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Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing

River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically impo...

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Autores principales: Menon, Ramesh, Patel, Anand B., Joshi, Chaitanya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941740/
https://www.ncbi.nlm.nih.gov/pubmed/27441113
http://dx.doi.org/10.7717/peerj.2147
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author Menon, Ramesh
Patel, Anand B.
Joshi, Chaitanya
author_facet Menon, Ramesh
Patel, Anand B.
Joshi, Chaitanya
author_sort Menon, Ramesh
collection PubMed
description River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects.
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spelling pubmed-49417402016-07-20 Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing Menon, Ramesh Patel, Anand B. Joshi, Chaitanya PeerJ Agricultural Science River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects. PeerJ Inc. 2016-07-07 /pmc/articles/PMC4941740/ /pubmed/27441113 http://dx.doi.org/10.7717/peerj.2147 Text en © 2016 Menon et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Menon, Ramesh
Patel, Anand B.
Joshi, Chaitanya
Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title_full Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title_fullStr Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title_full_unstemmed Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title_short Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
title_sort comparative analysis of snp candidates in disparate milk yielding river buffaloes using targeted sequencing
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941740/
https://www.ncbi.nlm.nih.gov/pubmed/27441113
http://dx.doi.org/10.7717/peerj.2147
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