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Wang H, Wu H, Zhang W, Jiang J, Qian H, Man C, Gao H, Chen Q, Du L, Chen S, Wang F. Development and validation of a 5K low-density SNP chip for Hainan cattle. BMC Genomics 2024; 25:873. [PMID: 39294563 PMCID: PMC11409743 DOI: 10.1186/s12864-024-10753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 09/02/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND This study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included. RESULTS A total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65-99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways. CONCLUSION The development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.
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Affiliation(s)
- Huan Wang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Hui Wu
- Xinjiang Barkol Kazakh Autonomous County Animal Husbandry Veterinary Station, Barkol Kazakh Autonomous County, Xinjiang, PR China
| | - Wencan Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Junming Jiang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Hejie Qian
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Churiga Man
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Hongyan Gao
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Qiaoling Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China
| | - Si Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
| | - Fengyang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, College of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, PR China.
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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