In other species: indicine cattle (zebu) , goat , sheep , domestic yak , bighorn sheep , water buffalo , kouprey

Categories: Craniofacial phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 110100 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal

Disease-related: no

Key variant known: yes

Year key variant first reported: 2012

Cross-species summary: Horns are paired appendages with a bony core that is attached to the skull and a keratin outer sheath. There is substantial variation in the extent of horn growth, making classification difficult. However, in general, the presence or absence of horns can be attributed to the action of two alleles at an autosomal locus. The type of gene action varies considerably between and among species. Absence of horns is called 'polled'. See also entries for 'scurs'.

Species-specific name: Haplotype BHP; Haplotype HHP; Haplotype JHP

Species-specific symbol: BHP; HHP; JHP

Species-specific description: The absence of horns (polledness) is of substantial benefit in cattle, from an economic and welfare point of view: bruising due to horns is eliminated, and the stress associated with de-horning is avoided. (Information complied by Ulrika Tjälldén and Vanja Kinch, Uppsala, March 1998). In addition to naturally occurring variants for this trait, variants have been created artificially: Genetically-modifed organism; GMO.

History: In cattle, one of the first Mendelian traits to attract attention was the presence/absence of horns. Polled cattle had long been recognised, e.g. having been described by Herodotus (c450BC) and Tacitus (c90AD). The inherited nature of this trait was well recognised (but not understood) long before the rediscovery of Mendelism (see, e.g. Darwin 1859 [p. 14]; Darwin 1868 [vol ii, p. 316]). In 1902, polledness was one of the first six animal traits (and the first cattle trait) to be shown to have Mendelian inheritance (Bateson and Saunders, 1902). In 1906, the American agricultural polymath W.J. Spillman (who is not only regarded as a founding father of agricultural economics, but also independently rediscovered Mendelism while crossing strains of wheat!) published a paper in Science (Spillman 1906a) and another in the newly-founded Journal of Heredity (Spillman 1906b), providing convincing evidence that the presence/absence of horns is a Mendelian trait, with polled being dominant to horned. This trait soon became a classic Mendelian trait, cited in many textbooks. Indeed, as delightfully recorded by Crow (1992), this trait even attracted the attention of the Nobel-prize winning physicist Erwin Schrödinger, who wrote two letters to J.B.S Haldane in 1945, in relation to “the hornless cattle problem”. In these letters, Schrödinger derived an equation that predicts the frequency of horned offspring in a closed herd after any number of generations of complete selection against horned bulls, but with no selection on cows. Nothing much was added to our knowledge of this trait until the first wave of genomics tools provided sufficient microsatellite markers to enable Georges et al. (1993) to map the presence/absence of horns to within a recombination fraction of 13% with two markers on chromosome BTA1 (see Mapping section). To present readers, such “loose” linkage might seem to be not worthy of much celebration. At the time, however, this result was sufficiently important and novel to warrant publication in Nature Genetics. Subsequent progress in mapping is summarised in the Mapping section. (Most of the wording under this heading is from Nicholas, F.W. (2012; Mendelian Inheritance in Cattle, chap 2 [pp. 11-19] in Bovine Genomics [ed. J. Womack], Wiley-Blackwell, Ames, Iowa.) As noted by Allais-Bonnet et al. (2013), the "Celtic" mutation (See Molecular section below) must be very old: "fixation of the Celtic mutation in ancient Nordic and British breeds and segregation of this allele in Icelandic cattle, which evolved independently from other Nordic breeds since the time of the Vikings, makes it possible to date back this mutation to at least one millenary. Because of historical relationships between the Vikings and the ancient Germans and between the ancient Germans and the Scythians, this mutation could be even older and explain the polledness of the cattle raised by these people . . . , which Herodotus, in the fifth century BC, mistakenly attributed to the extreme cold of the modern day Ukrainian steppes." In a landmark paper that presents the final results of a project initially reported by Tan et al. (2013), Carlson et al. (2016) described "the use of genome editing using transcription activator-like effector nucleases (TALENs) to introgress the putative PC POLLED allele [see Molecular section below] into the genome of bovine embryo fibroblasts to try and produce a genotype identical to what is achievable using natural mating, but without the attendant genetic drag and admixture". Importantly, they later commented that "To our knowledge this is the first empirical validation of a putative causative allele in livestock, and this report provides evidence that PC, a sequence variant duplication of unknown function in a genomic region with no known or predicted coding or noncoding genes, is causative for polled. Genetic improvement of livestock using TALENs, or other genome-editing methods, establishes an alternative to transgenic (genetic modification)-based methods for genetic improvement of livestock using variation already present in species without the admixture that can result from classic breeding methods. . . . This solution to the dehorning problem would be economically viable and could potentially improve the welfare of cattle in the United States."

Inheritance: As described in the History section, this trait was the first cattle trait to be shown to be inherited in a Mendelian manner. This form of inheritance has been confirmed many times, e.g. Stookey and Goonewardene (1996). (Information complied by Ulrika Tjälldén and Vanja Kinch, Uppsala, March 1998); supplemented by FN 14th June 2013

Mapping: Georges et al. (1993) mapped this locus to the linkage group corresponding to chromosome BTA1, within a recombination fraction of 13% with two markers. Schmutz et al. (1995) provided the first estimate of physical location of the locus as being "within 1q12-14, very near the centromere of Chromosome (Chr) 1". By 2005, the region in which the locus is located was narrowed to a 1 Mb segment (Drögemüller et al., 2005). In early 2012, the region was narrowed further to 385 kb by Seichter et al. (2012). The BTA1 location of horns/polled in cattle bears no homology to the OAR10 location of horns/polled in sheep (OMIA 000483-9940), suggesting that the same trait in the two species is determined by different genes. Mariasegaram et al. (2012) confirmed the location of this locus, and identified a 303bp allele of a new microsatellite (CSAFG29) that is stromngly associated with the polled trait in Australian Brahman cattle. Using the Illumina bovine 777K SNP beadchip on 15 homozygous polled cattle from nine breeds, together with 36 half-sibs), Allais-Bonnet et al. (2013) independently confirmed the mapping of this locus to the centromeric end of chromosome BTA1, in the region 1,693,164 to 2,018,403 (UMD3.1 bovine genome assembly). In an independent study, Wiedemar et al. (2014) homozygosity-mapped the polled locus in 1,019 polled cattle from 14 different breeds, each of which had been genotyped at 777,962 SNP loci with the Illumina BovineHD BeadChip. Their analysis enabled them to refine "the critical region of the Simmental polled mutation to 212 kb and identified an overlapping region of 932 kb containing the Holstein polled mutation". Rothammer et al. (2014) narrowed the Holstein-Friesian candidate region to 53kb. Stafuzza et al. (2018) mapped "polledness in Nelore (Bos taurus indicus)" to the "centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631-3,987,104 bp)", suggesting that "the postulated African horn locus is located very close to the Polled locus described for taurine breeds or it may be a mutation in the same region, since the literature that suggests the existence of an African horn locus is based on inconsistent inheritance patterns and dates from the last century." Utsunomiya et al. (2019) summarised the situation as "The absence of horns is a dominant phenotype determined by the P allele at the polled locus on bovine chromosome 1 (CHR1) positions 1,693,164–2,018,403".

Markers: Randhawa et al. (2019) "developed an optimized poll gene test that . . . successfully predicted a genotype in 99.96% of samples [from 39,943 animals of multiple breeds] assessed. We demonstrated that a robust set of 5 SNPs [rs801127025, rs383143898, rs799403053, rs210350155 and rs797088784; comprising the "optimized poll testing (OPT) assay"] can effectively determine PC and PF alleles and eliminate the ambiguous and undetermined results of poll gene testing previously identified as an issue in cattle".

Molecular basis: Finally, after many frustrating years, mutations completely associated with the last of Bateson and Saunder's (1902) six initial Mendelian traits have been determined. Resequencing (by Medugorac et al., 2012) of the region mapped by Seichter et al. (2012), and subsequent investigation of putative DNA sequence variants, revealed two alleles completely associated with polledness in cattle of European origin: a 202bp indel in breeds of “Celtic” origin (called P[sub]C or (P[sub]202ID)) and a 260kb haplotype block marked by two indels and three SNPs in cattle of Friesian origin (called P[sub]F). Heterozygosity or homozygosity for either of these alleles, or heterozygosity for both alleles, is completely associated with polledness. Despite this major discovery by Medugorac et al. (2012), and as if to reinforce the intransigence of this iconic Mendelian trait, no gene can yet be named, because none of these mutations disrupts "any known coding sequence or a splice site, or an intronic region, or any known regulatory regions". We are still a long way from having a complete understanding of this enigmatic locus. Until then, in OMIA the polled "gene" is called POLLED. Independent fine-mapping, followed by extensive sequencing in the candidate region, enabled Allais-Bonnet et al. (2013) to confirm their previously-reported "Celtic" (P[sub]C) mutation, but to specify it slightly differently as "a duplication of 212 bp replacing a segment of 10 bp (g.1706051_1706060 delins 1705834_1706045 dup" (UMD3.1 bovine genome assembly) and to confirm that it occurs in a region with no known genes or expressed sequence tags. A similar approach enabled Allais-Bonne et al. (2013) to reduce the list of candidate mutations for the "Friesian" (P[sub]F) allele to "three SNP (g.1764239T>C, g.1768587C>A, g.1855898G>A) and a large duplication of 80,128 bp (g.1909352_1989480dup)" (UMD3.1 bovine genome assembly), again in a region with no known genes or expressed sequence tags. Based on histological and gene-expression studies, Allais-Bonne et al. (2013) proposed that "the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis" and "provide[d] evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci." The Holstein situation was further investigated by Glatzer et al. (2013), who reported "Sequencing of the positional candidate genes within the 1 Mb polled region and whole genome sequencing of Holsteins revealed a single nucleotide polymorphism (SNP) AC000158: g.1390292G>A within intron 3 of the interferon gamma receptor 2 gene (IFNGR2) in perfect co-segregation with polledness in Holsteins. This complete association was validated in 443 animals of the same breed." Interestingly, as also reported by Glatzer et al. (2013), in a selective-sweep study by Stella et al. (2010) "The SNP featuring the largest difference in allelic frequency between polled and horned animals was located within the interferon gamma receptor 2 gene (IFNGR2)". Sequencing and additional genotyping enabled Wiedemar et al. (2014) to confirm the 212bp indel "Celctic" mutation P[sub]C as causal for polled in Simmentals and other European beef breeds. They also "identified a total of 182 sequence variants as candidate mutations for polledness in Holstein cattle, including an 80 kb genomic duplication and three SNPs reported before [see above]." Also, the authors reported that "For the first time we showed that hornless cattle with scurs are obligate heterozygous for one of the polled mutations." By testing almost 6000 cattle, Rothammer et al. (2014) confirmed the 80kb duplication mentioned above (now called P(sub)80kbID) to be the "single causal mutation" in Holstein-Friesian cattle", i.e. to be P[sub]F. In addition, their results did not support the SNP association reported by Glatzer et al. (2013). By introgressing the P(sub)C "allele into dairy cattle by genome editing [via TALEN-stimulated homology-dependent repair to produce four cell lines either homozygous or heterozygous for the [P.sub.C] allele]", followed by reproductive cloning to produce five live calves (all lacking horn buds), two of which were polled at 10 months, Carlson et al. (2016) provided "the first empirical validation of a putative causative allele in livestock, and this report provides evidence that [P.sub.C], a sequence variant duplication of unknown function in a genomic region with no known or predicted coding or noncoding genes, is causative for polled." This study involved genetically modified organisms (GMO). A third polled allele, the Mongolian allele, was discovered by Medugorac et al. (2017) in Mongolian Turano cattle. It is "a complex 219-bp duplication–insertion (P219ID) beginning at 1,976,128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position . . . . This rearrangement results in duplication of an 11-bp motif (5′-AAAGAAGCAAA-3′) that is entirely conserved among Bovidae . . . and that is also duplicated in the 80-kb duplication responsible for Friesian polledness". Intriguingly, this allele has been introgressed into yaks with which Mongolian Turano cattle have been herded for more than 1,500 years, via backcrossing female yak-cattle hybrids to male yaks (Medugorac et al., 2017). The suggested abbreviation for the Mongolian allele is P[sub]M (FN, in consultation with A. Capitan and I. Medugorac) or P[sub]219ID (Chen et al., 2017). Utsunomiya et al. (2019) reported a "novel polled variant . . . [that they named] Guarani (P[sub]G)", comprising a novel duplication the region BTA1: 1,893,790–2,004,553 in Nellore cattle. Koufariotis et al. (2018) "provide[d] evidence that the polled mutation in Brahmans, a desirable trait under very strong recent selection, is of Celtic origin and is introgressed from Bos taurus." By whole-genome sequencing with an Oxford Nanopore Technology's minION sequencer "four homozygous poll (PcPc), four homozygous horned (pp) and three heterozygous (Pcp) Brahmans" and comparing the sequence in the polled region, Lamb et al. (2020) confirmed that the polled allele in the Brahman breed is the Celtic allele. Schuster et al. (2020): "For the generation of polled offspring from a horned Holstein–Friesian bull, we isolated the Polled Celtic variant from the genome of an Angus cow and integrated it into the genome of fibroblasts taken from the horned bull using the CRISPR/Cas12a system (formerly Cpf1). Modified fibroblasts served as donor cells for somatic cell nuclear transfer and reconstructed embryos were transferred into synchronized recipients. One resulting pregnancy was terminated on day 90 of gestation for the examination of the fetus. Macroscopic and histological analyses proved a polled phenotype. The remaining pregnancy was carried to term and delivered one calf with a polled phenotype which died shortly after birth." This study involved genetically modified organisms (GMO).

Genetic engineering: Yes - in addition to the occurrence of natural variants, variants have been created artificially, e.g. by genetic engineering or gene editing
Have human generated variants been created, e.g. through genetic engineering and gene editing

Clinical features: Compared to horned cattlle, polled cattle have a narrower skull, and the frontal eminence is more pronounced (Brenneman et al., (1996). (Information complied by Ulrika Tjälldén and Vanja Kinch, Uppsala, March 1998). Also, "polled cattle have abnormal hair growth on the eyelashes and eyelids, and that some bulls carrying the Celtic mutation have pending prepuce and abnormal preputial withdrawal (Allais-Bonnet et al., 2013)" (A. Capitan, pers. comm. to FN, 2017)

Prevalence: Chen et al. (2017) reported that "all three candidate mutations [P[sub]202ID, P[sub]80kbID and P[sub]219ID] have been simultaneously introgressed into Shuxuan cattle . . . . Furthermore, one polled animal still remains to carry none of the three candidate mutations, which suggests that further mutation(s) would also exist." In a study of 26 horned and 39 Creole catte from Argentina, Falomir-Lockhart et al. (2019) reported that "variants PF and PG were not detected, thus dismissing the Holstein-Friesian and Nellore origins of the polled phenotype in this native breed. Conversely, the presence of the Celtic variant PC suggests an almost complete co-segregation. The cluster analysis rejected the hypothesis of recent introgression, which is compatible with the historical record of polled Creole cattle in northwest Argentina."

Breeds: Angus (Cattle) (VBO_0000104), Blanco Orejinegro, Colombia (Cattle) (VBO_0004602), Charolais (Cattle) (VBO_0000177), Galloway (Cattle) (VBO_0000207), Holstein Friesian (Cattle) (VBO_0000239), Kazakh (Cattle) (VBO_0000256), Limousin (Cattle) (VBO_0000274), Pinzgau (Cattle) (VBO_0000334), Polled Hereford (Cattle) (VBO_0000341), Polled Shorthorn (Cattle) (VBO_0000342), Simmental (Cattle) (VBO_0000380).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene: