Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant

Lee, Kyooyeol; Nguyen, Dinh-Truong; Choi, Mi Hyun; Cha, Se-Yeoun; Kim, Jin‐Hoi; Dadi, Hailu; Seo, Han Geuk; Seo, Kun‐Ho; Chun, Taehoon; Park, Chankyu

doi:10.1186/1471-2164-14-596

Cited by 48 publications

(46 citation statements)

References 37 publications

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“…We guessed that the difference among domesticated animals could remain in the OR genes. Previous study of cattle olfactory receptor gene reported that there was significant variation in the genetic component of olfactory receptor systems among artiodactyl species, indicating that the selection pressure for maintaining the integrity of olfactory receptor genes was lower in cattle compared to pigs [100]. These results supported that some CNVs in the selected QTL have been reflected in the evolutionary process during domestication by the missing functional domains of translated proteins resulting from genes affected by deleted CNVs.…”

Section: Discussionsupporting

confidence: 54%

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

et al. 2014

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BackgroundCopy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there have been few studies conducted on CNVs using next generation sequencing at the population level.ResultsIllumina NGS data was obtained for ten Holsteins, a dairy cattle, and 22 Hanwoo, a beef cattle. The sequence data for each of the 32 animals varied from 13.58-fold to almost 20-fold coverage. We detected a total of 6,811 deleted CNVs across the analyzed individuals (average length = 2732.2 bp) corresponding to 0.74% of the cattle genome (18.6 Mbp of variable sequence). By examining the overlap between CNV deletion regions and genes, we selected 30 genes with the highest deletion scores. These genes were found to be related to the nervous system, more specifically with nervous transmission, neuron motion, and neurogenesis. We regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed 94 putative selected CNVs and 954 breed-specific CNVs.ConclusionsThis study provides useful information for assessing the impact of CNVs on cattle traits using NGS at the population level.

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Section: Discussionsupporting

confidence: 54%

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

et al. 2014

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“…Olfactory receptor related genes are well known for extensive gains and losses in mammalian evolution 70 . And population specific copy-number variations of olfactory receptor genes were also reported in human (deletions) 71 and cattle (gains) 72 . Nevertheless, this is the first report, to our knowledge, of homozygous deletion of olfactory receptor genes in cattle.…”

Section: Resultsmentioning

confidence: 76%

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

et al. 2017

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Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.

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“…; Lee et al . ), the amino acid sequences of 864 translated OR functional genes in forest musk deer were compared to 22 human and mouse ORs (Krautwurst et al . ; Zhao et al .…”

Section: Methodsmentioning

confidence: 99%

The olfactory subgenome and specific odor recognition in forest musk deer

Jian

Koshy

et al. 2019

Animal Genetics

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Olfactory receptors (ORs) are encoded by OR genes. The OR genes in forest musk deer (Moschus berezovskii), which rely on olfaction for reproductive and social communication, are poorly understood. In this study, we analyzed the genome sequence of the forest musk deer to obtain its olfactory subgenome and compared it to other species. A total of 1378 ORrelated sequences were detected in the forest musk deer genome including 864 functional genes, 366 pseudogenes and 148 partial genes. These OR genes were classified into Class I and Class II and were further classified into 18 families and 244 subfamilies through sequence identity. Comparative analyses of the OR genes' protein sequences in species from different orders (forest musk deer, human, mouse and dog) showed that 12 clusters were specific to forest musk deer. However, when compared to other Artiodactyl species (i.e. cattle, yak and pig) only two clusters were specific to forest musk deer. The odor identification potential of the OR genes in the forest musk deer was focused mainly on floral, woody, lemon, sweet and fatty odors. We also found that OR genes specific to forest musk deer were involved in the identification of spearmint and caraway. Our work is the first genome-wide analysis of OR genes in forest musk deer. These findings will assist with better understanding the relationship between behavior and olfaction in the forest musk deer and the characteristics of the olfactory subgenome in Artiodactyl mammals.

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Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant

Cited by 48 publications

References 37 publications

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

The olfactory subgenome and specific odor recognition in forest musk deer

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