ASSEMBLY OF THE BOVINE PAN-TRANSCRIPTOMES FOR IMPROVED GENOME ANNOTATION AND PHENOME PREDICTION

<b>Project Methods</b><br> For Specific Objective 1, We will collect samples from Bos taurus (Angus), Bos indicus (Brahman) and Bos javanicus (Bali cattle). Ovis aries (sheep) will serve as a control. Three males and three females will represent each species/sub-species. At slaughter age, over 30 tissues will be collected from both sexes plus five sex-specific tissues. At the genome level, blood samples will be used to extract DNA for whole genome sequencing with 6x coverage. At the transcriptome level, a short-read library per tissue/individual will be constructed, but a tissue pool per species/sub-species will be formed to generate long-read transcripts. At the phenome level, carcass traits (including organ weights), meat quality and fatty acid profiles will be collected from each animal. Upon completion of Specific Objective 1, we will have information on 1) how genomes, transcriptomes and phenomes are evolutionarily conserved among four species/sub-species; 2) if distal pan-transcriptomes are more commonly used than proximal pan-transcriptomes; 3) whether or not gene biotypes, sex and tissues affect pan-transcriptomes and 4) whether or not pan-transcriptomes serve as bridges between genomes and phenomes.For Specific Objective 2, trials will be conducted in both USA and Australia to complete the funded research. We will screen over 1,000 beef cattle in each country for both internal parasites and dark cutting beef phenotypes and then select 50 top vs 50 bottom animals per trial per country to collect both DNA and RNA variants as described above. Upon completion of Specific Objective 2, we will have information on 1) whether or not there are common or specific pan-transcriptomes and the gene-networks altered by parasites and stressors; 2) whether or not there are common or specific DNA variants that might control expression of the altered pan-transcriptomes (eQTLs); 3) whether or not pan-transcriptomes can be used to narrow down QTLs associated with internal parasite infection and dark cutting beef; and 4) how important it is to include RNA variants in genome prediction of phenotypes.Efforts. We will share all data in standard formats. The image files will be saved as jpg, tif and stk. Data quantification files will be compiled in pzfx, xls and xlsx. Sequencing raw data will be packed in tar.gz files. Clean reads will be stored as FASTA/FASTQ/SAM/BAM, BAX, ta.bz2, GFF and xlsx file formats. We will hire undergraduate students, two graduate students and three technicians to conduct the proposed research for data collection, generation and processing. One Ph.D. student will be responsible for the data management and implementation under supervision of PD and co-PDs.Evaluation. We will perform pre-project evaluation, ongoing evaluation and post-project evaluation. In fact, we have completed the pre-project evaluation based on reviewers' concern. In brief, to minimize effects of environment, taurine and indicine samples will be collected from cattle raised in Hawaii, rather than in both Washington and Hawaii. As for the ongoing evaluation, we will focus on research plans, activity coordination, assay design, data review, manuscript preparation, budget spending and quality of work. Our post-project evaluation will examine research productivity, service efficiency, societal impact, scientific values and innovative outcomes.