PMID- 32439843
OWN - NLM
STAT- MEDLINE
DCOM- 20201201
LR  - 20240328
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 10
IP  - 1
DP  - 2020 May 21
TI  - Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new 
      co-expression and regulatory impact factor approach.
PG  - 8436
LID - 10.1038/s41598-020-65454-7 [doi]
LID - 8436
AB  - Mineral contents in bovine muscle can affect meat quality, growth, health, and 
      reproductive traits. To better understand the genetic basis of this phenotype in 
      Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression 
      data from 114 muscle samples. The analysis implemented a new application for two 
      complementary algorithms: the partial correlation and information theory (PCIT) 
      and the regulatory impact factor (RIF), in which we included the estimated 
      genomic breeding values (GEBVs) for the phenotypes additionally to the expression 
      levels, originally proposed for these methods. We used PCIT to determine putative 
      regulatory relationships based on significant associations between gene 
      expression and GEBVs for each mineral amount. Then, RIF was adopted to determine 
      the regulatory impact of genes and miRNAs expression over the GEBVs for the 
      mineral amounts. We also investigated over-represented pathways, as well as 
      pieces of evidences from previous studies carried in the same population and in 
      the literature, to determine regulatory genes for the mineral amounts. For 
      example, NOX1 expression level was positively correlated to Zinc and has been 
      described as Zinc-regulated in humans. Based on our approach, we were able to 
      identify genes, miRNAs and pathways not yet described as underlying mineral 
      amount. The results support the hypothesis that extracellular matrix interactions 
      are the core regulator of mineral amount in muscle cells. Putative regulators 
      described here add information to this hypothesis, expanding the knowledge on 
      molecular relationships between gene expression and minerals.
FAU - Afonso, Juliana
AU  - Afonso J
AUID- ORCID: 0000-0002-4435-5386
AD  - Department of Evolutionary Genetics and Molecular Biology, Federal University of 
      Sao Carlos, Sao Carlos, Brazil.
FAU - Fortes, Marina Rufino Salinas
AU  - Fortes MRS
AUID- ORCID: 0000-0002-7254-1960
AD  - School of Chemistry and Molecular Biosciences, Faculty of Sciences, The 
      University of Queensland, Brisbane, Australia.
FAU - Reverter, Antonio
AU  - Reverter A
AD  - Agriculture and Food, Commonwealth Scientific and Industrial Research 
      Organisation, Brisbane, Australia.
FAU - Diniz, Wellison Jarles da Silva
AU  - Diniz WJDS
AUID- ORCID: 0000-0003-1082-5535
AD  - Department of Evolutionary Genetics and Molecular Biology, Federal University of 
      Sao Carlos, Sao Carlos, Brazil.
FAU - Cesar, Aline Silva Mello
AU  - Cesar ASM
AUID- ORCID: 0000-0001-9921-214X
AD  - Department of Agroindustry, Food and Nutrition, University of Sao Paulo/ESALQ, 
      Piracicaba, Brazil.
FAU - Lima, Andressa Oliveira de
AU  - Lima AO
AD  - Department of Evolutionary Genetics and Molecular Biology, Federal University of 
      Sao Carlos, Sao Carlos, Brazil.
FAU - Petrini, Juliana
AU  - Petrini J
AD  - Department of Statistics, Institute of Exact Sciences, Federal University of 
      Alfenas, Alfenas, Brazil.
FAU - de Souza, Marcela M
AU  - de Souza MM
AUID- ORCID: 0000-0001-7512-5893
AD  - Department of Animal Science, Iowa State University, Ames, IA, USA.
FAU - Coutinho, Luiz Lehmann
AU  - Coutinho LL
AUID- ORCID: 0000-0002-7266-8881
AD  - Department of Animal Science, University of Sao Paulo/ESALQ, Piracicaba, Brazil.
FAU - Mourao, Gerson Barreto
AU  - Mourao GB
AD  - Department of Agroindustry, Food and Nutrition, University of Sao Paulo/ESALQ, 
      Piracicaba, Brazil.
FAU - Zerlotini, Adhemar
AU  - Zerlotini A
AUID- ORCID: 0000-0002-7739-0284
AD  - Bioinformatic Multi-user Laboratory, Embrapa Informatica Agropecuaria, Campinas, 
      Sao Paulo, Brazil.
FAU - Gromboni, Caio Fernando
AU  - Gromboni CF
AD  - Bahia Federal Institute of Education, Science and Technology, Ilheus, Brazil.
FAU - Nogueira, Ana Rita Araujo
AU  - Nogueira ARA
AUID- ORCID: 0000-0003-3648-2956
AD  - Embrapa Pecuaria Sudeste, Sao Carlos, Brazil.
FAU - Regitano, Luciana Correia de Almeida
AU  - Regitano LCA
AUID- ORCID: 0000-0001-9242-8351
AD  - Embrapa Pecuaria Sudeste, Sao Carlos, Brazil. luciana.regitano@embrapa.br.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200521
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
RN  - 0 (MicroRNAs)
RN  - 0 (Minerals)
RN  - 0 (RNA, Messenger)
SB  - IM
MH  - Animals
MH  - Cattle
MH  - *Gene Expression Regulation
MH  - *Gene Regulatory Networks
MH  - Genome
MH  - MicroRNAs/genetics/*metabolism
MH  - Minerals/*metabolism
MH  - Muscle, Skeletal/*metabolism
MH  - *Phenotype
MH  - RNA, Messenger/genetics/*metabolism
PMC - PMC7242321
COIS- The authors declare no competing interests.
EDAT- 2020/05/23 06:00
MHDA- 2020/12/02 06:00
PMCR- 2020/05/21
CRDT- 2020/05/23 06:00
PHST- 2019/11/06 00:00 [received]
PHST- 2020/05/04 00:00 [accepted]
PHST- 2020/05/23 06:00 [entrez]
PHST- 2020/05/23 06:00 [pubmed]
PHST- 2020/12/02 06:00 [medline]
PHST- 2020/05/21 00:00 [pmc-release]
AID - 10.1038/s41598-020-65454-7 [pii]
AID - 65454 [pii]
AID - 10.1038/s41598-020-65454-7 [doi]
PST - epublish
SO  - Sci Rep. 2020 May 21;10(1):8436. doi: 10.1038/s41598-020-65454-7.