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Outline
This study aimed to systematically identify expression short tandem repeats （eSTRs） in dairy cattle that are significantly associated with gene expression， in order to explore their regulatory roles in gene expression and complex economic traits， thereby providing functional variant resources for molecular breeding. A total of 108 Chinese Holstein cows were sampled for tail vein blood collection. Genomic DNA and total RNA were extracted and subjected to 30×whole-genome resequencing and transcriptome sequencing， respectively. After quality control， 105 samples were retained for further analysis. STRs were annotated and genotyped at the population scale using TRF and HipSTR. Gene expression levels were quantified after quality filtering with Trimmomatic， alignment using STAR， and normalization with edgeR. Based on a ±1 Mb window around transcription start sites （TSS）， a linear model was used to assess the association between STR dosage and gene expression to identify cis-eSTRs. Weighted correlation network analysis （WGCNA） and Gene Ontology （GO） were further applied to explore the functional relevance of cis-eSTRs in complex traits. A total of 25 154 significant cis-eSTR-gene expression associations were identified. These cis-eSTRs were predominantly located in intronic regions and near TSSs. WGCNA revealed that cis-eSTR regulated genes clustered into several functional modules， some of which were significantly associated with traits related to milk production and immune. GO enrichment analysis revealed that these modules are broadly involved in biological processes such as immune response， lipid metabolism， cell cycle， DNA replication and stability. Several key genes （e.g.， IRF7， BoLA-DRB， CCT2） might play important functional roles in immune regulation and mammary gland function. cis-eSTRs play important roles in regulating gene expression and complex traits in dairy cattle. The cis-eSTR resource generated in this study provides a valuable foundation for the functional annotation of complex traits and offers potential molecular markers for breeding applications.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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