PMID- 38158465 OWN - NLM STAT- Publisher LR - 20231229 IS - 1573-4927 (Electronic) IS - 0006-2928 (Linking) DP - 2023 Dec 29 TI - SNP Analysis of TLR4 Promoter and Its Transcriptional Factor Binding Profile in Relevance to Bovine Subclinical Mastitis. LID - 10.1007/s10528-023-10578-4 [doi] AB - Bovine mastitis is a complex infectious disease that develops in the mammary gland, predominantly caused by a bacterial infection of mammary tissue. Genetic variability of mastitis is well established and depends upon different quantitative trait loci (QTL) related to mastitis resistance or susceptibility. The susceptibility is often attributed to single-nucleotide polymorphisms (SNPs) in the variable cow breed genomes. Several global investigative attempts have resulted in studies mapping mastitis to the variations in the relevant genes. Reports have been attributed to dramatic genetic expression changes in Toll-Like Receptor 4 (TLR4) genes in mastitis-positive cows. However, the mechanism behind this variable genetic expression of TLR4 genes has been studied poorly. The present study aims to investigate SCM through various screening tests like somatic cell count (SCC), electric conductivity (EC), pH, and California mastitis test (CMT) in milk samples. This study also aims to investigate possible mechanisms behind this variable expression of TLR4 by comparative SNP evaluation and transcriptional factor profile mining. So that the important genetic mutations and effects thereof can be exploited in selecting specific breeds with higher mastitis resistance and milk yield. Seventy Holstein Frisian (HF) crossbred dairy cows were selected in the present study. The animals were screened based on various diagnostic tests (SCC, pH, EC, and CMT). Blood samples (5 mL) were collected for extraction of DNA followed by amplification of PPR1 and PPR2 of the promoter region and 5'UTR of the bovine TLR4 gene using specific primers. Sanger's enzymatic DNA sequencing technique sequenced the amplified PCR products. Further, the identification of SNPs was done through various bioinformatic tools used in this study. The findings of the present study revealed that CMT, EC, pH, and SCC could be used for the early detection of subclinical mastitis. In the present study, a significant increase in the EC, pH, and SCC in milk samples of animals affected with SCM was found in comparison to the healthy animals. The present study also revealed 16 SNPs falling in TLR4 promoter and 5' untranslated region (5'UTR) sequences in mastitis-positive genotypes compared to reference genomes. The study also investigates the potential transcriptional factor program deployed in response to variable mastitis development resistance. In the present study, the allelic and genotype frequencies of all SNP variants in the three regions viz., PPR1, PPR2, and 5'UTR, were the same indicating the absence of heterozygous condition at the respective loci. The present study has wide applicability for researchers developing mastitis-resistant breeding programs and the data generated may aid in the selection of better genetic breeds. The transcription factor binding profiles can serve as concrete leads about the studies on bovine mastitis at the molecular level and may also aid global research groups working on transcription factor (TF)-based molecular pathology of mastitis. CI - (c) 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. FAU - Bhat, Rahil Razak AU - Bhat RR AUID- ORCID: 0000-0002-2243-8850 AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. FAU - Bhat, Nadiem Nazir AU - Bhat NN AUID- ORCID: 0000-0002-9391-9109 AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. FAU - Shabir, Ambreen AU - Shabir A AD - Division of Fish Genetics and Biotechnology, Faculty of Fisheries, SKUAST-Kashmir, Rangil, Ganderbal, J&K, 191201, India. FAU - Mir, Manzoor Ur Rahman AU - Mir MUR AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. manzoorvbc43@gmail.com. FAU - Ahmad, Sheikh Bilal AU - Ahmad SB AUID- ORCID: 0000-0002-6360-8457 AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. FAU - Hussain, Ishraq AU - Hussain I AUID- ORCID: 0000-0001-8449-1617 AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. FAU - Hussain, Syed Ashaq AU - Hussain SA AUID- ORCID: 0000-0001-5299-974X AD - Division of Veterinary Clinical Medicine, Ethics and Jurisprudence, FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. FAU - Ali, Aarif AU - Ali A AUID- ORCID: 0000-0001-8789-2715 AD - Division of Veterinary Biochemistry FVSc & AH, SKUAST-Kashmir, Shuhama, Alusteng, Srinagar, J&K, 190006, India. buttaarif31@gmail.com. FAU - Shamim, Kashif AU - Shamim K AD - National Centre for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA. FAU - Rehman, Muneeb U AU - Rehman MU AD - Department of Clinical Pharmacy, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia. LA - eng GR - RSPD2023R722/Researchers supporting project number (RSPD2023R722), King Saud University, Riyadh Saudi Arabia/ PT - Journal Article DEP - 20231229 PL - United States TA - Biochem Genet JT - Biochemical genetics JID - 0126611 SB - IM OTO - NOTNLM OT - Bioinformatics OT - Biomarkers OT - Bovine mastitis OT - SNPs OT - Subclinical mastitis OT - TLR4 gene OT - Transcriptional factors EDAT- 2024/01/02 11:43 MHDA- 2024/01/02 11:43 CRDT- 2023/12/29 23:21 PHST- 2023/06/14 00:00 [received] PHST- 2023/10/28 00:00 [accepted] PHST- 2024/01/02 11:43 [medline] PHST- 2024/01/02 11:43 [pubmed] PHST- 2023/12/29 23:21 [entrez] AID - 10.1007/s10528-023-10578-4 [pii] AID - 10.1007/s10528-023-10578-4 [doi] PST - aheadofprint SO - Biochem Genet. 2023 Dec 29. doi: 10.1007/s10528-023-10578-4.