- indigenous fine-wool sheep populations using whole-genome resequencing. - In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.. - these regions accounted for 2.17% of the sheep reference genome. - The average length of the CNVRs was 4307.17 bp. - Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. - Keywords: Copy number variation, Fine-wool sheep, Whole-genome resequencing. - marker, CNVs extensively exist in various forms within the scope of the genome. - Large-scale CNV detection has been carried out mainly using array comparative genome hybridization (aCGH) chips and high-density SNP chips in the past, but these methods have certain limitations, such as low coverage and low resolution, and they can- not be used to detect some new or rare CNVs. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - decline of the cost of sequencing, next generation se- quencing (NGS) has overcome the limitations of chips, and shown enormous advantages for genomic CNV detection.. - It was found that 1 kb se- quence deletion in the guanylate binding protein 2 (GBP2) gene of cattle was significantly correlated with growth and development characteristics, indi- cating that CNV could serve as a marker for the molecular breeding of cattle [9]. - And CNV in the endothelin receptor A (EDNRA) gene in goats was positively correlated with white coat coverage [10].. - found a 38.7 kb CNV existing in the methio- nine sulfoxide reductase B3 (MSRB3) gene, which significantly correlated with pig ear size [12]. - In this study, the CNVs of three Chinese fine-wool sheep breeds were analyzed using genomic resequen- cing. - CNVnator software, which is based on the read depth method, was utilized, and a total of 1,747,604 CNV events (including 49,851 “duplication” events and de- letion” events) were detected in the 32 fine-wool sheep, with each sheep’s genome possessing 54,612.63 CNVs, on average (Table 1, Additional file 3: Table S3). - To explore the CNV distribution pattern in the four groups of fine- wool sheep, violin plots were drawn for the CNV lengths.. - The distribution showed that 69.44% of the CNVs were located within the 0–2 kb inter- val, 19.49% were within 2–4 kb, and 11.07% were greater than 4 kb in length (Fig. - Table 1 Summary of CNVs and CNVRs identified in 32 fine-wool sheep. - The distribution showed that 67.35% of the CNVRs were located within the 0–2 kb interval, 18.34% were within 2–4 kb, and 14.31% were greater than 4 kb in length (Fig. - Between 17 and 424 of the CNVRs detected in this study overlapped with previ- ously reported CNVRs, with overlapping ratios of . - Functional annotation of the identified CNVRs. - To further investigate the function of these CNVRs, functional enrichment analysis of the CNVR-harboring genes was performed. - A total of 119 GO terms were enriched in the CNVRs shared by the four groups of fine-wool sheep (p <. - 1 Violin plots showing distribution of the total CNV length in each group. - 2 Size distribution of CNVs and CNVRs in fine-wool sheep. - 3 Genomic landscape of CNVRs in fine-wool sheep. - a: A map of CNVRs in the fine-wool sheep genome. - Liu et al. - Ma et al. - Jenkins et al. - Zhu et al. - Fur- thermore, functional enrichment analysis of the spe- cific CNVR-harboring genes in the four groups of fine-wool sheep was also performed, and it was found that a large number of the CNVR-harboring genes participated in fat metabolism (GO:0006635, GO:0009062 and GO:0034440), amino acid metabol- ism (GO:0006658, GO:0006659 and GO:0005234), microelement metabolism (GO:0005506, GO:0010167 and GO:0006766), and response to stimuli (GO:. - CNVRs detected in the four groups of fine-wool sheep were compared with a database of previously reported sheep QTLs to further analyze their hereditary effects. - It was found that 1855 of the CNVRs were associated with 166 QTLs, with the QTL frequency ranging from 1 to 500. - These QTLs included milk, carcass and health- related QTLs, among others, providing important infor- mation for improving fine-wool sheep in the future (Additional file 9: Table S7).. - The 32 fine-wool sheep were divided into horned and polled groups, and selective sweep analysis of all the CNVRs was performed. - 4 and Table S8 (Additional file 10), the horned and polled fine-wool sheep showed genetic differentiation in many of their chromosomes, with the most significant vari- ation on chromosome 10, in the RXFP2 and B3GLCT gene. - The CNVRs with the top five VST values were selected as candidate CNVRs, and the functional enrichment analysis of the genes annotated by these CNVRs was carried out. - S3 (Add- itional file 13), eight (80%) of the randomly selected. - In this study, NGS technology was used to detect the CNVs in 32 indigenous fine-wool sheep in China. - This dif- ference was not surprising, as the genomic coverage of SNP chips is poor, which results in the detection of longer CNVRs [18, 19]. - The CNVRs detected in this study accounted for 2.17% of the sheep refer- ence genome, which falls within the range (0.8–. - However, the CNVRs identified in individ- ual species accounted for more than 10% of their reference genomes, which may be related to the dif- ferent genetic backgrounds of the studied animals [24, 25]. - In addition, these results could also be ascribed to differences in the CNV calling algorithms and standards used to determine the CNVs [26, 27].. - In the CNVs identified in this study, “deletion”. - In this study, many of the CNVR-harboring genes were significantly enriched for GO terms relating to sensory perception. - In addition, Wnt- related signaling pathways were also enriched in some of the CNVR-harboring genes in the AMS_no group. - Through the analysis of KEGG signaling pathways, it was found that some of the CNVR-harboring genes were enriched for signaling pathways correlated with wool growth and development. - It has been reported that, as one of the important pathways in the follicle development process, the Jak-STAT signaling pathway can stimulate MAPK to influence follicle development [44]. - The skin is the largest non-genital organ tar- geted by estrogens, which can significantly change the cyclic response of the hair follicles. - Therefore, the CNVRs detected in this study were compared with the QTLs reported in the sheep QTL database. - In this study, the first resequencing-based CNV map of Chinese indigenous fine-wool sheep was developed, pro- viding an important addition to the previously published sheep CNVs. - This information will be beneficial for fu- ture investigations of the genomic structural variations underlying traits of interest in sheep.. - We collected blood samples from 32 fine-wool sheep (2- year-old rams, Additional file 14: Table S11), including 16 Alpine Merino sheep (8 horned, AMS_horn. - The integrity and purity of the DNA was determined using 1.5% agarose gel electrophoresis and a NanoDrop 2000. - CNVnator software (version 0.3) was used to detect the CNVs in the sheep genome samples [31]. - The gene copy numbers (CN) of the genomes were estimated using the CNVnator “-geno- type” option. - The DAVI D database (http://david.abcc.ncifcrf.gov/) was used for the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses [59], and p-values ≤0.05 were considered to in- dicate significant enrichment in the candidate gene. - In addition, to study whether these CNVRs were associated with economically important characteristics in fine-wool sheep, these CNVRs were compared with QTLs in the sheep QTL database (https://www.animalgenome.org/. - The selective sweep analysis of the CNVs in this study was carried out according to Redon’s method [25]. - We used the 2 - ΔΔ Ct method to calculate the mul- tiple of change, and we calculated 2 × 2 - ΔΔ Ct for the copy number of the target gene in the test sample [16].. - Detail information of the detected CNVRs.. - Venn diagram of CNVR numbers in four different fine-wool sheep groups.. - CNVRs length for 27 chromosomes across four different fine-wool sheep groups.. - Introduction of the 3 sheep breeds examined in the present study.. - CNV: Copy number variation. - AHS_no: Aohan fine-wool sheep;. - The funders had no role in study design, data collec- tion and analysis, decision to publish, or preparation of the manuscript.. - All the whole genome sequencing raw data used in this study has been deposited in the Sequence Read Archive (SRA) public databases under BioProject (PRJNA680869).. - We obtained written permission from the owner of the sheep farm to take samples.. - Copy number variation: new insights in genome diversity. - Distribution and Functionality of Copy Number Variation across European Cattle Populations.. - Diversity of copy number variation in the worldwide goat population. - 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Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi- feralization. - The 1.78-kb insertion in the 3 ′ -untranslated region of RXFP2 does not segregate with horn status in sheep breeds with variable horn status. - A 1.8-kb insertion in the 3 ′ -UTR of RXFP2 is associated with polledness in sheep
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