Impact of Parental<i>Bos taurus</i>and<i>Bos indicus</i>Origins on Copy Number Variation in Traditional Chinese Cattle Breeds

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

doi:10.1093/gbe/evv151

Cited by 14 publications

(14 citation statements)

References 54 publications

(101 reference statements)

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“…Moreover, a copy-number deletion associated with reduced blood concentrations of hemoglobin, a characteristic of highaltitude adaptation in Tibetans, has been identified (Lou et al, 2015). CNV data have been used to analyze population relationships in some Chinese indigenous cattle breeds (Zhang et al, 2015a;Mei et al, 2019). However, to date, high-altitude adaptation analyses of genomic CNVs in Chinese indigenous cattle are limited.…”

Section: Introductionmentioning

confidence: 99%

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Zhang

Wang

et al. 2020

Front. Genet.

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Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp-4,477,860 bp in size), covering~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

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Section: Introductionmentioning

confidence: 99%

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Zhang

Wang

et al. 2020

Front. Genet.

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“…CNVs markers are more effective as compared to SNPs markers, due to more genomic sequences, including gene structure changing and dosage, changing gene regulation, and recessive alleles exposing [2] . Recently, a number of studies confirmed CNVs regions in bovine genome that cover a number of genes related to environment adaptation [3] . CNVs regions have tendency to demonstrate breed`s history and their formation patterns [4] .…”

Section: Introductionmentioning

confidence: 99%

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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“…As we know, molecular markers are a reflection of genetic polymorphism at the DNA level directly, since the genetic variation of nucleotide sequence among different breeds. Researchers used mitochondrial DNA makers (Xue et al 2014), microsatellite of Y chromosome (Acosta et al 2013), and copy number variation (Zhang 2015;Xu et al 2016) widely to assess genetic diversity and population structure of domestic animal in previous studies. Currently, with the advent of effective and high-throughput technology, more detail assessment of population structure and admixture history of cattle were conducted.…”

Section: Introductionmentioning

confidence: 99%

Genetic background analysis and breed evaluation of Yiling yellow cattle

Zhang

et al. 2017

Journal of Integrative Agriculture

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Traditionally, Chinese indigenous cattle is geographically widespread. The present study analyzed based on genome-wide variants to evaluate the genetic background among 157 individuals from four representative indigenous cattle breeds of Hubei Province of China: Yiling yellow cattle (YL), Bashan cattle (BS), Wuling cattle (WL), Zaobei cattle (ZB), and 21 individuals of Qinchuan cattle (QC) from the nearby Shanxi Province of China. Linkage disequilibrium (LD) analysis showed the LD of YL was the lowest (r 2 =0.32) when the distance between markers was approximately 2 kb. Principle component analysis (PCA), and neighbor-joining (NJ)-tree revealed a separation of Yiling yellow cattle from other geographic nearby local cattle breeds. In PCA plot, the YL and QC groups were segregated as expected; moreover, YL individuals clustered together more obviously. In the NJ-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed. We then used the F ST statistic approach to reveal long-term selection sweep of YL and other 4 cattle breeds. According to the selective sweep, we identified the unique pathways of YL, associated with production traits. Based on the results, it can be proposed that YL has its unique genetic characteristics of excellence resource, and it is an indispensable cattle breed in China.

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Impact of ParentalBos taurusandBos indicusOrigins on Copy Number Variation in Traditional Chinese Cattle Breeds

Cited by 14 publications

References 54 publications

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Pakistan’da Bazı Sığır Irklarında Kopya Sayısı Değişikliklerinin Genetik Özellikleri

Genetic background analysis and breed evaluation of Yiling yellow cattle

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