Cargando…

SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing

Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk...

Descripción completa

Detalles Bibliográficos
Autores principales: Ahmad, Syed Mudasir, Bhat, Basharat, Bhat, Shakil Ahmad, Yaseen, Mifftha, Mir, Shabir, Raza, Mustafa, Iquebal, Mir Asif, Shah, Riaz Ahmad, Ganai, Nazir Ahmad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369411/
https://www.ncbi.nlm.nih.gov/pubmed/34413874
http://dx.doi.org/10.3389/fgene.2021.666015
_version_ 1783739287276093440
author Ahmad, Syed Mudasir
Bhat, Basharat
Bhat, Shakil Ahmad
Yaseen, Mifftha
Mir, Shabir
Raza, Mustafa
Iquebal, Mir Asif
Shah, Riaz Ahmad
Ganai, Nazir Ahmad
author_facet Ahmad, Syed Mudasir
Bhat, Basharat
Bhat, Shakil Ahmad
Yaseen, Mifftha
Mir, Shabir
Raza, Mustafa
Iquebal, Mir Asif
Shah, Riaz Ahmad
Ganai, Nazir Ahmad
author_sort Ahmad, Syed Mudasir
collection PubMed
description Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways.
format Online
Article
Text
id pubmed-8369411
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-83694112021-08-18 SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing Ahmad, Syed Mudasir Bhat, Basharat Bhat, Shakil Ahmad Yaseen, Mifftha Mir, Shabir Raza, Mustafa Iquebal, Mir Asif Shah, Riaz Ahmad Ganai, Nazir Ahmad Front Genet Genetics Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways. Frontiers Media S.A. 2021-08-03 /pmc/articles/PMC8369411/ /pubmed/34413874 http://dx.doi.org/10.3389/fgene.2021.666015 Text en Copyright © 2021 Ahmad, Bhat, Bhat, Yaseen, Mir, Raza, Iquebal, Shah and Ganai. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Ahmad, Syed Mudasir
Bhat, Basharat
Bhat, Shakil Ahmad
Yaseen, Mifftha
Mir, Shabir
Raza, Mustafa
Iquebal, Mir Asif
Shah, Riaz Ahmad
Ganai, Nazir Ahmad
SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title_full SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title_fullStr SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title_full_unstemmed SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title_short SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing
title_sort snps in mammary gland epithelial cells unraveling potential difference in milk production between jersey and kashmiri cattle using rna sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369411/
https://www.ncbi.nlm.nih.gov/pubmed/34413874
http://dx.doi.org/10.3389/fgene.2021.666015
work_keys_str_mv AT ahmadsyedmudasir snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT bhatbasharat snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT bhatshakilahmad snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT yaseenmifftha snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT mirshabir snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT razamustafa snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT iquebalmirasif snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT shahriazahmad snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing
AT ganainazirahmad snpsinmammaryglandepithelialcellsunravelingpotentialdifferenceinmilkproductionbetweenjerseyandkashmiricattleusingrnasequencing