Biology subjects

Onteru, S. K.

Publications and source records attributed to Onteru, S. K..

4 recordsLinked to original sources

bioRxiv2026

Integrative Whole-Genome Analysis reveals Genomic Signatures of Innate Immunity in Indicine Cattle.

Indicine cattle (Bos indicus) are known for resilience to infectious diseases and environmental stress. However, the genomic basis underlying this advantage remains poorly understood. To characterize variations in immune-related genetic elements in four indicine breeds (Kangayam, Gir, Tharparkar, and Sahiwal), a taurine breed (Holstein Friesian), and a taurine-indicine crossbreed (Karan Fries), we performed integrative whole-genome analysis. Using whole-genome data representing 108 animals, we identified structural variants, copy number variants, single-nucleotide variations, and insertions/deletions. High-impact single-nucleotide variations in the key innate immune genes, CARD9 and NLRP8, shared across all indicine breeds, were absent in the other breeds. Genetic differentiation analysis identified several innate immune genes showing strong divergence between the indicine breeds and the taurine breed. Selective sweep detection analysis highlighted multiple breed-specific immune-related sweep regions. Functional enrichment analysis showed significant enrichment of immune pathways in indicine breeds. A comparison of the candidate genes with basal gene expression profiles of unchallenged peripheral blood mononuclear cells indicated that genomic variation influences the differential expression of several genes in indicine breeds. We synthesized the data from population genome structure analysis, nucleotide diversity, genetic differentiation, selective sweep analysis, and correlations with gene expression profiles. Indicine breeds exhibited a higher number of immune-related variants and stronger signals of selection in immune pathways. These findings provide a curated set of innate immune gene candidates in indicine breeds for future functional studies and breeding programs.

bioinformatics↗

bioRxiv2024

Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome

Indicine cattle (Bos indicus) show notable resilience and disease resistance compared with taurine breeds, but the genomic basis of these traits remains largely unexplored. Identification of genomic elements for immunity will enable future controlled crossbreeding programs using molecular breeding methods. Therefore, we performed a genome-wide comparison among Nelore, Gir, and Hereford breeds using their whole-genome sequences, majorly focusing on immune-related structural and sequence variation. Our aims were to catalog insertions, deletions, and single nucleotide variants (SNVs) that intersect immune loci and known quantitative trait loci (QTLs), identify runs of homozygosity and selective-sweep signals, and prioritize candidate genes for follow-up functional studies. We retrieved whole-genome sequencing data for Nelore breed (n=14) and Gir breed (n=20) from NCBI using the SRA toolkit. Reads were checked with FastQC, filtered with fastp to remove low-quality bases and adaptors, and retained high-quality reads based on Q20 and Q30. The reads were mapped to the Bos taurus reference (ARS-UCD2.0) with BWA-MEM; alignments were processed with SAMtools for sorting, duplicate marking, and MAPQ [≥] 20 filtering. Variants (insertions, deletions, SNVs) were called with GATK HaplotypeCaller, hard-filtered, normalized with bcftools, and annotated with SnpEff and SnpSift. Common variants were identified via in-house Python scripts; immune loci were detected from InnateDB and keyword searches; QTL overlaps were identified using Animal QTLdb; DAVID was used for GO and KEGG enrichment (P < 0.05). ROH islands were defined in PLINK as regions shared by >50% of individuals or samples, and selective sweeps were detected with RAiSD; genes overlapping ROH islands and RAiSD peaks were prioritized as candidate selection signatures. GATK identified 1,884,058 indels and 13,997,533 SNVs in Nelore breed, and 1,457,337 indels and 11,627,881 SNVs in Gir breed, with Ti/Tv ratios of [~]2.26 and [~]2.25, respectively. Nelore breed has more number of variants than Gir. We observed frameshift insertions in TLR3 and LOC508441 (CD33) in both the breeds and frameshift deletions in JAM3 in Nelore breed and PAX5 in Gir breed. The variants are also identified in the regulatory regions of both breeds. The high-impact SNVs were in CD46 and IL26 genes in Nelore breed, and PLG gene in Gir breed. Genome-wide scans using RAiSD identified selective sweeps in 707 candidate genes in Nelore breed and 165 in Gir breed. Comparing the ROH and RAiSD results, we prioritized the genes ANKRD11, MAGI2, LOC132345096, FOXP2, TCF12, and ATP5PO in Nelore breed, and the genes MEFV and ORIF1 in Gir breed. These genes are found in QTLs linked to milk and health traits. Functional enrichment showed that the genes exhibiting all the three variants belong to immune pathways such as, NF-kappaB signaling, T-cell receptor signaling, and MAPK signaling in both breeds. These results reveal breed-specific genomic variation locating immune loci and its associated QTLs and provide a list of candidate genes and regions for experimental validation and marker development to improve disease resistance and productivity in Indicine cattle. Keywords: Hereford, Nelore, Gir, immune-related genes, QTLs, Whole genome sequence

bioinformatics↗

bioRxiv2024

Comparative cell free salivary miRNA profile in Bubalus bubalis between diestrus and estrus stages

Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. Hence, the present study was planned to identify differential levels of salivary cell free miRNAs in estrus as compared to the diestrus phase of buffalo oestrous cycle (n=3) in order to discover a possible estrus specific miRNAs as biomarkers. miRNA-Seq data analysis showed that in total 10 miRNAs i.e bta-miR-375, bta-miR-200c, bta-miR-30d, bta-let-7f, bta-miR-200a, bta-miR-12034, bta-let-7b, bta-miR-142-5p, bta-miR-2467-3p, bta-miR-30a-5p are significantly altered (log2foldchange >3 and p<0.05) during estrus in comparison to the diestrus phase in buffaloes, suggesting their estrus biomarker potential. Overall, 8 miRNAs i.e bta-miR-375 (6.87 Fold; p-value 0.003), bta-miR-200c (5.98 Fold; p-value 0.003), bta-miR-30d (4.17 Fold; p-value 0.015), bta-let-7f (3.34 Fold; p-value 0.022), bta-miR-200a (4.92 Fold; p-value 0.024), bta-miR-12034 (3.58 Fold; p-value 0.0025), bta-let-7b (3.06 Fold; p-value 0.031), bta-miR-30a-5p (4.7 Fold; p-value 0.036) were upregulated, whereas bta-miR-142-5p (-3.4 Fold; p-value 0.032) and bta-miR-2467-3p (-5.24 Fold; p-value 0.035) were downregulated during estrus. However, further validation study using qPCR is required in a large sample size in order to determine their estrus biomarker potential. In summary, our results revealed differential salivary cell free miRNAs profile during the oestrous cycle that may lead to the development of estrus specific miRNAs based point-of-care test applicable for the reproductive management of buffaloes in the field condition in the near future.

genomics↗

bioRxiv2020

Effect of dioxins in milk on 3D-cultured primary buffalo granulosa cells, a pilot study for a prospective RT-LAMP colour reaction for dioxin toxicity

Dioxins are highly toxic environmental persistent organic pollutants. In several countries, their presence was also reported in cow and human milk samples in the range of 0.023-26.46 and 0.88-19.0 pg/gm of fat, respectively. The detection of dioxns in food samples has been relied on several expensive technologies, which do not represent their toxic effects on consumers. However, mammalian cell based bioassays have such potential to detect the toxins, while representing their toxic effects. Therefore, we tried a three-dimensionally (3D) cultured buffalo granulosa cell based RT-LAMP colour reaction for detecting the presence of added model dioxin, 2,3,7,8-tetrachlorodibenzodioxin (TCDD), in commercial milk. The 3D spheroids on the fifth day of culture were treated with different concentrations of TCDD (i.e. 0.02- 20 pg/ml) directly as well as indirectly through milk fat. After 24hrs of treatment, gene expression studies were performed on certain granulosa cell-specific (CYP19A1, ER-beta, FSHR and LHR) and selective TCDD-responsive (CYP1A1, CYP1B1 and AHR) genes to identify the potential dioxin responsive gene for further RT-LAMP reaction. As the AHR expression in 3D cultured buffalo granulosa cells appears to be a potential gene marker for sensing the added TCDD in the milk, a colour based RT-LAMP reaction was successfully attempted for its expression. However, future studies are needed to develop a dose-responsive colour reaction by considering the treatment time less than 24 hrs.

pharmacology and toxicology↗