In:
PLOS ONE, Public Library of Science (PLoS), Vol. 15, No. 11 ( 2020-11-24), p. e0242500-
Abstract:
The domestic Nili-Ravi water buffalo ( Bubalus bubalis ) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0242500
DOI:
10.1371/journal.pone.0242500.g001
DOI:
10.1371/journal.pone.0242500.g002
DOI:
10.1371/journal.pone.0242500.g003
DOI:
10.1371/journal.pone.0242500.g004
DOI:
10.1371/journal.pone.0242500.g005
DOI:
10.1371/journal.pone.0242500.g006
DOI:
10.1371/journal.pone.0242500.g007
DOI:
10.1371/journal.pone.0242500.g008
DOI:
10.1371/journal.pone.0242500.t001
DOI:
10.1371/journal.pone.0242500.t002
DOI:
10.1371/journal.pone.0242500.t003
DOI:
10.1371/journal.pone.0242500.s001
DOI:
10.1371/journal.pone.0242500.s002
DOI:
10.1371/journal.pone.0242500.s003
DOI:
10.1371/journal.pone.0242500.s004
DOI:
10.1371/journal.pone.0242500.s005
DOI:
10.1371/journal.pone.0242500.s006
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2020
detail.hit.zdb_id:
2267670-3
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