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  • ReceivedAug 9, 2020
  • AcceptedNov 16, 2020
  • PublishedJan 21, 2021

Abstract


Funded by

the National Natural Science Foundation of China(31822052,31572381)

the National Thousand Youth Talents Plan

and the Program of the National Beef Cattle and Yak Industrial Technology System(CARS-37)


Acknowledgment

This work was supported by the National Natural Science Foundation of China (31822052, 31572381) and the National Thousand Youth Talents Plan, and the Program of the National Beef Cattle and Yak Industrial Technology System (CARS-37). We thank the High-Performance Computing platform of Northwest A&F University. We thank Yu Wang, Xiangyu Pan, Ming Li, Xiaomeng Tian, Dongke Zhou, Zhirui Yang, Han Xu, Chunna Cao and other members of the genome of big data laboratory for discussions. We also thank members of the NextGen project for sharing their data.


Interest statement

The author(s) declare that they have no conflict of interest. Animal care and the experiments were conducted according to the guidelines established by the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004) and approved by the Institutional Animal Care and Use Committee (College of Animal Science and Technology, Northwest A&F University, China). Every effort was made to minimize animal pain, suffering, and distress and to reduce the number of animals used.


Supplement

SUPPORTING INFORMATION

The supporting information is available online at https://doi.org/10.1007/s11427-020-1850-x. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    Analysis pipeline. Diagram of the pipeline used to identify species-shared CNVRs. There may be multiple shared regions with similar ranges because of the similarity of the alignment sequence. We only use the merged region for subsequent analysis.

  • Figure 2

    CNVR comparison among genomes of cattle, goat, and sheep. A, Geographic distribution of 886 genomes of ruminant livestock. B, Distribution of CNVR in genomic region based on the size of all CNVR sites. C, Interspecific comparison of CNVRs. For each species, the proportion of its CNVRs shared with none, one or two other species is plotted. The genome sequences of cattle and sheep were compared to the autosomal genome sequences of goat ARS1, and some of the sequences not matched were not involved in the calculation.

  • Figure 3

    (Color online) Validation and evaluation of genotypes by CNVplex. Three deletion (A–C) and three duplication (D–F) CNVRs with distinguishable copy numbers were genotyped using CNVplex in 56 sheep samples. The copy-number genotype from the same animal as were predicted by CNVcaller and CNVplex; the two methods showed genotype concordance at confidently called sites. See Table S5 in Supporting Information for CNVplex confirmation results for 44 CNVRs in 56 sheep.

  • Figure 4

    Genome-wide screening and functional annotations of selected CNVRs in cattle (A), goat (B), and sheep (C). VST is plotted against the position on each of the 27 (sheep) or 30 (goat) chromosomes. The horizontal solid lines indicate the genome-wide threshold of selection signals, with the highly stratified genes having VST values≥0.15. Selected CNVRs that overlapped with characterized GWAS loci are shown in Latitude (°), PR (mm), ATMP (°C), AMIT (°C), AMAT (°C), DTMM (°C), ASD (h). Three GWAS results that overlapped with the strong selective CNVs are shown. The Bonferroni significance threshold (cattle: 1.04×10−5, goat: 4.21×10−5, sheep: 2.18×10−5) is indicated by red horizontal dashed lines.

  • Figure 5

    Allele frequency distribution of CNVRs and SNPs number among three species. A, With the increasing frequency of the allele, the number of CNVRs present a different downward trend. B, With the increasing frequency of the allele, the number of SNPs present a different downward trend. C, Venn diagram showing unique and shared CNVR (bp) among the three species. D, Random distribution of shared CNVRs by the assumed model, the observed species-shared CNVR is significantly higher than what is expected by 300 simulations (**, P<1.0×10−2). E, Venn diagram showing unique and shared SNPs among the three species, the digit in brackets represent the total number of SNPs with the same location and genotype.

  • Figure 6

    Heatmaps of two CNVRs around ASIP region in goat and sheep. The heatmaps depict two CNVRs under candidate balancing selection with the same starting and ending positions of ASIP gene in the sheep and goat genomes. The X-axis values indicate the position and the Y-axis values indicate the sample count and different populations. Red solid line: the ASIP gene and its upstream and downstream genes, and this region correspond to the goat and sheep genome, respectively; Green shadow region: the ~40 kb shared CNVR distribution of goat and sheep genomes; Yellow shadow region: the ~190 kb shared CNVR distribution of goat and sheep genomes (copy 1), there were two ~190 kb CNVRs in the sheep genome; Pink shadow region: the ~190 kb shared CNVR distribution of goat and sheep genomes (copy 2), there were two ~190 kb CNVRs in the sheep genome.

  • Table 1   CNVRs differentiated between ruminant livestock populationsa)

    NO.

    Species

    Chr

    Start

    End

    Size (kb)

    Type

    Gene

    VST

    Copy range

    GWAS (P-valve)

    Function description

    1

    Cattle

    X

    133,087,001

    133,098,000

    11

    exonic

    PRDM7

    BI: LH vs. HH (0.35)

    2.28–6.02

    NA

    Hybrid sterility gene (Ahlawat et al., 2016; Ma et al., 2015).

    2

    13

    22,741,001

    22,748,000

    7

    UTR5

    MLLT10

    BT: LH vs. HH (0.18)

    0.64–4.24

    NA

    Subcutaneous fat (Sung et al., 2016).

    3

    19

    35,329,001

    35,339,000

    10

    exonic

    KCNJ12

    BI: LH vs. HH (0.25); BT: LH vs. HH (0.37); All cattle: LH vs. HH (0.22)

    0.70–3.42

    NA

    KCNJ12 was reported to regulate insulin secretion (Reimann and Ashcroft, 1999).

    4

    19

    41,452,501

    41,477,000

    24.5

    exonic

    KRTAP9-1

    BT vs. BI (0.46); BT vs. BB (0.21)

    1.78–11.86

    NA

    Tick resistance in cattle (Bickhart et al., 2012; Wang et al., 2007).

    5

    Sheep

    2

    113,389,001

    113,393,000

    4

    intronic

    ARHGEF4

    LH vs. HH (0.19)

    0.7–9.0

    NA

    ARHGEF4 is involved in several metabolic processes (Thiesen et al., 2000). The CNVs of this gene are associated with delayed development and neural alterations (Dharmadhikari et al., 2012), as well as resistance to insulin (Irvin et al., 2011).

    6

    9

    63,878,501

    63,886,000

    7.5

    intronic

    CSMD3

    DOA vs. WOA (0.20)

    0.04–2.58

    DTMM: 6.14×10−6; NDPR: 6.14×10−6

    CUB and Sushi multiple domains 3 (CSMD3) as a candidate gene for autism found in their common 8q23 breakpoint area (Sarowar et al., 2016).

    7

    1

    65,686,501

    65,699,000

    12.5

    UTR5

    GBP5

    DOA vs. WOA (0.18)

    0–2.48

    PR: 1.07×10−5

    GBP5 promotes NLRP3 inflammasome assembly and immunity in mammals (Kojo et al., 2017).

    8

    10

    196,501

    209,000

    12.5

    intergenic

    LOC101118284 (dist=172,535), PCDH20 (dist=501,727)

    DOA vs. WOA (0.17)

    0–2.64

    PR: 6.78×10−6

    olfactory receptor 5W2-like.

    9

    Goat

    21

    64,885,501

    64,888,500

    3

    intergenic

    BEGAIN (dist=145,698), DLK1 (dist=10,651)

    CA vs. CI (0.29)

    0.48–5.36

    DTMM: 6.72×10−6; PR: 2.65×10−8

    Ectopic expression of DLK1 protein in skeletal muscle of Padumnal Heterozygotes causes the callipyge phenotype (Davis et al., 2004).

    10

    21

    5,414,501

    5,419,000

    4.5

    intronic

    CERS3

    CA vs. CI (0.65); CH vs. CI (0.53)

    0.14–2.56

    AMIT: 2.54×10−5

    Recessive forms of congenital ichthyosis encompass a group of rare inherited disorders of keratinization leading to dry, scaly skin (Simpson et al., 2020).

    11

    20

    23,758,001

    23,765,500

    7.5

    intronic

    PLPP1

    CA vs. CI (0.98); CH vs. CI (0.86)

    0.02–2.46

    AMAT: 1.37×10−6; AMIT: 1.17×10−6; ATMP: 9.09×10−7

    Lipid phosphate phosphatase 3 in vascular pathophysiology (Busnelli et al., 2018).

    12

    22

    31,979,501

    31,985,500

    6

    intergenic

    MITF (dist=223,910), FRMD4B (dist=142,279)

    CA vs. CI (0.98); CH vs. CI (0.86)

    0–2.48

    PR: 5.41×10−7; AMIT: 1.13×10−6; ATMP: 5.35×10−7

    MITF gene that cause the splashed white phenotype in Horses (Hauswirth et al., 2012). FRMD4B variant suppressesdysplastic photoreceptor lesions(Kong et al., 2018).

    BT: Bos taurus; BI: Bos indicus. BB: Bos taurus×Bos indicus. BG: Bos grunniens. DOA: Domestic Ovis aries. WOA: Wild Ovis aries; including Ovis musimon (mouflon), Ovis ammon (Argali), Ovis canadensis (Bighorn Sheep), and Ovis dalli (Thinhorn sheep). CA: Capra aegagrus. CI: including Capra falconeri (Markhor), Capra sibirica (Siberian ibex), and Capra ibex (Alpine ibex). CH: Capra hircus. LH: Low-height. HH: High-height. CNVRs intersecting genes that show a dramatic difference in copy number (as measured by VST and GWAS) between ruminant livestock populations. See Table S1 in Supporting Information for the definition of populations and the abbreviation of environmental parameters.