Joel Leal

PhD Candidate

Joel Leal

PhD Candidate

A little bit about me...

My research is focused on uncovering the genomic architecture of complex phenotypes and beef quality is my model trait. I am applying bioinformatic tools to multiple phenotypic traits measured in beef cattle from the Multibreed Angus-Brahman population of the University of Florida. From this analysis, the main proteolytic system associated with meat tenderness, μ-calpain and calpastatin, and a number of transmembrane anchoring proteins were identified as associated with meat quality. These anchoring proteins may be proteolytic substrates of the μ-calpain and calpastatin system or they could be involved in adipocyte and myocyte proliferation having a direct effect on eating quality.


I am currently working on differential expression analyses for meat quality using RNAseq. Some quantitative trait-associated genes, and differentially expressed genes and isoforms were uncovered. In addition, an eQTLs and sQTLs analysis in skeletal muscle was carried out paying special attention to differentially expressed genes related to meat quality.



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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.

Structural Equation Modeling and Who

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.


Accepted review: Genetic basis of improving the palatability of beef cattle: Current insights In this review, we discuss the current knowledge of quantitative and molecular genetic aspects of palatability and discuss implications of genetic manipulation for the cattle industry.

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Active research: Expression association and differential expression assessment for meat quality identify genes and pathways related to cytoskeletal structure, proliferation-apoptosis and energy metabolism in beef Partial 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.

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Active research: Expression and splicing qualitative trait loci in skeletal muscle focused on meat quality in beef. Partial results: * A total number of 14,536 eQTLs were identified. * For Cis-acting regulation, 12.1% were found in a non-Diff gene and only 2.9% involved a Diff gene. * A total number of 23 master regulators were uncovered.


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 molecule activity. * The porcine 200Q (RN-) polymorphism can alter some molecular features at mRNA and protein level in-silico.


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 population 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: 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 in water holding capacity.