Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00281/full |
| _version_ | 1811264207520268288 |
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| author | Wentao Cai Cong Li Shuli Liu Chenghao Zhou Hongwei Yin Jiuzhou Song Qin Zhang Shengli Zhang |
| author_facet | Wentao Cai Cong Li Shuli Liu Chenghao Zhou Hongwei Yin Jiuzhou Song Qin Zhang Shengli Zhang |
| author_sort | Wentao Cai |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality. |
| first_indexed | 2024-04-12T19:59:02Z |
| format | Article |
| id | doaj.art-78980d5ad47a4a45957f09cadb8c6e72 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T19:59:02Z |
| publishDate | 2018-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-78980d5ad47a4a45957f09cadb8c6e722022-12-22T03:18:35ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-07-01910.3389/fgene.2018.00281 357739Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein CowsWentao Cai0Cong Li1Shuli Liu2Chenghao Zhou3Hongwei Yin4Jiuzhou Song5Qin Zhang6Shengli Zhang7Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaShaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaDepartment of Animal and Avian Science, University of Maryland, College Park, MD, United StatesKey Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLong non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality.https://www.frontiersin.org/article/10.3389/fgene.2018.00281/fulllong non-coding RNAmammary glandtranscriptomemilk proteinsintegrate study |
| spellingShingle | Wentao Cai Cong Li Shuli Liu Chenghao Zhou Hongwei Yin Jiuzhou Song Qin Zhang Shengli Zhang Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows Frontiers in Genetics long non-coding RNA mammary gland transcriptome milk proteins integrate study |
| title | Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows |
| title_full | Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows |
| title_fullStr | Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows |
| title_full_unstemmed | Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows |
| title_short | Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows |
| title_sort | genome wide identification of novel long non coding rnas and their potential associations with milk proteins in chinese holstein cows |
| topic | long non-coding RNA mammary gland transcriptome milk proteins integrate study |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00281/full |
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