Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks
The development of the four stomachs of yak is closely related to its health and performance, however the underlying molecular mechanisms are largely unknown. Here, we systematically analyzed mRNAs of four stomachs in five growth time points [0 day, 20 days, 60 days, 15 months and 3 years (adult)] o...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-09-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2023.1204706/full |
| _version_ | 1797677032884142080 |
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| author | Yili Liu Qi Min Jiao Tang Lu Yang Xinxin Meng Tao Peng Mingfeng Jiang |
| author_facet | Yili Liu Qi Min Jiao Tang Lu Yang Xinxin Meng Tao Peng Mingfeng Jiang |
| author_sort | Yili Liu |
| collection | DOAJ |
| description | The development of the four stomachs of yak is closely related to its health and performance, however the underlying molecular mechanisms are largely unknown. Here, we systematically analyzed mRNAs of four stomachs in five growth time points [0 day, 20 days, 60 days, 15 months and 3 years (adult)] of yaks. Overall, the expression patterns of DEmRNAs were unique at 0 d, similar at 20 d and 60 d, and similar at 15 m and adult in four stomachs. The expression pattern in abomasum was markedly different from that in rumen, reticulum and omasum. Short Time-series Expression Miner (STEM) analysis demonstrated that multi-model spectra are drastically enriched over time in four stomachs. All the identified mRNAs in rumen, reticulum, omasum and abomasum were classified into 6, 4, 7, and 5 cluster profiles, respectively. Modules 9, 38, and 41 were the most significant three colored modules. By weighted gene co-expression network analysis (WGCNA), a total of 5,486 genes were categorized into 10 modules. CCKBR, KCNQ1, FER1L6, and A4GNT were the hub genes of the turquoise module, and PAK6, TRIM29, ADGRF4, TGM1, and TMEM79 were the hub genes of the blue module. Furthermore, functional KEGG enrichment analysis suggested that the turquoise module was involved in gastric acid secretion, sphingolipid metabolism, ether lipid metabolism, etc., and the blue module was enriched in pancreatic secretion, pantothenate and CoA biosynthesis, and starch and sucrose metabolism, etc. Our study aims to lay a molecular basis for the study of the physiological functions of rumen, reticulum, omasum and abomasum in yaks. It can further elucidate the important roles of these mRNAs in regulation of growth, development and metabolism in yaks, and to provide a theoretical basis for age-appropriate weaning and supplementary feeding in yaks. |
| first_indexed | 2024-03-11T22:39:03Z |
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| id | doaj.art-b716878acad9463c908b4f17b27f645a |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-03-11T22:39:03Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj.art-b716878acad9463c908b4f17b27f645a2023-09-22T10:07:40ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692023-09-011010.3389/fvets.2023.12047061204706Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaksYili Liu0Qi Min1Jiao Tang2Lu Yang3Xinxin Meng4Tao Peng5Mingfeng Jiang6Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, ChinaInstitute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, ChinaInstitute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, ChinaThe development of the four stomachs of yak is closely related to its health and performance, however the underlying molecular mechanisms are largely unknown. Here, we systematically analyzed mRNAs of four stomachs in five growth time points [0 day, 20 days, 60 days, 15 months and 3 years (adult)] of yaks. Overall, the expression patterns of DEmRNAs were unique at 0 d, similar at 20 d and 60 d, and similar at 15 m and adult in four stomachs. The expression pattern in abomasum was markedly different from that in rumen, reticulum and omasum. Short Time-series Expression Miner (STEM) analysis demonstrated that multi-model spectra are drastically enriched over time in four stomachs. All the identified mRNAs in rumen, reticulum, omasum and abomasum were classified into 6, 4, 7, and 5 cluster profiles, respectively. Modules 9, 38, and 41 were the most significant three colored modules. By weighted gene co-expression network analysis (WGCNA), a total of 5,486 genes were categorized into 10 modules. CCKBR, KCNQ1, FER1L6, and A4GNT were the hub genes of the turquoise module, and PAK6, TRIM29, ADGRF4, TGM1, and TMEM79 were the hub genes of the blue module. Furthermore, functional KEGG enrichment analysis suggested that the turquoise module was involved in gastric acid secretion, sphingolipid metabolism, ether lipid metabolism, etc., and the blue module was enriched in pancreatic secretion, pantothenate and CoA biosynthesis, and starch and sucrose metabolism, etc. Our study aims to lay a molecular basis for the study of the physiological functions of rumen, reticulum, omasum and abomasum in yaks. It can further elucidate the important roles of these mRNAs in regulation of growth, development and metabolism in yaks, and to provide a theoretical basis for age-appropriate weaning and supplementary feeding in yaks.https://www.frontiersin.org/articles/10.3389/fvets.2023.1204706/fullyakstomachDEmRNAsSTEMWGCNA |
| spellingShingle | Yili Liu Qi Min Jiao Tang Lu Yang Xinxin Meng Tao Peng Mingfeng Jiang Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks Frontiers in Veterinary Science yak stomach DEmRNAs STEM WGCNA |
| title | Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks |
| title_full | Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks |
| title_fullStr | Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks |
| title_full_unstemmed | Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks |
| title_short | Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks |
| title_sort | transcriptome profiling in rumen reticulum omasum and abomasum tissues during the developmental transition of pre ruminant to the ruminant in yaks |
| topic | yak stomach DEmRNAs STEM WGCNA |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2023.1204706/full |
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