Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

Dixit, S. P.; Singh, Sanjeev; Ganguly, Indrajit; Bhatia, A. K.; Sharma, Anjani Kumar; Kumar, Narendra; Dang, Ajay Kumar; Jayakumar, S.

doi:10.3389/fgene.2020.00092

Cited by 69 publications

(64 citation statements)

References 33 publications

(54 reference statements)

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“…Altogether, MDS, AMOVA, PCA and MJ network analyses demonstrated that geographical distribution is not a reliable predictor of paternal variation, and Y-lineages appear to be more related to function of the Indian cattle breeds. The clustering of Indian cattle breeds based on genome-wide runs of homozygosity further supports the view 38 .…”

Section: Discussion Finding New Haplotypes In Indicine Cattlesupporting

confidence: 66%

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

Ganguly

Jeevan

Singh

et al. 2020

Sci Rep

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Y-chromosome genetic diversity in and around its domestication origin and a better understanding of indicine-specific microsatellite alleles are imperative concerns but less-targeted. We analysed Y-chromosome markers in 301 bulls representing 19 native Indian cattle (Bos indicus) and identified new alleles and haplotypes. compared to other indicine studies, the high Y-haplotype diversity found in indian cattle supports the hypothesis of greater genetic variability across the centre of origin decreasing along migratory routes with increasing distance. Hence, a considerable paternal genetic diversity of indian cattle appears to have been lost in transboundary commercial indicine breeds. the Khillar and Gir are the most diversified populations where the first tends to be the well-differentiated traditional breed carrying strikingly distinct Y-lineages with typical BM861-158 bp allele, characteristics of taurine cattle, while retaining standard indicine lineages for all other markers. Geographical distribution found to be an unreliable predictor of parental variation, and Y-lineages seemed closely related to indian breed function/utility. the comprehensive Y-chromosome information will be useful to examine the demographic expansion/spread of Bos indicus lineages from close proximity to the domestication centre across different countries worldwide and such diversity should be preserved through effective management and conservation programs.

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Section: Discussion Finding New Haplotypes In Indicine Cattlesupporting

confidence: 66%

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

Ganguly

Jeevan

Singh

et al. 2020

Sci Rep

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“…ROH analyses were performed separately for each population, using SVS software. No linkage disequilibrium (LD)-based pruning was performed and, as in [ 17 ], the minimum ROH length was set to 1 Mb to avoid the detection of short and common ROH across the genome due to LD. The ROH were defined setting a minimum of 1000 Kb in length and 60 homozygous consecutive SNPs.…”

Section: Methodsmentioning

confidence: 99%

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

Strillacci

Vevey²,

Blanchet³

et al. 2020

Animals

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The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were −0.003, −0.01 and −0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.

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“…2019; Dixit et al . 2020). Crossbreeding with taurine dairy breeds enhances dairy production (Wakchaure et al .…”

Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

Evolution and domestication of the Bovini species

et al. 2020

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Summary Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y‐chromosomal DNA. The high diversity of European breeds has been shaped through isolation‐by‐distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

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Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

Cited by 69 publications

References 33 publications

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

Evolution and domestication of the Bovini species

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