Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis
During lactation, dairy cattle’s digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to understand the biological functions of the epithelia of the rumen, s...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-05-01
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| Series: | Journal of Advanced Research |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2090123224002571 |
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| author | Yahui Gao George E. Liu Li Ma Lingzhao Fang Cong-jun Li Ransom L. Baldwin, VI |
| author_facet | Yahui Gao George E. Liu Li Ma Lingzhao Fang Cong-jun Li Ransom L. Baldwin, VI |
| author_sort | Yahui Gao |
| collection | DOAJ |
| description | During lactation, dairy cattle’s digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to understand the biological functions of the epithelia of the rumen, small intestine, and colonic tissues in response to changes in physiological state driven by changes in nutrient demands for milk synthesis. In this study, we obtained a total of 108 transcriptome profiles from three tissues (epithelia of the colon, duodenum, and rumen) of five Holstein cows, spanning eight time points from the early, mid, late lactation periods to the dry period. On average 97.06% of reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We analyzed 27,607 gene expression patterns at multiple periods, enabling direct comparisons within and among tissues during different lactation stages, including early and peak lactation. We identified 1645, 813, and 2187 stage-specific genes in the colon, duodenum, and rumen, respectively, which were enriched for common or specific biological functions among different tissues. Time series analysis categorized the expressed genes within each tissue into four clusters. Furthermore, when the three tissues were analyzed collectively, 36 clusters of similarly expressed genes were identified. By integrating other comprehensive approaches such as gene co-expression analyses, functional enrichment, and cell type deconvolution, we gained profound insights into cattle lactation, revealing tissue-specific characteristics of the gastrointestinal tract and shedding light on the intricate molecular adaptations involved in nutrient absorption, immune regulation, and cellular processes for milk synthesis during lactation. |
| format | Article |
| id | doaj-art-8656639ddea94bbcafc630ad71004e88 |
| institution | OA Journals |
| issn | 2090-1232 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
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| series | Journal of Advanced Research |
| spelling | doaj-art-8656639ddea94bbcafc630ad71004e882025-08-20T01:55:52ZengElsevierJournal of Advanced Research2090-12322025-05-0171678010.1016/j.jare.2024.06.020Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesisYahui Gao0George E. Liu1Li Ma2Lingzhao Fang3Cong-jun Li4Ransom L. Baldwin, VI5Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USADepartment of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USACenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, DenmarkAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USAAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Corresponding author.During lactation, dairy cattle’s digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to understand the biological functions of the epithelia of the rumen, small intestine, and colonic tissues in response to changes in physiological state driven by changes in nutrient demands for milk synthesis. In this study, we obtained a total of 108 transcriptome profiles from three tissues (epithelia of the colon, duodenum, and rumen) of five Holstein cows, spanning eight time points from the early, mid, late lactation periods to the dry period. On average 97.06% of reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We analyzed 27,607 gene expression patterns at multiple periods, enabling direct comparisons within and among tissues during different lactation stages, including early and peak lactation. We identified 1645, 813, and 2187 stage-specific genes in the colon, duodenum, and rumen, respectively, which were enriched for common or specific biological functions among different tissues. Time series analysis categorized the expressed genes within each tissue into four clusters. Furthermore, when the three tissues were analyzed collectively, 36 clusters of similarly expressed genes were identified. By integrating other comprehensive approaches such as gene co-expression analyses, functional enrichment, and cell type deconvolution, we gained profound insights into cattle lactation, revealing tissue-specific characteristics of the gastrointestinal tract and shedding light on the intricate molecular adaptations involved in nutrient absorption, immune regulation, and cellular processes for milk synthesis during lactation.http://www.sciencedirect.com/science/article/pii/S2090123224002571 |
| spellingShingle | Yahui Gao George E. Liu Li Ma Lingzhao Fang Cong-jun Li Ransom L. Baldwin, VI Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis Journal of Advanced Research |
| title | Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| title_full | Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| title_fullStr | Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| title_full_unstemmed | Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| title_short | Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| title_sort | transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis |
| url | http://www.sciencedirect.com/science/article/pii/S2090123224002571 |
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