Genome-wide patterns of copy number variation in the Chinese yak genome

Zhang, Xiao; Wang, Kun; Wang, Lizhong; Yang, Yongzhi; Ni, Zhengqiang; Xie, Xiaofeng; Shao, Xuemin; jinsoo, Han; Wan, Dongshi; Qiu, Qiang

doi:10.1186/s12864-016-2702-6

Cited by 69 publications

(93 citation statements)

References 90 publications

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“…The CNVs deletion events have some advantage over duplication, due to its bi-allelic nature and compatibility with genetic analysis procedures designed for SNPs markers [9] . In this study, CNVs was used to explore the population genetic properties in some indigenous cattle breeds in Pakistan with moderate intra population frequencies as reported by Bickhart et al [6] .…”

Section: Discussionmentioning

confidence: 99%

“…It is important here that selection pressure, the amount divergence between breeds (divergence time, effective population size and gene flow) can affect VST value and overall differentiation among selected populations [13,14] . At this stage a hypotheses can be developed that high VST value between populations does not necessarily involve in divergent (selection for different alleles in both populations) or can occur in the absenteeism of selection by bottlenecks or founder effects by drift [9] . All these hypotheses needs further research using large population samples size of these breeds as similar observed by Xu et al [8] .…”

Section: Discussionmentioning

confidence: 99%

“…However, there are also some evidence of fewer lineage differentiated CNVs in laboratory mouse, some zebra fish strains and cattle breeds which compared with their wild populations [6] . This may suggest CNVs differently fixed as large effective population size or indicate inbreeding effects of wild populations [9] . There is still very little information about genetic landscape and exact domestication events of these breeds.…”

Section: Discussionmentioning

confidence: 99%

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Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

Mustafa¹,

Khan²,

Kim³

et al. 2018

Kafkas Univ Vet Fak Derg

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A copy number variation (CNV) is information of DNA segment containing deletion, duplication or insertion exist within diverse populations. This study detected 53 CNVs regions that overlapped with immune response, body size and parasitic resistance traits in Pakistani cattle breeds. This study characterized genetic diversity and provides lineage differentiated CNVs in these indigenous cattle breeds. Keywords: Copy number variation, Diversity, Traits, Breed, Pakistan Pakistan'da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri ÖzKopya sayısı değişikliği (CNV) farklı popülasyonlar içerisinde delesyon, duplikasyon ve insersiyonları içeren DNA segmentlerinin bilgisidir. Bu çalışma ile Pakistan sığır ırkları arasında bağışıklık yanıtı, vücut boyutu ve parazit direnci özelliklerini içeren 53 CNV tespit edildi. Bu çalışma; belirtilen yerel sığır ırkları arasında genetik çeşitliliği göstermiş ve hat farklı CNV'leri belirlemiştir.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

Mustafa¹,

Khan²,

Kim³

et al. 2018

Kafkas Univ Vet Fak Derg

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“…; Zhang et al . ). However, despite the characterization of the potential selective sweep regions in the domestic yak genome, little is known about the specific effects on genome‐wide patterns of deleterious variations in yak populations that are associated with their domestication.…”

Section: Introductionmentioning

confidence: 97%

Accumulation of deleterious mutations in the domestic yak genome

et al. 2018

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Deleterious mutations play an important functional role, affecting trait phenotypes in ways that decrease the fitness of organisms. Estimating the frequency of occurrence and abundance has been a topic of much interest, especially in crops and livestock. The processes of domestication and breeding allow deleterious mutations to persist at high frequency, and identifying such deleterious mutations is particularly important for breed improvement. Here, we assessed genome-wide patterns of deleterious variation in 59 domestic and 13 wild yaks using genome resequencing data. Based on the intersection of results given by three methods (provean, polyphen2 and sift4g), we identified 3187 putative deleterious mutation sites affecting 2586 genes in domestic yaks and 2067 affecting 1701 genes in wild yaks. Multiple lines of evidence indicate a significant increase in the load of deleterious mutations in domesticated yaks compared to wild yaks. Private deleterious genes were found to be associated with the perception of smell and detection of chemical stimulus. We also identified 36 genes related to Mendelian genetic diseases involved in sensory perception, skeletal development and the nervous and immune systems. This study not only adds to the understanding of the genetic basis of yak domestication but also provides a rich catalog of variants that will facilitate future breeding-related research on the yak genome and on other bovid species.

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“…Although the draft genome sequence of the Yak has been available for four years, and resequencing studies have since been undertaken [6,33,34] , genetic variation in the Yakmost notably structural variation and genetic comparisons with other bovid species-Remains poorly understood. Moreover, the genome sequence of the Dzo has not been reported until now.…”

Section: Discussionmentioning

confidence: 99%

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

Zhong¹,

Ma²,

Chai³

et al. 2018

Kafkas Univ Vet Fak Derg

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Xin J: Whole genome sequencing of the Dzo: Genetic implications for high altitude adaptation, sterility, and milk and meat production. Kafkas Univ Vet Fak Derg, 24 (6): 835-844, 2018. DOI: 10.9775/kvfd.2018 AbstractThe Dzo, a hybrid between the domestic Yak and cattle found on the Qinghai-Tibetan plateau are commercially important owing to increased meat and milk production, as well as their adaptation to extremely high-altitude environments. To better understand the genomic architecture and adaptive capabilities of this unique domesticated hybrid, we performed whole genome resequencing and compared the genomic architecture and variation of the Dzo to its progenitors: the cattle and Yak. In total, 33.17 M single nucleotide variations (SNVs) were detected between the Dzo and cattle reference genomes. Even though the Dzo is known to be sterile, no genetic signatures associated with sterility were found on the Dzo Y chromosome. On the contrary, our results suggest that the autosomal DMC1 locus (Chromosome 5. 110729098. C>CT) plays a role in the sterility of Dzo, which warrants further exploration of its functions. We integrated the whole genome resequencing data of cattle and Yak to obtain candidate genes with a high degree of variation that might be associated with altitudinal adaptation. We found that the EPAS1 gene, which encodes hypoxia-inducible factor 2α, exhibited significant variation (Chromosome 11.28664187 C>T) between Yak and cattle, and may play a key role in the genetic basis of altitudinal adaptation. In addition, in analyzing differences between the Dzo, Yak, and cattle genomes, we uncovered several additional genomic signatures relevant to high altitude adaptation and meat and milk production. These findings underscore the need for further studies to improve ruminant stock for sustainable agriculture on the Qinghai-Tibet plateau.. Keywords: Dzo: Genome sequencing, Dzo, Altitude adaptation, Sterility, Milk and meat production Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Verimine Etkisi ÖzEvcil Yak ile Qinghai-Tibet platosunda bulunan sığırın bir hibriti olan Dzo artmış et ve süt üretimi ile birlikte aynı zamanda oldukça yüksek rakımlı bölgelere adaptasyonu nedeni ile ticari olarak önem arz etmektedir. Bu özgün evcil hibritin genomik yapısını ve uyum kapasitelerini daha iyi anlamak amacıyla tüm genom sekanslaması yapılarak genomik yapısı ve varyasyonlar Dzonun progenitörleri olan sığır ve Yak ile karşılaştırıldı. Dzo ile sığır referans genomları arasında toplam 33.17 M tek nükleotid varyasyonu belirlendi. Dzo steril olarak bilinmesine rağmen Dzo Y kromozomunda sterilite ile ilgili hiç bir genetik işarete rastlanmadı. Aksine, elde edilen bulgular otozomal DMC1 lokusunun (Kromozom 5. 110729098. C>CT) Dzonun sterilitesinde rol oynadığına işaret etmekte ve bu nedenle de daha ileri araştırılmaların yapılması gerekmektedir. Yüksek rakıma adaptasyon ile ilişkili yüksek oranda varyasyona sahip genlerin araştırılması amacıyla sığır ve Yakın tüm genom sekanslama ve...

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Genome-wide patterns of copy number variation in the Chinese yak genome

Cited by 69 publications

References 90 publications

Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

Accumulation of deleterious mutations in the domestic yak genome

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

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