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

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Title Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus
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Creator Not Available
 
Subject autozygosity, genomic inbreeding, runs of homozygosity islands, selection sweep, FROH
 
Description Not Available
Genome-wide runs of homozygosity (ROH) are suitable for understanding population
history, calculating genomic inbreeding, deciphering genetic architecture of complex traits
and diseases as well as identifying genes linked with agro-economic traits. Autozygosity
and ROH islands, genomic regions with elevated ROH frequencies, were characterized in
112 animals of seven Indian native cattle breeds (B. indicus) using BovineHD BeadChip.
In total, 4138 ROH were detected. The average number of ROH per animal was maximum
in draft breed, Kangayam (63.62 ± 22.71) and minimum in dairy breed, Sahiwal (24.62 ±
11.03). The mean ROH length was maximum in Vechur (6.97 Mb) and minimum in Hariana
(4.04 Mb). Kangayam revealed the highest ROH based inbreeding (FROH> 1Mb = 0.113 ±
0.059), whereas Hariana (FROH> 1Mb = 0.042 ± 0.031) and Sahiwal (FROH> 1Mb = 0.043 ±
0.048) showed the lowest. The high standard deviation observed in each breed highlights
a considerable variability in autozygosity. Out of the total autozygous segments observed
in each breed except Vechur, > 80% were of short length (< 8 Mb) and contributed almost
50% of the genome proportion under ROH. However, in Vechur cattle, long ROH
contributed 75% of the genome proportion under ROH. ROH patterns revealed
Hariana and Sahiwal breeds as less consanguineous, while recent inbreeding was
apparent in Vechur. Maximum autozygosity observed in Kangayam is attributable to
both recent and ancient inbreeding. The ROH islands were harbouring higher proportion
of QTLs for production traits (20.68% vs. 14.64%; P≤ 0.05) but lower for reproductive
traits (11.49% vs. 15.76%; P≤ 0.05) in dairy breeds compared to draft breed. In draft
cattle, genes associated with resistant to diseases/higher immunity (LYZL1, SVIL, and
GPX4) and stress tolerant (CCT4) were identified in ROH islands; while in dairy breeds, for
milk production (PTGFR, CSN1S1, CSN2, CSN1S2, and CSN3). Significant difference in
ROH islands among large and short statured breeds was observed at chromosome 3 and
5 involving genes like PTGFR and HMGA2 responsible for milk production and stature,
respectively. PCA analysis on consensus ROH regions revealed distinct clustering of dairy,
draft and short stature cattle breeds.
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Date 2021-08-09T05:31:09Z
2021-08-09T05:31:09Z
2020-02-21
 
Type Research Paper
 
Identifier Not Available
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http://krishi.icar.gov.in/jspui/handle/123456789/53704
 
Language English
 
Relation Not Available;
 
Publisher Not Available