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Please use this identifier to cite or link to this item:
http://krishi.icar.gov.in/jspui/handle/123456789/71674
Title: | Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo |
Other Titles: | Not Available |
Authors: | Sarika Jaiswal Jaisri Jagannadham Juli Kumari Mir Asif Iquebal Anoop Kishor Singh Gurjar Varij Nayan Ulavappa B. Angadi Sunil Kumar Rakesh Kumar Tirtha Kumar Datta Anil Rai Dinesh Kumar |
ICAR Data Use Licennce: | http://krishi.icar.gov.in/PDF/ICAR_Data_Use_Licence.pdf |
Author's Affiliated institute: | ICAR-Indian Agricultural Statistics Research Institute, New Delhi ICAR-Central Institute for Research on Buffaloes, Hisar ICAR-National Dairy research Institute, Karnal |
Published/ Complete Date: | 2021-06-18 |
Project Code: | Not Available |
Keywords: | GWAS mammary gland markers mastitis TGP water buffalo |
Publisher: | Not Available |
Citation: | Jaiswal S, Jagannadham J, Kumari J, Iquebal MA, Gurjar AKS, Nayan V, Angadi UB, Kumar S, Kumar R, Datta TK, Rai A and Kumar D (2021) Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo. Front. Vet. Sci. 8:593871. doi: 10.3389/fvets.2021.593871 |
Series/Report no.: | Not Available; |
Abstract/Description: | Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo. |
Description: | Not Available |
ISSN: | Not Available |
Type(s) of content: | Research Paper |
Sponsors: | Not Available |
Language: | English |
Name of Journal: | Frontiers in Veterinary Science |
Impact Factor: | 3.412 |
Volume No.: | 8 |
Page Number: | Not Available |
Name of the Division/Regional Station: | Not Available |
Source, DOI or any other URL: | doi: 10.3389/fvets.2021.593871 |
URI: | http://krishi.icar.gov.in/jspui/handle/123456789/71674 |
Appears in Collections: | AEdu-IASRI-Publication |
Files in This Item:
File | Description | Size | Format | |
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Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo.pdf | 2.86 MB | Adobe PDF | View/Open |
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