derivation and stable our breeding system, one can create an embryo-stem Fig. 4 A schematic workflow of the animal embryo-stem cell conservation system. The endangered animals under biodiversity monitoring (phenotyping/ genotyping) are used to generate embryos and ESCs sequentially. Population of endangered or rare animal embryos can be quickly expanded through in vitro recycled propagation. Live offspring can be obtained through embryo transfer to recipient of same or relative species/breeds as needed Hou et al. 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Journal of Animal Science and Biotechnology – Springer Journals
Published: Dec 14, 2018
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