An Update on Bison Genetics and Genomics"

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1 An Update on Bison Genetics and Genomics" Dr. James Derr, Professor Texas A&M University Texas Bison Association 26 October 2013 Crockett, Texas

2 American Bison are found in all shapes, sizes and colors National Buffalo Museum, ND

3 This presentation A couple of short examples of using genetic technology to understand bison better. An update on bison genome sequencing. Overview of bison genetic services offered at Texas A&M University Examples of how to collect genetic samples from bison. TAMU-CVM Continuing Education course.

4 What can we do with genetic data from wildlife? One quick example from our bison studies at Wind Cave National Park. We sampled the entire herd >400 animals in 1999 (sex ratio is 1:1). Sampled all calves each year through Parentage tested all offspring for 10 years. Our findings were unexpected!

5 Total number of bulls Total number offspring produced by individual bulls, bulls produced 280 calves 7.5% (8 bulls) produced 26.4% (74 calves) Number of offspring

6 Percentage of calves produced Bull breeding age vs. percentage of calves produced Average Age of bull at breeding

7 Percentage of calves produced Cow breeding age vs. percentage of calves produced Average Age of cow at breeding

8 We have good idea of the breeding structure of this fairly large bison herd. It is different than we expected. Herd management decisions regarding the long-term conservation of genetic diversity can now be based on empirical knowledge. Modern genetic biotechnology is the only way to learn this information.

9 Phenotypic Effects of Cattle Mitochondrial DNA in American Bison We conducted two separate studies to determine if mitochondrial status of a bison has a biological effect. Nutritionally stressful environment. Santa Catalina Island 329 animals sampled in 2004 and 2009 All animals were weighed and in 2009 all animals were measured for height. 47% of the bison had domestic cattle mtdna Nutritionally rich environment. Private feedlot All bull calves 618 animals started the study at weaning and were weighed 8 times over 26 months. 6% of the bison had domestic cattle mtdna

10 Mean weight (SE) for male and female bison from Santa Catalina Island with bison mtdna (shaded bars) or cattle mtdna (open bars) for samples from 2004 and 2009, for 2004 and 2009 combined, and for combined males and females and years. Combined mean difference across both years is 7.8% (25.7 lbs.). Bison with domestic cattle mtdna were consistently smaller in the harsh nutritional study (Santa Catalina Island).

Mean weight (SE) every 90 120 days for young bison males with bison (shaded bars) or cattle (unshaded bars) mtdna from a feedlot (n, sample size).

11 Mean weight (SE) every days for young bison males with bison (shaded bars) or cattle (unshaded bars) mtdna from a feedlot (n, sample size). All differences were statistically significant (p < 0.01). The mean difference at weaning weight was 7% (28.7 lbs.) and at the final weight was 4% (43 lbs.). Bison with domestic cattle mtdna were consistently smaller in the high nutritional study (feedlot). Both studies resulted in the same conclusion, bison with domestic cattle mtdna are, on average, smaller.

12 The hybridization experiments conducted by some of the owners of the five foundation herds of the late 1800s, have left a legacy of a small amount of cattle genetics in many of our existing bison herds.

13 So What if a Bison Herd Has Cattle mtdna? First, the ability to identify bison populations with hybrid ancestry provides information to make responsible conservation decisions regarding the introduction of animals into bison populations that have no evidence of past hybridization. Second, perpetuating animals in production herds with domestic cattle mtdna, across different nutrition platforms, results in the production of smaller animals on average.

14 Bison Genomics

15 The first American bison to have its genome completely sequenced was this animal from Yellowstone NP. His name is Templeton

17 Funding USDA National Buffalo Foundation Turner Foundation Texas A&M University Foundation Texas A&M University College of Veterinary Medicine This is part of Ms. Lauren Dobson s Ph.D research. Collaborators Iowa State University James Reecy Julie Blanchong USDA Infectious Bacterial Diseases Research Unit Steven Olsen David Alt USDA Meat and Animal Research Center Tim Smith University of Maryland Aleksey Zimin

18 Additional Bison Genomes Wood Buffalo from Elk Island National Park (4 composite DNAs). Texas State Bison Herd (4 composite DNAs). Historical Bison sample (died 1856 in Hayden Valley). European Bison (Wisent from Poland).

19 We are sequencing bison genomes that predate the population bottleneck of the late 1800s (Turner Foundation Funding). Lauren Dobson and I traveled to the Smithsonian Institution in last year to collect historic bison samples.

21 Why Sequence Bison Genomes? Identify all genes that define bison. Immune system, disease traits, production traits, behavior traits, fertility traits, feed conversion traits, etc. Compare bison species, subspecies and geographic differences (North vs. South) and differences over time (the last 150 years). Document genetic differences between bison and domestic cattle (and other bovids) and develop a bison SNP test to define introgression (there are 3.2 million SNP differences between these two species).

22 Bison Genetic Service Offered at The College of Veterinary Medicine at Texas A&M University Parentage testing. A valuable management tool providing information on male reproductive success and to help avoid inbreeding over time in small populations. Diversity and domestic cattle introgression testing. Mitochondrial and nuclear DNA testing provides helpful information for managing overall levels of genetic diversity in a herd as well as identify, quantify and manage away from unwanted domestic cattle genes in your bison herds.

Min Cai Phone: (979) 862-3991 Phone: (979) 845-9972 E-mail:

.. Mitochondrial DNA (mtdna) Determine if individual has domestic cattle or bison mtdna Nuclear Microsatellites (NMI) - 14 loci For evidence of cattle introgression Parentage Testing (PRTG) - 11 loci

23 Min Cai Phone: (979) Phone: (979) Contact Name:... Phone:... Fax: Mitochondrial DNA (mtdna) Determine if individual has domestic cattle or bison mtdna Nuclear Microsatellites (NMI) - 14 loci For evidence of cattle introgression Parentage Testing (PRTG) - 11 loci All Three Tests (mtdna, NMI, PRTG) mtdna and NMI only DNA Technologies Core Lab VMR Building 1197, Room 226 College Station, TX Genotyping Service Dr. James N. Derr Phone: (979) jderr@cvm.tamu.edu Herd/Ranch Name:... Address:... City:... State:... Zip:... Bison DNA Testing Services Price List <100 Animals >100 Animals (Hair) >100 Animals (FTA card) <100 Animals >100 Animals <100 Animals >100 Animals <100 Animals >100 Animals <100 Animals >100 Animals *Pricing can be negotiated downward for a large number samples and FTA cards. Samples will be archived in the laboratory following analysis. Results typically provided within 2-3 months unless rush service is required. # of Animals x $12 = # of Animals x $8 = # of Animals x $7 = # of Animals x $35 = # of Animals x $25 = # of Animals x $35 = # of Animals x $25 = # of Animals x $45 = # of Animals x $35 = # of Animals x $35 = # of Animals x $25 = I have some of these forms with me if you are interested. Also, these forms are available on our website. This is a non-profit University run facility and all income is invested back in bison research and in support of students and technicians in the laboratory. Make checks payable to: Texas AgriLife Research Total Charges $

24 Collection of Bison Samples for Genetic Analysis.

25 THE TAIL HAIRS. Grab the tail and pull straight out about hairs.

26 Cut off the hair about 1 inch above the hair follicle. (Save the follicle end).

27 Make sure the hair follicles are still on the hairs.

28 It s best to store hairs in a paper envelope.

29 Always label with a pencil

30 GETTING THE BLOOD. A tail stick with a 18 gauge needle is much safer for the workers that neck bleeding. However, sometimes on small animals you must neck bleed.

31 The DNA work requires about 2 MLs of whole blood.

32 Remove the needle from the syringe.

33 Apply the blood with even strokes across the card. Less is better than too much. Optimally, we would like enough blood that you can see red through the back of the card, but not so much that it flows through.

34 After the blood is on the card it MUST dry out completely before storage. Be sure the samples are clearly labeled in pencil & set the cards up tee-pee style to dry.

35 Be sure to turn them loose happy..

37 DART RIFLE TRAINING

38 ANESTHETIZED CROCODILES

39 DEHORNING WHITE RHINOS

40 TRANSPORTED CAPE BUFFALO

41 SABLE ANTELOPE

42 HYSTERECTOMIES ON LIONESS

43 SNARE FROM A GIRAFFE

44 NECROPSY ON A FRESHLY KILLED IMPALA

45 LECTURE ON AFRICAN SNAKES

46 THE CROCODILE RIVER IN KRUGER NP

47 TERRA LUNA LODGE AND THE DORMITORIES

48 ALSO HAD A BIT OF FUN

49 You never know what you might see

Bison Conservation Genetics and Disease

Bison Conservation Genetics and Disease James Derr Department of Veterinary Pathobiology and the Graduate Faculty of Genetics Texas AgriLIFE Research Texas A&M System The Bison Genetics Program at Texas