GENETIC IMPROVEMENTS OF HAWAII BEEF CATTLE USING CUTTING-EDGE GENOMIC APPROACHES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1021758
• Project Start Date: Feb 18, 2020
• Project End Date: Sep 30, 2024
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIV OF HAWAII
3190 MAILE WAY
HONOLULU,HI 96822

Performing Department
Human Nutrition, Food & Animal Sciences

Non Technical Summary
Hawaii local beef cattle are 100% Grass-Fed & finished and produce top-quality of the carcass, but the overall production of local beef cannot meet the total consumption of Hawaii tourists and locals because of economic and geographic reasons. This project will apply molecular and quantitative genetics strategies combing cutting-edge genomic approaches including deep sequencing and CRISPR technologies to study mechanisms of skeletal muscle development and improve Hawaii beef cattle production.

Animal Health Component

30%

Research Effort Categories

Basic

40%

Applied

30%

Developmental

30%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3310	1081	40%
304	3310	1080	40%
311	3310	1040	20%

Knowledge Area
303 - Genetic Improvement of Animals; 311 - Animal Diseases; 304 - Animal Genome;

Subject Of Investigation
3310 - Beef cattle, live animal;

Field Of Science
1040 - Molecular biology; 1081 - Breeding; 1080 - Genetics;

Keywords

beef

muscle

genomics

gs

gwas

epigenetics

Goals / Objectives
Investigate the genetic background of Hawaii local beef cattle.Screen the significant genetic and epigenetic marks associated with production and reproduction traits by using Genome-Wide Association Study (GWAS) and Next Generation Sequencing (NGS) approaches.Apply more accurate Genomic Selection (GS) in Hawaii beef cattle populations across different islands.

Project Methods
We expect to select better breeding cattle and improve production and reproduction traits as well as the health of offspring and promote its genetic progress in the long-term for Hawaii's local beef cattle genetic improvements. To justify the strategy, I state that as four approaches below.Approach 1: If we know the genetic background of Hawaii local beef cattle, we can pick up the closest beef population in the genetic background for Genomic Selection Application based on Genetic Evaluation Parameters released by USDA.Approach 2: If we do not know the genetic background of Hawaii local beef cattle, we can investigate it using Illumina BovineSNP50 in roughly 300 individuals from different ranchers across multiple islands. It is better to have phenotypic data records (eg. birth weight) for these 300 cattle for Approach 3, Genome-Wide Association Study (GWAS). Once we get genotypes of our population individuals, that would be incorporated into published datasets (Decker, McKay et al. 2014) to comprehensively analyze the patterns of ancestry, divergence, and admixture of Hawaii beef cattle, and hopefully, we would get the closest beef population for Genomic Selection Application same described as Approach 1.Approach 3: For those 300 genotyped individuals, we would combine phenotypic data to identify SNP markers associated with production traits, eg. birth weight, meat production, and tenderness, using GWAS. The genetic progress will be monitored and measured every year and GWAS and GS will be applied again to eventually screen out the most significant SNP marks for production traits.Approach 4: Molecular genetic improvements: by comparing to the beef cattle from the mainland or other countries, explore genetic or epigenetic marks that could regulate carcass weight, meat tenderness or marbling content, reproduction traits, flavors, and disease resistance, which would provide info for GS to select best breeding cattle.

Progress 02/18/20 to 09/30/20

Outputs
Target Audience: The target audiences for this project will be scientists in the field of genomics and epigenomics onbeef and dairy cattle. Farmers, ranchers, and animal breeding companies will also be my target audiences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?01/2020 I was awarded theFaculty Travel Grant in the amount of $1,700 from the UHM, supporting the travel for the Plant and Animal Genome XXVIII Conference in San Diego, California, USA 07/2020 I was awarded a NanoString Research Grant in the amount of $3,000 from NanoString Technologies, Inc., supporting miRNA studies in myostatin transgenic mice 03/2020-03/2021 I was awarded Beef team science project grant in the amount of $8,000 from UH CTAHR, supporting genetics studies in Hawaiian beef cattle My student, Mandeep Adhikari, was awarded the scholarships below: July 2020:awarded more module registration scholarships to attend the 2020 Online Summer Institute in Statistical Genetics (SISG). August 2020:selected as a participant in the East-West Center (EWC) Fall 2020 Student Affiliate Program October 2020:awarded registration scholarship to participate in the SACNAS Conference My student,Huong Thanh Vu, was awarded the scholarships below: January 2020:awarded 2020 Student Fellow of the International Livestock Forum July 2020:awarded more module registration scholarships to attend the 2020 Online Summer Institute in Statistical Genetics (SISG). How have the results been disseminated to communities of interest?The results have or will be disseminated to the communities of interests by publications, CTAHR News, Hawaii News, and/or some professional conferences and workshops. What do you plan to do during the next reporting period to accomplish the goals?1. Collect blood and hair samples from ~200 beef cattle in Hawaii 2. Genotype the beef cattle collected in Hawaii 3. Analyze genotypicdata and collect phenotypic data as much as possible 4. Publish some articles

Impacts
What was accomplished under these goals? Aim 1: Explore whether Diverse Geographic Features of Hawaiian Ranches Affect Their Cattle Performance Collaborators: HNFAS extension faculties and Dr. Thomas W. Giambelluca's group from the Department of Geography and Environment at UHM Progress: we have collected all of the climate data and completed over 80% of comprehensive data analysis in major ranches in the Hawaiian Islands. Accomplishments: a research article was prepared and will be submitted to the journal - Frontiers in Genetics soon. Aim 2: Explore genetic diversity of beef cattle in Hawaii using SNP chips Progress: we plan to genotype 300-400 beef cattle in Hawaii to investigate their genetic drift and diversity. The sample collection has been delayed because of COVID-19, but it will begin soon once the situation is better.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Liu, J., Liu, F., Cai, W., Jia, C., Bai, Y., He, Y., Zhu, W., Li, R.W., and Song, J. 2020. Jejunal Microbiome and Bile Acids Induced by Diets in Angus Beef Cattle. Animal Microbiome volume 2, Article number: 33 (2020)
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Bai, H., He, Y., Ding, Y., Chu, Q., Lian, L., Heifetz, E.M., Yang, N., Cheng, H.H., Zhang, H., Chen, J., and Song, J. 2020. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genetics. 2020 Jul 16; 21(1):77. doi: 10.1186/s12863-020-00884-w.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Bai, Y., Carrillo, J.A., Li, Y., He, Y., and Song, J. 2020. Diet induced the change of mtDNA copy number and metabolism in Angus cattle. Journal of Animal Science and Biotechnology volume 11, Article number: 84 (2020)
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lazzarotto, C.R., Malinin, N.L., Li, Y., Zhang, R., Yang, Y., He, Y., Lan, X., Jividen, K., Katta1, V., Kolmakova, N.G., Petersen, C.T., Qi, Q., Strelcov, E., Maragh, S., Krenciute, G., Ma, J., Cheng, Y., and Tsai, S.Q. 2020. CHANGE-seq reveals genetic and epigenetic effects on CRISPRCas9 genome-wide activity. Nature Biotechnology (IF 36.558). volume 38, pages13171327(2020) https://doi.org/10.1038/s41587-020-0555-7