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Table 6 Potential causal genes underlying selective sweep regions and their associated function or phenotype

From: Detection of selective sweeps in cattle using genome-wide SNP data

SNP50 discovery breed(s) AFFXB1P discovery breed(s) BTA Sweep position (Mb) Potential causative gene(s) Gene or region type* Associated function or phenotype
SNP50 Specific Sweep Regions
Hereford --- 6 70.65-70.87 spotted 1 ---1 white points on face, underline, feet & tail in cattle [8]
Angus, Salers, Shorthorn, Simmental --- 12 25.87-26.23 NBEA PC autism spectrum disorder in human [35, 36]
MAB21L1 PC psychiatric disorders in human [37]
Angus, Hanwoo, Hereford, Holstein, Limousin, Simmental --- 24 0.06-0.32 LOC10013911 PS olfactory receptor-like variants
LOC783097 PS olfactory receptor-like variants
LOC100337172 PS olfactory receptor-like variants
Co-Discovered Regions (SNP50 and AFFXB1P)
Angus Angus 1 1.67-2.02 POLL 2 ---2 presence or absence of horns in cattle [5, 6, 38]
Holstein Wagyu 13 15.49-15.74 DGKZ PC leptin signaling – linked to human obesity [39]
Angus, Hereford, Jersey, Holstein, Limousin, Simmental Angus, Simmental 16 45.39-45.65 RERE PC embryogenesis and embryonic survival [4042]
Hanwoo Simmental, Wagyu 16 52.63-52.86 AGRN PC cell adhesion between embryo & maternal tissues [43]
HES4 PC oscillation and repression of embryogenesis [44]
ISG15 PC acknowledgement & maintenance of pregnancy [45, 46]
Hanwoo Angus, Simmental 18 14.72-14.97 MC1R PC black coat colour in cattle [7]
AFFXB1P Specific Sweep Regions
--- Simmental 1 83.46-83.68 HTR3E PC serotonin receptors – social cognition (tameness)
HTR3C PC in foxes and dogs [4750]
--- Angus 1 111.66-111.90 LEKR1 CCNL1 PC reduced birth weight in humans [51]
--- Angus 3 28.19-28.40 TSPAN2 PC oligodendrocyte signaling & maturation [52, 53]
--- Brahman 5 48.68-48.90 MSRB3 PC ear floppiness and morphology in dogs [54, 55]
--- Angus, Hanwoo, Simmental, Wagyu 6 5.64-5.99 MAD2L1 PC proper onset of anaphase during cell division
--- Angus, Simmental, Wagyu 6 106.84-107.30 RGS12 PC positional candidate for ovulation rate in swine [56]
--- Wagyu 11 33.02-33.26 NRXN1 PC synaptic function – linked to autism spectrum disorders [57, 58]
--- Simmental 13 66.46-66.70 SAMHD1 PC innate immune response [59]
--- Angus 14 24.63-25.17 PLAG1 PC variation in human height [60] and cattle stature [61]
--- Angus, Simmental 16 44.69-44.88 PIK3CD PC immune response
SPSB1 PC immune regulation [62]
--- Simmental, Wagyu 17 73.76-73.97 VpreB PC B cell development
PRODH PC schizophrenia [63]
--- Angus, Simmental 20 71.67-72.01 IgCgamma PC immune response
PDCD6 PC T cell receptor-induced apoptosis
--- Angus, Hanwoo 21 70.11-71.28 AHNAK2 PC skeletal muscle fiber organization [64]
IGHE other immune response
CRIP1 PC immune regulation [65, 66]
CRIP2 PC immune regulation [65, 66]
--- Brahman 22 10.70-10.96 TRANK1 PC bipolar disorder in humans [67]
DCLK3 PC brain development [68]
GOLGA4 PC golgi identity/structure [69]
ITGA9 PC gamete interaction & reduced fertilization success [70]
--- Wagyu 22 49.08-49.45 TLR9 PC innate immunity
--- Simmental 25 26.43-26.74 HSA163 HO autism spectrum disorders [7173]
--- Angus, Hanwoo Simmental, Wagyu 26 0.21-0.45 OR5D18 PC olfactory receptor [74]
various loci4 PS olfactory receptor-like variants
--- Wagyu 27 17.91-18.11 CBX1 PC epigenetic reprogramming of embryo/gene expression [7577]
--- Simmental 28 30.48-30.71 ADK PC physiological state – blood flow, neurotransmission in brain [78]
--- Hanwoo, Simmental, Wagyu 29 0.32-0.56 ANKRD26P3 PS ncRNA regulatory activity
CCDC144C PS ncRNA regulatory activity
  1. *Gene and region types are defined as: PC protein coding, PS pseudogene, HO human orthologue, other = known type, unspecific.
  2. 1The causal mutation has not yet been identified but the locus has been fine mapped to this region, see reference.
  3. 2The POLL locus in cattle has been identified but is characterised by allelic heterogeneity among breeds.
  4. 3This region is orthologous to human chromosome 16 (HSA16).
  5. 4There are 13 loci identified as olfactory receptor-like variants which have been determined to be pseudogenes.