Abstract
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.
Highlights
Runs of homozygosity (ROH), the indicator of genomic autozygosity, may be defined as two contiguous identical by descent (IBD) stretches of homozygous genotypes/segments/ haplotypes of a common ancestor in an individual inherited from both of its parents (Gibson et al, 2006).This autozygosity may arise in inbred as well as non-inbred populations due to several population phenomena like inbreeding, genetic drift, consanguineous mating, population bottleneck, as well as natural and artificial selection (Falconer and Mackay, 1996; Curik et al, 2014)
The quality control measures led to final data on 112 cattle belonging to Sahiwal (13), Tharparkar (17), Gir (15), Ongole (17), Hariana (18), Kangayam (16), and Vechur (16) breeds
The mean number of runs of homozygosity (ROH) per animal was highest in draft breed, Kangayam (63.62 ± 22.71 with a range of 11- 92) and lowest in Sahiwal (24.62 ± 11.03 with a range of 12–49)
Summary
Runs of homozygosity (ROH), the indicator of genomic autozygosity, may be defined as two contiguous identical by descent (IBD) stretches of homozygous genotypes/segments/ haplotypes of a common ancestor in an individual inherited from both of its parents (Gibson et al, 2006). This autozygosity may arise in inbred as well as non-inbred populations due to several population phenomena like inbreeding, genetic drift, consanguineous mating, population bottleneck, as well as natural and artificial selection (Falconer and Mackay, 1996; Curik et al, 2014). The selection sweeps were studied using ROH information in cattle (Iacolina et al, 2016)
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