Methods for generating, evaluating, gene editing and cloning pluripotent stem cells comprising a lethal haplotype

1. A method of evaluating a bovine embryo comprising:

fertilizing an egg obtained from a first bovine heterozygote of a recessive lethal haplotype with sperm cells obtained from a second bovine heterozygote of the recessive lethal haplotype;

producing the embryo from the fertilized egg, wherein the embryo is homozygous for the lethal haplotype;

establishing a stem cell culture from the embryo;

collecting a plurality of cultured stem cells; and

obtaining omics data, comprising one or more features, from the plurality of cultured stem cells.

2. The method of claim 1 , wherein the recessive lethal haplotype is selected from the group consisting of: AH1, HH1, HH2, HH3, HH4, HH5, HH6, JH1, JH2, BH1 and BH2.

3. The method of claim 1 , wherein the step of establishing a cell culture from the embryo comprises culturing the embryo at the blastocyst stage.

4. The method of claim 1 , wherein the omics data is comprised of genotypic, proteomic or transcriptomic data.

5. The method of claim 1 , wherein the step of establishing a cell culture comprises placing the embryo, or a cell sample from the embryo, on a first substrate in a first culture media comprising a low free-fatty acid BSA (bovine serum albumin), Fibroblast Growth Factor 2 and an inhibitor of Wnt signaling for 5-15 days and thereafter dissociating cell outgrowths on the first substrate and placing the cell outgrowths on a second substrate in a second culture media comprising a ROCK (Rho-associated coiled-coil containing kinase) inhibitor.

6. The method of claim 5 , wherein the first substrate and the second substrate are comprised of irradiated mouse embryonic fibroblasts.

7. The method of claim 5 , wherein the cell sample from the embryo comprises cells from the inner cell mass of the embryo.

8. A method of evaluating a plurality of bovine embryos comprising:

fertilizing a plurality of eggs obtained from one or more female bovine heterozygotes of a recessive lethal haplotype with sperm cells obtained from one or more male bovine heterozygotes of the recessive lethal haplotype;

producing the plurality of embryos from the plurality of fertilized eggs, wherein the embryos are homozygous for the lethal haplotype;

identifying a first group of one or more embryos from the plurality of embryos that are underdeveloped or dead after a first period of time;

establishing a stem cell culture from each of the embryos in the identified first group;

collecting cultured stem cells from each of the established stem cell cultures; and

obtaining omics data from the collected cultured stem cells.

9. The method of claim 8 , wherein the omics data comprises one or more features.

10. The method of claim 8 , further comprising the steps of:

identifying a second group of one or more embryos from the plurality of embryos that are underdeveloped or dead after a second period of time; and

obtaining omics data from the identified second group.

11. The method of claim 10 , wherein the omics data is comprised of genotypic, proteomic or transcriptomic data.

12. The method of claim 8 , wherein the recessive lethal haplotype is selected from the group consisting of: AH1, HH1, HH2, HH3, HH4, HH5, HH6, JH1, JH2, BH1 and BH2.