top of page
A little bit about Joel...
Joel's research is focused on uncovering the genetic architecture of complex phenotypes using animal models and farm animals. He has applied bioinformatics and statistical tools to multiple complex phenotypes.
During his graduate studies, Joel researched complex phenotypes in farm animals, including meat quality, tenderness, and water-holding capacity in beef cattle. After finishing his graduate studies, he researched complex biomedical traits using animal models. His research included phenotypes such as unilateral kidney agenesis, cocaine contextual conditioning, cocaine-conditioned cue preference, and metabolomics features recorded in a heterogeneous stock rat population.
Joel has performed, amongst other analyses, protein modeling, whole genome associations, gene mapping based on structural equation modeling, differential expression analyses, eQTL and sQTL mapping, and identifying genomic hubs influencing cecum metabolome composition in both farm species and animal models.
Original research (click to follow the publication)
 Completed research: Genetic basis of cecum metabolome composition in heterogeneous stock rats identifies ABC and SLC transporters and enzymes including CES, CYP, and UGT as associated with metabolome abundance. Main results: * Enzymes and transporters such as UGTs, LSS and SLCs were identified by using a conditional association analysis. * In most cases the conditional associated polymorphisms identified might drive expression of the tagged genes. |  Completed research: Whole genome association meta-analysis on Pavlovian conditioned approach (PavCA) behaviors and related phenotypes in heterogeneous stock and Sprague Dawley rat populations Main results: * Identified genes for PavCA behaviors included Neuromedin B (NMB), Olfactory receptors (OLRS), Fucosyltransferase 9 (FUT9), Trafficking Protein Particle Complex Subunit 9 (TRAPPC9), and Cerebellin 2 Precursor (CBLN2). |  Completed research: Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and several TFs. Main results: * A significantly associated region on chr 14, between positions 32 and 37 Mb was identified. * This associated locus harbors an ERV insertion (LTR1-ERV-LTR2). * TFs such as AHR, ATF3, GATA3, HNF1B and TFCP2 are potential candidates to explain incomplete penetrance. |
|---|---|---|
 Completed research: Structural equation modeling for understanding the genetic architecture of cocaine contextual conditioning and cocaine conditioned cue preference in heterogeneous stock rats undercover candidate genes for behavioral variation caused by cocaine exposure. Main results: * CFA models for CCC and for CCP were constructed. * CFA-CCC allowed for identifying the candidate genes OLR109s, PENK, TRPV2, and ZSWIM6. * CFA-CCP model allowed for mapping HNRNPA1, LARGE1, and SLITRK3. |  Published paper: Identification of eQTLs and sQTLs associated with meat quality in beef (2020). Main results: * A total number of 14,536 eQTLs were identified. * For Cis-acting regulation, 12.1% were found in a non-DEG gene and only 2.9% involved a DEG gene. * A total number of 23 master regulators were uncovered. |  Published paper: RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef (2020). Main results: * Expression of 208 genes was associated with a meat quality index. * A total number of 1,286, 230 and 219 genes were DE for WBSF, tenderness and marbling, respectively. * Seven pathways were enriched across analysis and they are related to cytoskeletal proteins. |
 Published paper: Whole genome sequence data provides novel insights into the genetic architecture of meat quality traits in beef (2020). Main results: * An associated region on BTA29 (36,432,655–44,313,046 bp) was found. * This region harbors 13 highly significant markers for meat quality traits. * Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. * The final protein–protein network included 431 interations between 349 genes. |  Published paper: Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef (2019). Main results: * A total of 52 genes distributed in 68 genomic regions were associated with meat quality. * Some pathways including “Endoplasmic reticulum membrane” were determined as enriched. * Eleven clusters related to transmembrane or structural proteins were uncovered. |  Published review: Genetic basis of improving the palatability of beef cattle: Current insights (2019) It discusses the current knowledge of quantitative and molecular genetic aspects of palatability. It also examines the implications of genetic manipulation for the cattle industry. |
 Published paper: Structural equation modeling and whole-genome scans uncover chromosome regions and enriched pathways for carcass and meat quality in beef (2018). Main results: * 159 regions were associated with carcass quality. * 106 regions were associated with both carcass and meat quality. * 242 regions were associated with meat quality. * 64 regions were associated with carcass quality, having an indirect effect on meat quality. |  Published paper: Association of μ-calpain and calpastatin polymorphisms with meat tenderness in a Brahman–Angus population (2018). Main results: * One LD-block in calpastatin had a significant effect on tenderness. * The TG-CG diplotype was associated with more tender meat. * Four markers inside this LD-block were found to be significantly associated with tenderness. |  Published paper: Computational analysis of polymorphisms in genes of the μ-calpain/calpastatin system in bovine meat quality (2015). Main results: * SNPs such as C283T and C872T in calpastatin modify molecular features at mRNA and protein level. * The A2959G SNP in calpastatin is associated with meat quality in a number of populations and was able to modify mRNA stability in-silico. |
 Published paper: Polymorphisms in CAPN1, CAST, DES, PRKAG3 and RYR1 genes associated with water holding capacity in raw and cooked meat from crossbred Bos indicus and Bos taurus in Colombia (2015). Main results: * The CAST2959 polymorphism was associated with water holding capacity in raw meat being the favorable genotype AA. * The RYR1-11195 marker was associated with water holding capacity in cooked meat and the favorable genotype was AA. |  Published paper: Computational analysis of mutations in the bovine PRKAG3 gene associated with meat quality (2014). Main results: * The bovine 1796C and 2338T polymorphism at mRNA level and 389T at protein level can theoretically modify molecular activity. * The porcine 200Q (RN-) polymorphism can alter some molecular features at mRNA and protein level in-silico. |  Published paper: In-silico Analysis of Missense Mutation of Bovine RYR1 Protein (2014). Main results: * Several bovine alleles (827E, mainly) have an important alteration of electrostatic potential. * This trait is also altered in the 615C allele in pork. |
 Published paper: Effect of genetic type and aging on water holding capacity in meat from castrated bulls (2014). Main results: * Breed composition had a significant effect on water holding capacity in raw and cooked meat. * Limousin-Brahman crossbred animals had the best performance on water holding capacity. |
bottom of page