METHODS FOR GENERATING ANIMALS WITH DESIRABLE TRAITS

Abstract

Method for selecting mammalian cells having a genetically-desirable trait, the method comprising culturing an embryo in vitro, dividing the cells from the embryo into aliquots, subjecting the cells from at least one of the aliquots to a genetic analysis, and, based on the results of such analysis, selecting an aliquot of cells. Method for selecting mammalian cells having a genetically-desirable trait, the method comprising culturing an embryo in vitro, transferring the cultured embryo into a recipient female, collecting the embryo, dividing the cells from the embryo into aliquots, subjecting the cells from at least one of the aliquots to a genetic analysis, and, based on the results of such analysis, selecting an aliquot of cells. Method for selecting a mammalian embryo having a genetically-desirable trait, the method comprising removing one or more cells from each of a plurality of embryos, culturing the cells, subjecting the cultured cells to a genetic analysis, and, based on the results of such analysis, selecting an embryo.

Claims

1. A method for selecting mammalian cells having a genetically desirable trait, the method comprising: (a) culturing an embryo in vitro to produce a cell line, wherein the embryo comprises from 1 to about 500 cells at the onset of step (a); (b) dividing the cells from the cell line produced in step (a) into two or more aliquots; (c) subjecting the cells from one of the two or more aliquots produced in step (b) to a genetic analysis; and (d) if the genetically desirable trait is found in the aliquot subjected to genetic analysis, selecting cells from a different aliquot from the two or more aliquots produced in step (b) wherein the selected cells are capable of producing a mammal having the genetically desirable trait.

2. A method for selecting mammalian cells having a genetically desirable trait, the method comprising: (a) culturing an embryo in vitro, wherein the embryo comprises from 1 to about 500 cells at the onset of step (a); (b) transferring the cultured embryo into a recipient female; (c) about 10 or more days after step (b), collecting the embryo from the recipient female; (d) dividing the cells from the collected embryo into two or more aliquots; (e) subjecting the cells from one of the two or more aliquots produced in step (d) to a genetic analysis; (f) if the genetically desirable trait is found in the aliquot subjected to genetic analysis, selectins cells from a different aliquot from the two or more aliquots produced in step (d) wherein the selected cells are capable of producing a mammal having the genetically desirable trait.

3-4. (canceled)

5. The method of claim 2, wherein the embryo is collected from the recipient female about 21 days or more after the transfer thereto.

6. A method for producing a mammal having a genetically desirable trait, the method comprising using one or more cells selected using the method of claim 1.

7. The method of claim 6, comprising a step of nuclear transfer.

8. The method of claim 1, wherein the aliquot(s) of step (c) that are not subject to genetic analysis are frozen.

9. The method of claim 8, wherein the aliquot(s) that are frozen are later thawed.

10. The method of claim 1, wherein the genetic analysis comprises one or more assays selected from the group consisting of whole genome analysis (WGA), gene expression profiling using microarray, sequencing of a coding region of a gene, sequencing of a non-coding region of a gene, and whole genome sequencing.

11. The method of claim 1, wherein the embryo is cultured during step (a) for at least 5 days.

12. The method of claim 11, wherein the embryo is cultured during step (a) for at least 7 days.

13. The method of claim 1, wherein the embryo comprises about 100 to about 200 cells at the onset of step (a).

14. The method of claim 1, wherein the embryo comprises about 400 to about 800 cells at the end of step (a).

15. A method for selecting a mammalian embryo having a genetically desirable trait, the method comprising: (a) removing a cell from each of a plurality of embryos about 2 to 6 days after fertilization of the embryos; (b) culturing the cell for about 2 to 6 days; (c) subjecting the cultured cell of step (b) to a genetic analysis; (d) culturing the plurality of embryos of step (a) after the cell has said one or more cells have been removed; and (e) if the genetically desirable trait is found in the cell subjected to genetic analysis, selecting the embryo from which the cell was removed, wherein the selected embryo is capable of producing a mammal carrying the genetically desirable trait, and.

16. The method of claim 15, further comprising a step of freezing the embryos of step (d).

17. The method of claim 16, wherein the embryos that are frozen are later thawed.

18. The method of claim 15, wherein the genetic analysis comprises one or more assays selected from the group consisting of whole genome analysis (WGA), gene expression profiling using microarray, sequencing of a coding region of a gene, sequencing of a non-coding region of a gene and whole genome sequencing.

19. The method of claim 15, wherein the embryos are cultured in a medium comprising 15% fetal calf serum during step (b).

20. A method for producing a mammal having a genetically desirable trait, the method comprising using one or more cells selected using the method of claim 2.

21. A method for producing a mammal having a genetically desirable trait, the method comprising using one or more cells selected using the method of claim 15.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0025] FIGS. 1A-1 C illustrate methods of culturing whole embryos for expanding the cell numbers in the embryos.

[0026] FIG. 2 illustrates the embryo biopsy and culture method.

DETAILED DESCRIPTION OF THE INVENTION

[0027] The present disclosure provides methods for selecting embryos having desirable traits prior to nuclear transfer for cloning or implantation of embryos. Methods for extended culture of embryos are also disclosed. Extended culture of embryos enable the use of genetic tests for selecting embryos having desirable traits. Genetic tests, such as whole genome analysis (WGA), may be employed to identify an embryo that possesses desirable genetic characteristics. WGA and other genetic tests that can be used for genom is selection are disclosed, for example, in Humblot et al. Vet. Med. Int 2010, Article ID 192787; Ponsart et al. 28.sup.th Annual Meeting AETE. Saint Malo, France, Sep. 7-8, 2012; Schefers and Weigel. Animal Frontiers. 2(1):4-9, 2012. The methods disclosed herein may be applied to many mammals, such as cattle, as well as in horses, dogs, cats, goats, sheep, bison, deer, donkeys, mules, swine, hogs, among others.

[0028] In one embodiment, a female animal may be induced to superovulate, eggs may be collected from the superovulated female. The collected eggs may be fertilized in vitro using sperms from a suitable male animal. The fertilized eggs may be cultured in vitro to allow the cells numbers to expand in the embryos.

[0029] In one embodiment, embryos may be cultured while the genetic tests are being performed on a portion of the cells from the same embryos. If the test results are positive, the cultured embryos may be transferred to a recipient for production of offspring. Alternatively, cells from these positive embryos may be used for cloning to produce genetically superior animals. In another embodiment, methods are disclosed for expanding and freezing of embryonic cells. Genetic tests may be performed on a portion of the expanded cells. If the test results are positive, the remaining cells from the same embryos may be thawed and used to produce offspring.

[0030] In another embodiment, biopsy sample(s) may be obtained from embryos that have been cultured for about 3-7 days after fertilization. General methods of embryo biopsy are known in the art and disclosed, for example, in Polisseni et al. Fertility and Sterility. 93(3): 783-788, 2010; Lopes et al. Theriogenology. 56(9): 1383-1392, 2001. The biopsied cells may be cultured individually to expand the cells for about 2-10 days, or even longer. The expanded cells from the biopsy sample may be subject to genetic test, such as whole genome analysis (WGA), while the rest of the embryos are cultured. Multiple displacement amplification (M DA) is one type of WGA technique, which may be used to increase the amount of DNA from biopsies for analysis (see, e.g., Lauri et al. Genomics. 101 (1):24-29, 2013). After WGA is performed, superior embryos may be selected to produce calves based on the WGA results from corresponding biopsy samples. The embryos may be continuously cultured after the biopsy is performed, for example, until WGA is completed on the biopsied sample. Such embryos may be cultured for about 1 week (or, in some instances, longer, e.g., 2 or 3 weeks) post-biopsy before they are frozen. The fate of the frozen embryos may be decided depending upon results from the WGA of the biopsied sample. If the genetic tests indicate that the corresponding embryos may develop into an animal possessing superior traits, the frozen embryos may be used for cloning or implantation to generate offspring that possess such traits.

[0031] In another embodiment, the whole embryo may be cultured in vitro for 5-7 extra days after the approximately 7-day post-fertilization culturing period. At this stage, each embryo typically contains approximately 300-400 cells. These embryos may be divided into several aliquots using micromanipulation techniques and frozen separately in freezing medium and stored in liquid nitrogen for further downstream analysis and usage (see FIG. 1A).

[0032] In another embodiment, the embryos may be cultured individually for about 2-6 weeks in vitro with modified tissue culture medium in multi-well plates containing mitotically arrested mono-layer of feeder cells (see FIG. 1B). At this stage, embryos are attached to the surface of the tissue culture plate and each well contains several thousand cells. These cells may be divided into several portions by enzymatic treatment and frozen in several vials and stored in liquid nitrogen.

[0033] Thus, the several vials of frozen cells may be derived from the same well and are clonally expanded from the same embryo. One of these vials may be used for genetic tests, such as whole genome analysis (FIG. 1).

[0034] In another embodiment, embryos that have been in culture for 5-9 days (e.g., 7 days) may be transferred into synchronized recipient females using standard non-surgical embryo transfer methods (see FIG. 1C). These embryos may be collected about 10-40 days (e.g., about 21-26 days, e.g., about 21 days) after this transfer to establish cell lines. Each of these cell lines may be divided into several portions by enzymatic treatment, frozen in several vials, and stored in liquid nitrogen for future use.

[0035] Based on the results of this analysis, genetically superior frozen vials may be selected and used as nuclear donor cells to clone calves using established nuclear transfer procedures. These methods of culturing the embryos and producing calves by nuclear transfer may significantly reduce the production of genetically less valuable animals by increasing (e.g., by at least 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% or more) the selection intensity and accuracy of selection and decreasing (e.g., by at least 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% or more) the generation interval.

[0036] For purpose of this disclosure, genetic test(s) may include analyzing data associated with one or more genetic characteristics in individual embryos or cells obtained from individual embryos. In one embodiment, the methods and systems of the present disclosure may utilize genetic information obtained from individual embryos to identify embryos that may possess desirable traits. The genetic information may include but is not limited to single nucleotide polymorphisms (SN Ps), insertions, deletions, inversions and other mutations.

[0037] As used herein, the term “polymorphism” refers to an allelic variant that occurs in a population, which may be a single nucleotide difference present at a locus, or an insertion or deletion of one, a few or many consecutive nucleotides, or an inversion. A single nucleotide polymorphism (SN P) may be characterized by the predominance of certain nucleotides at a specific locus of a genome in a certain population. Under most circumstances, less than all four nucleotides (i.e., adenosine, cytosine, guanosine or thymidine) predominate at a particular locus. For instance, a specific locus in a genome of a given population may contain either a cytosine or thymidine at the polymorphic site and thus two of the four nucleotides predominate at this particular locus. However, polymorphism of one, two, three or four nucleotides may exist. It will be recognized that, while the methods disclosed herein are exemplified by the detection of SNPs, the disclosed methods or others known in the art similarly can be used to identify other types of polymorphisms, such as an insertion or a deletion, which typically involve more than one nucleotide.

[0038] A “single nucleotide polymorphism” or “SN P” typically occurs at a polymorphic site occupied by a single nucleotide, which is the site of variation between allelic sequences. The site is usually flanked by highly conserved sequences of the allele. For instance, the highly conserved sequences may vary in fewer than 1/100 or 1/1000 members of the population. A single nucleotide polymorphism usually arises due to a substitution of one nucleotide for another at the polymorphic site. Single nucleotide polymorphisms may also result from a deletion of a nucleotide or an insertion of a nucleotide relative to a reference allele.

[0039] According to one aspect of the present disclosure, a genetic test may include detecting at least one SN P in one or more genes implicated in certain genetic traits. For instance, the method may include determining the identity of a nucleotide at one or more specific positions of one or more genes, and comparing the identity to the nucleotide identity at corresponding positions of a reference allele.

[0040] The term “haplotype” refers to the genetic constitution of an individual chromosome. Haplotype may refer to only one locus or to an entire genome. The term “haplotype” may also refer to a set of SNPs that are statistically related.

[0041] For purpose of this disclosure, the term genotyping may be used to refer to the process of determining the genetic information an individual animal carries at one or more positions in the genome. For example, genotyping may include determination of which allele or alleles an individual carries for a single SNP or the determination of which allele or alleles an individual carries for a plurality of SNPs.

[0042] Genetic tests may be performed to determine one or more genetic characteristics or traits. For instance, a plurality of assay compositions may be used to identify a plurality of nucleotide markers, such as SNPs. In one embodiment, the presence or absence of a nucleotide polymorphism may be detected by polymerase chain reaction (PCR) followed by nucleotide sequencing. The presence or absence of a plurality of nucleotide polymorphisms may be detected by performing PCR assays using a panel of primers followed by nucleotide sequencing. In another embodiment, a polymorphism may be identified, at least in part, by using the polymerase chain reaction without sequencing.

[0043] PCR reactions may be performed simultaneously using assay plates or a flat-block thermal cycler. PCR primers may be pre-labeled using fluorescent dye such that the fluorescence output may be read using a computer-based imaging system. Using such a design, high-throughput cost-efficient analysis of hundreds or thousands of polymorphic sites may be assayed simultaneously.

[0044] A sample for practicing the method of the present disclosure may be obtained from a cell, a portion or a biopsy of an embryo or from the culture medium in which the embryos are cultured. Optionally, call rates of the PCR amplified DNA samples may be determ fined to evaluate the genotyping quality (e.g., genotyping accuracy) in WGA using standard techniques known in the art (see, e.g., Lewis and Knight. Cold Spring Harbor Protoc. 297-306, 2012). In one embodiment, the sample is a nucleic acid sample. The nucleic acid sample may be deoxyribonucleic (DNA) acid or ribonucleic acids (RNA). The DNA may be genom is DNA, or reversely transcribed cDNA. The DNA may be coding or non-coding sequences of a gene or whole genome sequence of an individual mammal. Methods of genetic engineering, which may include but are not limited to PCR, DNA hybridization, DNA sequencing, vector construction, recombinant DNA techniques, may be found in the literature, such as Maniatis et al. Molecular Cloning A Laboratory Manual. Cold Spring Harbor Laboratory, N.Y. (1989), which is incorporated herein in its entirety by reference. By way of example, assays for WGA may include but are not limited to, the use of the Illumina Bovine SNP50 and Bovine LD assays (Ilium ina, Inc., San Diego, Calif.) for generation of genomic enhanced genetic evaluations.

[0045] It is to be noted that the term “a” or “an” refers to one or more of an entity; for example. “an animal,” is understood to represent one or more animals. As such, the terms “a” (or “an”), “one or more,” and “at least one” may be used interchangeably in this disclosure.

[0046] The term “about” means substantially the same with a deviation of no more than 10-20%.

EXAMPLES

[0047] The following examples are provided for purposes of illustration of embodiments only and are not intended to be limiting. The reagents, chemicals and other materials are presented as exemplary components or reagents, and various modifications may be made in view of the foregoing discussion within the scope of this disclosure. Unless otherwise specified in this disclosure, components, reagents, protocol, and other methods used in the system and the assays, as described in the Examples, are for the purpose of illustration only. It is to be understood that although per-pubertal heifers are used in the Examples, the disclosed methodology may be applied to mature heifers as well.

Example 1. Whole Embryo Culture In Vitro and Splitting of Embryos

[0048] Oocytes were collected from pre-pubertal heifers. Following a 7-day culturing window that is standard practice in the field, embryos were cultured in vitro for an additional 5-7 days in standard embryo culture medium (e.g., synthetic oviductal fluid (SOF), e.g., SOF with amino acids, sodium citrate, and myo-inositol (SOFaaci)) with 15% Fetal calf serum. At this stage, each embryo contained approximately 300-400 cells (FIG. 1). These embryos were divided into three aliquots using micromanipulation techniques (FIG. 1A). The three aliquots were frozen separately in freezing medium (EC2 with 20% DMSO and 60% FCS) and stored in liquid nitrogen for further downstream analysis and usage.

[0049] Using the method described above, several aliquots of cells from the same embryo are generated. One or more of these aliquots are used for whole genome analysis (WGA) or other types of genetic analysis (FIG. 1A). Based on the results of the genetic tests, frozen cells corresponding to the cells that possess the desirable traits are selected and used as nuclear donor cells to clone calves using well-established nuclear transfer procedures. This method of culturing the embryos and producing calves by nuclear transfer may reduce the production of less valuable animals by increasing the selection intensity and accuracy of selection and decreasing the generation interval.

Example 2. Extended Culture of Whole Embryo In Vitro

[0050] Jersey females were super-ovulated, and oocytes aspirated and matured in vitro per standard protocols. After maturation, oocytes were insem inated in vitro using semen from different Jersey bulls. After fertilization, presumptive zygotes were cultured for 7-8 days. Expanded blastocyst stage embryos were then selected and cultured individually in multi-well plates containing modified tissue culture medium without any feeder cells for approximately 10 days (see FIG. 1B). Once the cultured embryos were attached to the surface of the tissue culture plate and started to divide, the culture media was replaced once every 4 days until cell colony monolayers were established. Table 1 below shows the number of cell lines established with cultured whole Jersey embryos using this method.

TABLE-US-00001 TABLE 1 Cell line establishment with Jersey embryos No. of No. of cell lines Date of oocyte Sire/donor embryos established in aspiration combination cultured 8-10 days Mar. 22, 2012 Camilo/6528 6 4 Camilo/6810 9 9 Apr. 5, 2012 Zuma/6528 6 3 Zuma/6810 2 1 Arp. 12, 2012 Camilo/7242 1 1 Camilo/7005 2 0 Camilo/7124 14 4 Total 40 22

[0051] After approximately 10 days in culture, the established cell colony monolayers were mechanically disrupted into cell clumps by repeated pipetting. These clumps of cells were pelleted and the pellet was dissolved in freezing medium containing 20% DMSO and 40% serum. This suspension with clumps was divided into 3-5 vials and frozen using slow freezing. These frozen vials were stored in liquid nitrogen.

[0052] Using the method described above, several vials of cells that were clonally expanded from one embryo were generated. One or more of these vials were used for WGA. Based on the results of this analysis, genetically superior frozen vials are selected and used as nuclear donor cells to clone calves using well-established nuclear transfer procedures.

Example 3. Embryo Transfer to Recipient Mothers

[0053] Jersey females were super-ovulated, and oocytes aspirated and matured in vitro per established protocols. After maturation, oocytes were inseminated in vitro using semen from different Jersey bull. After fertilization, presumptive zygotes were cultured for seven days. On day 7, embryos were selected, graded, and transferred to a recipient mother, with each recipient mother receiving 3-5 embryos (1-3 embryos per uterine horn).

[0054] Embryos were collected between pregnancy days 21-26. Briefly, recipient mothers were confined in a cattle chute and given an epidural block of 2% procaine. A sterile 24-gauge Foley catheter was inserted through the cervix into the uterine body and ViGro complete flush solution (Bioniche Animal Health Inc., Pullman, Wash.) supplemented with 16 μI/ml of antibiotic-antimycotic (Gibco, Grand Island, N.Y.) and δμI/ml fungizone (Gibco, Grand Island, N.Y.) was flushed through the uterus non-surgically. Upon recovery, embryos were isolated from the uterine flush medium under a stereomicroscope.

[0055] Jersey cell lines were established as follows. Briefly, flushed embryos were transported to the laboratory in Dulbecco's phosphate buffered solution (DPBS) with 16 μI/ml of antibiotic-antimycotic (Gibco, Grand Island, N.Y.), 5 μI/lτlI penicillin Streptomycin (Sigma, St. Louis, Mo.) and δμI/ml fungizone (Gibco). Embryos were rinsed in DPBS and finely chopped into pieces with a scalpel blade. The fibroblasts were separated from the tissue pieces by standard trypsinization procedure using TrypLE (Gibco). The cells were seeded onto 25-cm vented tissue culture flaks (BD) in DMEM (Gibco) supplemented with 10% FCS (fetal calf serum, Hyclone, Logan, Utah), 0.003% β-mercaptoethanol (Gibco) and penicillin/streptomycin solution (Sigma). On day four of seeding, the cells were harvested, using TrypLE solution and reseeded onto 75 cm.sup.2 tissue culture flasks. After 3-4 days of culture, cells were harvested and approximately one hundred thousand cells were used for DNA isolation. The remaining cells were frozen in DM EM with 10% FCS and DMSO (Sigma).

[0056] Table 2 below summarizes the number of Jersey embryo cell lines established by this embryo transfer method.

TABLE-US-00002 TABLE 2 Summary of Embryo transfers, collections and cell line establishments No. of No. of No. of No. of cell lines usable Date of No. of recip- embryos estab- cell lines transfer embryos ients collected lished frozen 24 Jan. 2013 19 5 10 10 *8  31 Jan. 2013 9 3 7 7 7 14 Feb. 2013 12 3 3 3 3 20 Feb. 2013 16 4 10 10 10  7 Mar. 2013 18 5 8 8 8 13 Mar. 2013 3 1 2 2 2 21 Mar. 2013 6 2 2 2 2 27 Mar. 2013 3 1 5 5 5 10 Apr. 2013 12 3 6 6 6 24 Apr. 2013 17 4 8 8 8 8 May 2013 9 2 6 6 6 10 May 2013 11 3 3 3 3 24 May 2013 17 4 3 3 3 7 Jun. 2013 3 1 0 0 0 Total 155 41 73 73 71  *Fungal contamination was observed in two cell lines after establishment and they were discarded.

[0057] The DNA samples isolated from cell lines were submitted for whole genome analysis (WGA) and genotyping through Geneseek, Inc. (Lincoln, Nebr.) to the animal improvement program laboratory at USDA. The results are summarized in Table 3 below.

TABLE-US-00003 TABLE 3 DNA sample analysis and selection of cell lines Date of No. of No. of samples No. of cell sample DNA analyzed lines with submission samples successfully (%) JPI >210 (%) 4 Apr. 2013 28 23 (82.14) 1 (4.3) 29 Apr. 2013 17 17 (100) 1 (5.9) 29 May 2013 13 13 (100) 0 24 Jun. 2013 13 13 (100)  3 (23.1) Total 71 66 (92.95) 5 (7.6)

[0058] After genotyping these cell lines, five cell lines were selected based on the general Jersey Performance Index (J PI) in Table 4. Each of these cell lines (FL065, FL062, FL064, FL017, and FL036) were determined to have a favorable J PI score of 210 or greater.

TABLE-US-00004 TABLE 4 Summary of the top five selected cell lines Cell JPI CM NM PTAT MILK FAT PRO PL SCS DPR UDC line ID Gen Gen Gen Gen Gen Gen Gen Gen Gen Gen Gen Haplotypes FL065 251 750 680 2.1 880 75 41 6.5 2.86 1.2 6.13 JH1T JH1_PC.N JHPT JHP_PC.N FL062 224 688 623 1.8 669 65 34 6.2 2.86 1.6 5.02 JH1T JH1_PC.N JHPT JHP_PC.N FL064 221 708 618 1.0 501 63 33 6 2.73 1.5 4.92 JH1T JH1_PC.N JHPT JHP_PC.N FL017 215 692 607 0.9 470 60 31 5.8 2.72 1.9 4.35 JH1T JH1_PC.N JHPT JHP_PC.N FL036 210 594 571 1.4 909 32 29 6.6 2.76 1.1 5.76 JH1T JH1_PC.N JHPT JHP_PC.N

[0059] Two cell lines were used for making cloned embryos using the standard nuclear transfer procedure as described earlier. The in vitro embryo development of these cell lines looked similar to that of other fibroblast cell lines (Table 5).

TABLE-US-00005 TABLE 5 Clone embryo development in vitro with some of the established cell lines Total No. of fused No. of blastocysts Cell line ID reconstructed couplets (%) developed on day 7 (%) FL010 224 150 (66.9) 26 (17.3) FL010 103  68 (66.0) 14 (20.6) FL065 165 115 (69.7) 11 (9.6)  FL065 156  92 (58.9) 38 (41.3) Total 648 425 (65.6) 89 (20.9)

[0060] A total of 16 embryos from cell line FL065 were transferred to synchronized recipient females on 04 and 18 Sep. 2013 (Table 5). The pregnancy status of these recipients will be confirmed approximately at 40 and 60 days of gestation using ultrasonography and thereafter by rectal palpation every other month.

TABLE-US-00006 TABLE 6 Embryo transfers and pregnancies with cell line FL065 No of recipients Pregnant at (%) Cell line ID implanted 40 days 60 days FL065 11 6 (55) ND FL065  5* ND ND Total 16 These animals will be pregnancy checked on 22 Oct. 2013. ND: Not detected and in progress.

Example 4. Embryo Biopsy and Culture

[0061] Biopsy sample(s) from Day 2-7 embryos were obtained and the biopsied cells (e.g., 4-6 cells from each embryo) were cultured individually. The remaining embryos were also cultured separately from the biopsied cells. Standard SOFaaci medium was used. The biopsied cells were allowed to expand for 1-6 days. Since few cells result in limited amounts of genomic DNA, only a limited number of markers can be tested. To evaluate this, call rates of the amplified DNA samples using Bovine SN P50 bead chip with cells collected after biopsy and cells cultured for a day or two after biopsy were determined (Table 7). DNA amplified from whole embryos and fetal fibroblast cell lines were used as control.

TABLE-US-00007 TABLE 7 Call rates of the samples analyzed Sample ID DNA amplified from Call rates (%) F21 Fibroblast cells 99.0 E11 Whole embryo 94.6 B1 Biopsy 6-8 cells 79.8 B2 Biopsy 6-8 cells 81.9 B3 Biopsy 6-8 cells 36.7 B4 Biopsy after two days of culture 75.5 B5 Biopsy after two days of culture 80.0

[0062] When the call rates of the biopsy samples are optimized (e.g., are uniformly above 80%) for accurate genetic analysis, we may use the expanded cells from the biopsy for WGA, while freezing the biopsied embryos. Based on the results from WGA, superior embryos are selected to produce calves.

OTHER EMBODIMENTS

[0063] Although each of the embodiments described above has been illustrated with various components having particular respective orientations, it should be understood that the system and methods as described in the present disclosure may take on a variety of specific configurations with the various components being located in a variety of positions and mutual orientations and still remain within the spirit and scope of the present disclosure. Furthermore, suitable equivalents may be used in place of or in addition to the various components, the function and use of such substitute or additional components being held to be familiar to those skilled in the art and are therefore regarded as falling within the scope of the present disclosure. Therefore, the present examples are to be considered as illustrative and not restrictive, and the present disclosure is not to be limited to the details given herein but may be modified within the scope of the appended claims.

[0064] All patents, patent applications, patent application publications, and other publications cited or referred to in this specification are herein incorporated by reference to the same extent as if each independent patent, patent application, patent application publication or publication was specifically and individually indicated to be incorporated by reference. Such patent applications specifically include United States Provisional Patent Application No. 61/716,294, filed Oct. 19, 2012, from which this application claims benefit.