Panda Genetic Research Using Methods of Genetic Analysis for Livestock Species

pandaUsing methods of genetic analysis often used for livestock species, Professor Yang Da, an animal geneticist in the Department of Animal Science, and collaborators at the Minnesota Supercomputer Institute, Sichuan Agricultural University and Chengdu Giant Panda Research Base, recently published two studies on panda inbreeding and relatedness in wild panda populations (panda genomic study [1]) and on genetic composition of the captive panda population (panda genetic study [2]).

The panda genomic study found that wild pandas in some regions had higher levels of inbreeding and relatedness, which appeared to be related to habitat loss in those regions. Pandas from the four largest habitats were genetically unrelated, and most pandas separated by 200 kilometers or more shared no common ancestral alleles. The panda genetic study identified underrepresentation of the smallest wild populations in the captive population and proposed three alternative plans of habitat-controlled breeding to increase the genetic contribution of the smallest wild populations to the captive population. The method of analysis for the panda genomic study was genomic relationship calculated from single nucleotide polymorphism (SNP) markers, an approach widely used in genomic selection in livestock species; whereas the method of analysis for the panda genetic study was conancestry coefficient, a classical concept in quantitative genetics, and habitat-controlled breeding used an approach similar to selection index that is a classical selection method and is still used today in the form of ‘net merit’ for USDA’s national genetic evaluation in dairy cattle.

Students interested in those methods can learn them from Professor Da’s courses. The computing tools used for implementing the data analysis were fully or partially supported by a USDA/AFRI bioinformatics grant to Professor Da. The panda genomic study was highlighted by the Minnesota Supercomputer Institute [3], and the panda genetic study was selected as a featured article of BMC Genetics [4].

1. Garbe, J.R., D. Prakapenka, C. Tan, and Y. Da. 2016. Genomic inbreeding and relatedness in wild panda populations. PLoS ONE 11(8): e0160496. doi:10.1371/journal.pone.0160496.
URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0160496
2. Yang, J., F. Shen, R. Hou, and Y. Da. 2016. Genetic composition of captive panda population. BMC Genetics: 17(1):1-9. doi: 10.1186/s12863-016-0441-y.
URL: https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-016-0441-y
3. Panda Genomics. https://www.msi.umn.edu/content/panda-genomics.
4. Featured Article: Genetic composition of captive panda population. https://bmcgenet.biomedcentral.com/