Copy number variations in the amylase gene (<i><scp>AMY</scp>2B</i>) in Japanese native dog breeds

Tonoike, Akiko; Hori, Yoshiaki; Inoue‐Murayama, Miho; Konno, Akira; Fujita, Kazuo; Miyado, Mami; Fukami, Maki; Nagasawa, Miho; Mogi, Kazutaka; Kikusui, Takefumi

doi:10.1111/age.12344

Cited by 10 publications

(5 citation statements)

References 6 publications

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“…The effective population size in wolves is higher than that in dogs so higher genome diversity in wolves is expected compared to dogs [3,25]. Our results from two components of genetic variation sources including SVs and CNVs confirmed that the novel adaptations permitted the primal ancestors of recent dogs to live on a diet high starch compared to the carnivorous diet of wolves and formed a essential step in the primal domestication of dogs [8,9,25,52,60]. The terms "Negative regulation of neuron apoptotic process", "positive regulation of dendrite development" and "nervous system development" were enriched among SVs in wolf and are indicative of reducing aggression in the first steps of animal domestication.…”

Section: Discussionsupporting

confidence: 60%

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Ghanatsaman

Wang

Fozi

et al. 2019

Preprint

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Background 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 also high haplotype sharing between wolves and dog breeds has been reported. Results Higher diversity was found within the wolf genome compared with the dog genome. A total of 10.45, 7.82, 3.11 and 2.24 million SNPs and small Indels were identified within wolf and dog genomes, 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. The genes related to olfactory and immune systems were enriched in the set of structural variants (SVs) identified in this work. Annotation of genomic variations showed that in general the proportion of genomic variations in the intron and intergenic regions in wolf genome is higher than that in dog genome while their proportion in the coding sequences and 3'-UTR in dog genome is higher than that in wolf genome. Generally, genes engaged in digestion and metabolism and neurological process had an important role in the process of dog domestication. Conclusions By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.

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Section: Discussionsupporting

confidence: 60%

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Ghanatsaman

Wang

Fozi

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…The effective population size in wolves is higher than that in dogs so higher genome diversity in wolves is expected compared to dogs [3,30]. Our results from two components of genetic variation sources including SVs and CNVs confirmed that the novel adaptations permitted the primal ancestors of recent dogs to live on a diet with high starch compared to the carnivorous diet of wolves, which is an essential step in the primal domestication of dogs [9,10,30,64,73]. The term "nervous system development" was enriched among SVs in wolf and is indicative of reducing aggression in the first steps of animal domestication [70].…”

Section: Discussionsupporting

confidence: 60%

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

et al. 2020

View full text Add to dashboard Cite

Background: 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 also high haplotype sharing between wolves and dog breeds has been reported. Results: Higher 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. Conclusions: Our 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. Publisher's NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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“…The effective population size in wolves is higher than that in dogs so higher genome diversity in wolves is expected compared to dogs [3,29]. Our results from two components of genetic variation sources including SVs and CNVs confirmed that the novel adaptations permitted the primal ancestors of recent dogs to live on a diet with high starch compared to the carnivorous diet of wolves, which is an essential step in the primal domestication of dogs [8,9,29,60,69]. The term "nervous system development" was enriched among SVs in wolf and is indicative of reducing aggression in the first steps of animal domestication [66].…”

Section: Discussionsupporting

confidence: 54%

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Ghanatsaman

Wang

Nanaei

et al. 2020

Preprint

View full text Add to dashboard Cite

Background 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 also high haplotype sharing between wolves and dog breeds has been reported.Results Higher diversity was found within the wolf genome compared with the dog genome. A total 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 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, annotation of genomic variations showed that the proportion of genomic variations in the intron and intergenic regions 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. Generally, genes engaged in digestion and metabolism and neurological process had an important role in the process of dog domestication.Conclusions Our 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.

show abstract

Copy number variations in the amylase gene (AMY2B) in Japanese native dog breeds

Cited by 10 publications

References 6 publications

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

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