Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle
The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle. Longissimus thoracis muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate ( n = 10) and low ( n = 10) group...
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| Veröffentlicht in: | Functional & integrative genomics 2022-08, Vol.22 (4), p.451-466 |
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| creator | Muniz, Maria Malane Magalhães Fonseca, Larissa Fernanda Simielli dos Santos Silva, Danielly Beraldo Magalhães, Ana Fabrícia Braga Ferro, Jesus Aparecido Chardulo, Luiz Artur Loyola Baldi, Fernando Cánovas, Angela de Albuquerque, Lucia Galvão |
| description | The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle.
Longissimus thoracis
muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (
n
= 10) and low (
n
= 10) groups) and beef color (desirable (
n
= 10) and undesirable (
n
= 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (
P
-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer. |
| doi_str_mv | 10.1007/s10142-022-00844-w |
| format | Article |
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Longissimus thoracis
muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (
n
= 10) and low (
n
= 10) groups) and beef color (desirable (
n
= 10) and undesirable (
n
= 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (
P
-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.</description><identifier>ISSN: 1438-793X</identifier><identifier>EISSN: 1438-7948</identifier><identifier>DOI: 10.1007/s10142-022-00844-w</identifier><identifier>PMID: 35305194</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Beef ; Biochemistry ; Bioinformatics ; Biomedical and Life Sciences ; Carbon dioxide ; Cell Biology ; Color ; Erythrocytes ; Gene deletion ; Genetic diversity ; Insertion ; Isoforms ; Life Sciences ; Metabolic pathways ; Microbial Genetics and Genomics ; Original Article ; Phenotypes ; Phenylalanine ; Plant Genetics and Genomics ; Transcriptomics ; Tyrosine</subject><ispartof>Functional & integrative genomics, 2022-08, Vol.22 (4), p.451-466</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022</rights><rights>2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.</rights><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c326t-d3069414614e4887ff1fa185c7205bb03d7650103c122ce0db82ba9b942700cf3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10142-022-00844-w$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10142-022-00844-w$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35305194$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Muniz, Maria Malane Magalhães</creatorcontrib><creatorcontrib>Fonseca, Larissa Fernanda Simielli</creatorcontrib><creatorcontrib>dos Santos Silva, Danielly Beraldo</creatorcontrib><creatorcontrib>Magalhães, Ana Fabrícia Braga</creatorcontrib><creatorcontrib>Ferro, Jesus Aparecido</creatorcontrib><creatorcontrib>Chardulo, Luiz Artur Loyola</creatorcontrib><creatorcontrib>Baldi, Fernando</creatorcontrib><creatorcontrib>Cánovas, Angela</creatorcontrib><creatorcontrib>de Albuquerque, Lucia Galvão</creatorcontrib><title>Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle</title><title>Functional & integrative genomics</title><addtitle>Funct Integr Genomics</addtitle><addtitle>Funct Integr Genomics</addtitle><description>The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle.
Longissimus thoracis
muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (
n
= 10) and low (
n
= 10) groups) and beef color (desirable (
n
= 10) and undesirable (
n
= 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (
P
-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.</description><subject>Animal Genetics and Genomics</subject><subject>Beef</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Carbon dioxide</subject><subject>Cell Biology</subject><subject>Color</subject><subject>Erythrocytes</subject><subject>Gene deletion</subject><subject>Genetic diversity</subject><subject>Insertion</subject><subject>Isoforms</subject><subject>Life Sciences</subject><subject>Metabolic pathways</subject><subject>Microbial Genetics and Genomics</subject><subject>Original Article</subject><subject>Phenotypes</subject><subject>Phenylalanine</subject><subject>Plant Genetics and 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diversity</topic><topic>Insertion</topic><topic>Isoforms</topic><topic>Life Sciences</topic><topic>Metabolic pathways</topic><topic>Microbial Genetics and Genomics</topic><topic>Original Article</topic><topic>Phenotypes</topic><topic>Phenylalanine</topic><topic>Plant Genetics and Genomics</topic><topic>Transcriptomics</topic><topic>Tyrosine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Muniz, Maria Malane Magalhães</creatorcontrib><creatorcontrib>Fonseca, Larissa Fernanda Simielli</creatorcontrib><creatorcontrib>dos Santos Silva, Danielly Beraldo</creatorcontrib><creatorcontrib>Magalhães, Ana Fabrícia Braga</creatorcontrib><creatorcontrib>Ferro, Jesus Aparecido</creatorcontrib><creatorcontrib>Chardulo, Luiz Artur Loyola</creatorcontrib><creatorcontrib>Baldi, Fernando</creatorcontrib><creatorcontrib>Cánovas, Angela</creatorcontrib><creatorcontrib>de Albuquerque, Lucia 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Loyola</au><au>Baldi, Fernando</au><au>Cánovas, Angela</au><au>de Albuquerque, Lucia Galvão</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle</atitle><jtitle>Functional & integrative genomics</jtitle><stitle>Funct Integr Genomics</stitle><addtitle>Funct Integr Genomics</addtitle><date>2022-08-01</date><risdate>2022</risdate><volume>22</volume><issue>4</issue><spage>451</spage><epage>466</epage><pages>451-466</pages><issn>1438-793X</issn><eissn>1438-7948</eissn><abstract>The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle.
Longissimus thoracis
muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (
n
= 10) and low (
n
= 10) groups) and beef color (desirable (
n
= 10) and undesirable (
n
= 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (
P
-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>35305194</pmid><doi>10.1007/s10142-022-00844-w</doi><tpages>16</tpages></addata></record> |
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| ispartof | Functional & integrative genomics, 2022-08, Vol.22 (4), p.451-466 |
| issn | 1438-793X 1438-7948 |
| language | eng |
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| source | SpringerNature Journals |
| subjects | Animal Genetics and Genomics Beef Biochemistry Bioinformatics Biomedical and Life Sciences Carbon dioxide Cell Biology Color Erythrocytes Gene deletion Genetic diversity Insertion Isoforms Life Sciences Metabolic pathways Microbial Genetics and Genomics Original Article Phenotypes Phenylalanine Plant Genetics and Genomics Transcriptomics Tyrosine |
| title | Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle |
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