Juan F. Medrano

Current Research Areas

  1. Bovine reference genome assembly
  2. Coffee genome assembly and transcriptome analysis
  3. Manipulation of spatial grazing behavior in cattle
  4. RNA sequencing as a tool to explore the functionality of milk composition
  5. Gene co-expression network analysis

1. Bovine reference genome assembly

Collaboration in the development of a new significantly improved bovine genome reference assembly of Dominette using an 80X coverage of PacBio sequencing reads. A FALCON de-novo assembly was followed by scaffolding with Dovetail Genomics Chicago library/HiRise technology, the BtOM1.0 Optical Map of Dominette, and a recombination map of 59K autosomal SNPs. Chromosome length scaffolds have been produced. A public version of the new ARS-UCD assembly is expected to be released at the beginning of 2017. [PAG 2017, W138]

2. Coffee genome assembly and transcriptome analysis

We are developing the genome sequence of Coffea arabica variety Geisha that is grown in Goleta, California. RNA samples from different tissues and developmental stages were collected and sequenced to enhance gene model prediction. We are also studying the variation between Geisha plants and 12 different varieties at the whole genome level relevant to coffee quality and environmental adaptation. We are also examining gene expression differences between coffee varieties grown at different altitudes. It is known that coffee grown at higher altitudes acquire unique flavor characteristics, whose molecular differences would be economically important to identify. [Publications: PAG-2013 P0802, PAG-2017 W176]

3. Manipulation of spatial grazing behavior in cattle (High Altitude vs Bottom Dwellers)

Identification of genetic markers that can be used for selection of animals adapted for mountainous terrain or extensive paddocks as a grassland management tool. (Collaboration with D. Bailey, New Mexico State U and M Thomas Colorado State U) [Publications: Rangeland Ecology Management 68:142-149] [Hill Climbing Cows]

4. RNA sequencing as a tool to explore the functionality of milk composition

We have utilized RNA sequencing of different milk cellular components (somatic cells, milk fat globule membrane, mammary epithelial cells and others) to examine the milk transcriptome to study functional metabolic pathways affecting the composition and manufacturing properties of milk. The opportunity to sample the milk transcriptome in a non-invasive way has allowed extending this work to several other organisms, including cattle, macaque and human. [Publications PMID: 21057797, 21541029, 22276848, 22261723, 23403202, 24330573, 24620897, 25001089, 25908898]

5. Gene co-expression network analysis

Gene co-expression networks have been used to study QTL associations and the underlying regulation of those genes involved, as a means to expand our understanding of genotype-phenotype associations. We are currently examining the regulation of the PRE and POST puberty states in Angus and Brahman heifers. The analysis combines results from RNA-Seq (8 tissues), GWAS, and bovine transcription factors. (Collaboration with M.Thomas, Colorado State U., A. Reverter, CSIRO, S. Moore U. Queensland) [Publications PMID: 22739780 , 25048735, 27898892]

Recent Collaborations

Transcriptomics of high altitude/brisket disease

High altitude disease is partly associated with vascular inflammation of the pulmonary artery due to hypoxia, resulting in pulmonary hypertension that can lead to congestive heart failure. To understand the etiology of this disease, we are using RNA-Seq and network analysis to examine the transcriptome of pulmonary artery fibroblasts derived from Healthy and Hypertensive neonatal Holstein calves. (Collaboration with K. Stenmark, U. of Colorado and M. Thomas, Colorado State U.) [Publications PMID:27562971]

Molecular phylogeny and SNP variation of wild populations

We sequenced DNA pools of Polar, Brown and Black bears using next generation sequencing to perform a molecular phylogeny analysis. (Collaboration with Matt Cronin, University of Alaska) [Publications PMID:24477675].

Analysis SNP variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves, dogs, and coyotes in North America in relation to taxonomy and conservation management. [Publication PMID: 25429025]