Abstract
BackgroundAdvances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported.ResultsHigher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3′-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work.ConclusionsOur results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
Highlights
Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication
The range of total high-quality sequence data was from 42.1 Gb (Sample ID: #GW1) to 51 Gb (#DogQI), and the coverage varied from 14.51 x (#GW1) to 17.15 x (#GW2) (Additional file 1: Table S2)
Our results indicated that the proportion of deleterious mutations varied between wolf and dog chromosomes (Fig. 4), and more deleterious mutations are in dog genome, compared with their wild ancestor
Summary
Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and high haplotype sharing between wolves and dog breeds has been reported. In the Southwest Asia, major–scale farming extended within the sonamed Fertile Crescent (FC) where the independent domestication of plants and animals had led to shifting from gathering and hunting to sedentary farming following expansion of the first complex societies [23, 78]. The dog is a notable instance of variation under domestication, the evolutionary processes underlying the genesis of this diversity are weakly realized
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