Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle

Guo, Shaoke; Wu, Xiaoyun; Pei, Jie; Wang, Xingdong; Bao, Pengjia; Xiong, Lin; Chen, Min; Liang, Chunnian; Yan, Ping; Guo, Xian

doi:10.1016/j.ejbt.2021.07.006

Cited by 7 publications

(3 citation statements)

References 76 publications

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“…Compared to the analysis of the genome CNV in Qaidam cattle (18) for the first time, the role that CNVs have in the evolution of Qaidam cattle is becoming clear through our present study. The Qaidam cattle have strong adaptability to the arid environment, exhibiting dry, hypoxia, low air pressure, and large diurnal temperature difference (relative humidity 29-42%, precipitation 140-210.4 mm).…”

Section: Discussionmentioning

confidence: 85%

“…However, screening the selected genomic copy number genetic markers is complex. Over the past decades, high-throughput sequencing techniques and bioinformatics tools have been increasingly used to construct genome-wide CNV maps (1,15,17,18). The diversity of CNVs has been extensively explored in Bos Taurus, Bos Indicus, and their crossing populations.…”

Section: Discussionmentioning

confidence: 99%

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Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Liu

Wang

et al. 2023

Front. Vet. Sci.

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Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.

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Section: Discussionmentioning

confidence: 85%

Section: Discussionmentioning

confidence: 99%

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Liu

Wang

et al. 2023

Front. Vet. Sci.

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“…Through the analysis of mitochondrial DNA, it was found that the maternal genetic diversity of Qaidam cattle was high, with two maternal origins of B. taurus and Bos indicus (Xia, Achilli, et al., 2021; Yang et al., 2023). Genome copy number variation analysis of Qaidam cattle revealed some genes related to immunity, coat color and environment adaptability (Guo et al., 2021; Liu et al., 2023). The whole genome resequencing data analysis of nine Qaidam cattle revealed the closest relationship between Qaidam and Qinchuan cattle.…”

Section: Introductionmentioning

confidence: 99%

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

Wei,

Li,

Yan

et al. 2024

Animal Genetics

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Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low‐oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole‐genome resequencing technology, along with 192 published sets of whole‐genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross‐population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

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Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep

Tian,

Sun,

Ren

et al. 2023

Sci Rep

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Copy number variation (CNV) is a genetic structural polymorphism important for phenotypic diversity and important economic traits of livestock breeds, and it plays an important role in the desired genetic variation. This study used whole genome sequencing to detect the CNV variation in the genome of 6 local Tibetan sheep groups. We detected 69,166 CNV events and 7230 copy number variable regions (CNVRs) after merging the overlapping CNVs, accounting for 2.72% of the reference genome. The CNVR length detected ranged from 1.1 to 1693.5 Kb, with a total length of 118.69 Mb and an average length of 16.42 Kb per CNVR. Functional GO cluster analysis showed that the CNVR genes were mainly involved in sensory perception systems, response to stimulus, and signal transduction. Through CNVR-based Vst analysis, we found that the CACNA2D3 and CTBP1 genes related to hypoxia adaptation, the HTR1A gene related to coat color, and the TRNAS-GGA and PIK3C3 genes related to body weight were all strongly selected. The findings of our study will contribute novel insights into the genetic structural variation underlying hypoxia adaptation and economically important traits in Tibetan sheep.

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Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle

Cited by 7 publications

References 76 publications

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep

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