Abstract
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.
Highlights
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical
We observed the highest proportion of the genome covered by runs of homozygosity (ROH) in Nanda cattle (NDC) from South China, whereas the lowest was found in Yanhuang cattle (YHC)
The high density SNP arrays are more sensitive for the determination of small segments, as previously reported[35], while the BovineSNP50K array may underestimate the numbers of segments of 1 to 4 Mb in length
Summary
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. We identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. Recent studies suggested the total number and length of ROH per individual display considerable variation in worldwide human populations[6], and the genomic distribution of ROH followed an obvious South to North gradient which was in consistent with European population history[7]. The formation of ROH of various sizes (long vs short) may reflect different evolutionary events on recent vs ancient inbreeding[6,12], with long ROH indicate more recent inbreeding, while short ROH suggest more ancient inbreeding The investigation of these ROH segments can further improve our understanding of selection histories for special traits among diverse populations[23,24]
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