Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I^d allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I^p), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th–19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.     

A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern

A specific white spotting phenotype, termed finching or line‐backed spotting, is known for all Pinzgauer cattle and occurs occasionally in Tux‐Zillertaler cattle, two Austrian breeds. The so‐called Pinzgauer spotting is inherited as an autosomal incompletely dominant trait. A genome‐wide association study using 27 white spotted and 16 solid‐coloured Tux‐Zillertaler cattle, based on 777k SNP data, revealed a strong signal on chromosome 6 at the KIT locus. Haplotype analyses defined a critical interval of 122 kb downstream of the KIT coding region. Whole‐genome sequencing of a Pinzgauer cattle and comparison to 338 control genomes revealed a complex structural variant consisting of a 9.4‐kb deletion and an inversely inserted duplication of 1.5 kb fused to a 310‐kb duplicated segment from chromosome 4. A diagnostic PCR was developed for straightforward genotyping of carriers for this structural variant (KIT^PINZ) and confirmed that the variant allele was present in all Pinzgauer and most of the white spotted Tux‐Zillertaler cattle. In addition, we detected the variant in all Slovenian Cika, British Gloucester and Spanish Berrenda en negro cattle with similar spotting patterns. Interestingly, the KIT^PINZ variant occurs in some white spotted animals of the Swiss breeds Evolèner and Eringer. The introgression of the KIT^PINZ variant confirms admixture and the reported historical relationship of these short‐headed breeds with Austrian Tux‐Zillertaler and suggests a mutation event, occurring before breed formation.     

Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F_st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.     

Linkage disequilibrium structures in cattle and their application to breed identification testing

We examined the extent of linkage disequilibrium (LD) block lengths in four breed populations: Japanese Black, Angus, Hereford and Holstein. Three chromosomal regions in which QTL were previously mapped in Japanese Black populations were scanned with 84 microsatellite markers. The estimated LD lengths in these four purebred populations varied from 535 to 683 kb, which is much shorter than the values reported previously. Our findings suggest that QTL can be mapped in sub-centimorgan regions in these populations using an LD-mapping method. We also developed breed identification methods to distinguish Japanese Black from Angus, Hereford, Holstein and F₁ animals (Japanese Black × Holstein) respectively using the haplotypic frequencies of a pair of markers in the breed populations. After assessing the distributions of posterior probabilities to be Japanese Black, we obtained several pairs of markers that completely distinguished Japanese Black from the other breeds. We also obtained several combinations of six markers that completely distinguished Japanese Black animals from F₁ animals.     

Growth and reproductive development from weaning through 20 months of age among breeds of bulls in subtropical Florida

To determine the effect of breed on growth and reproductive development, weaned bulls in each of 2 yr were managed as a single group for approximately a year. In Year 1, the study group consisted of 24 Angus, 24 Brahman, 20 Hereford and 14 Senepol bulls, while in Year 2, it contained 25 Angus, 17 Brahman. 13 Romosinuano and 9 Nellore x Brahman bulls. Body and testicular growth measurements were recorded at 6-wk intervals. At approximately 1 yr of age and quarterly thereafter (4 periods), bulls were evaluated for libido, pubertal status, and GnRH-induced LH and testosterone secretion. Significant breed-by-age interactions occurred for most growth measurements. Brahman bulls (Bos indicus ) were (P < 0.05) older and heavier at puberty than Angus, Hereford, Senepol and Romosinuano bulls (Bos taurus ). Libido scores were lowest for Brahman and Nell ore x Brahman bulls (Bos indicus ). highest for Angus and Hereford bulls (temperate Bos taurus breeds) and intermediate for Senepol and Romosinuano bulls (tropical Bos taurus breeds; P < 0.05). Differences were not consistent among breeds or between years for GnRH-induced LH secretion. In both years, basal testosterone concentrations and areas under the GnRH-induced testosterone curve were higher (P < 0.05) for Angus and Hereford bulls (temperate breeds) than for Brahman, Senepol, Romosinuano and Nellore x Brahman bulls (tropical breeds). In conclusion, reproductive development of Senepol and Romosinuano bulls (tropical Bos taurus breeds) was more similar to Angus and Hereford bulls (temperate Bos taurus breeds) than to Brahman and Nellore x Brahman bulls (Bos indicus ).     

Fine‐mapping the POLL locus in Brahman cattle yields the diagnostic marker CSAFG29

The POLL locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) in both taurine breeds and taurine–indicine crosses in an interval of approximately 1 Mb. It has not yet been mapped in pure‐bred zebu cattle. Despite several efforts, neither causative mutations in candidate genes nor a singular diagnostic DNA marker has been identified. In this study, we genotyped a total of 68 Brahman cattle and 20 Hereford cattle informative for the POLL locus for 33 DNA microsatellites, 16 of which we identified de novo from the bovine genome sequence, mapping the POLL locus to the region of the genes IFNAR2 and SYNJ1. The 303‐bp allele of the new microsatellite, CSAFG29, showed strong association with the POLL allele. We then genotyped 855 Brahman cattle for CSAFG29 and confirmed the association between the 303‐bp allele and POLL. To determine whether the same association was found in taurine breeds, we genotyped 334 animals of the Angus, Hereford and Limousin breeds and 376 animals of the Brangus, Droughtmaster and Santa Gertrudis composite taurine–zebu breeds. The association between the 303‐bp allele and POLL was confirmed in these breeds; however, an additional allele (305 bp) was also associated but not fully predictive of POLL. Across the data, CSAFG29 was in sufficient linkage disequilibrium to the POLL allele in Australian Brahman cattle that it could potentially be used as a diagnostic marker in that breed, but this may not be the case in other breeds. Further, we provide confirmatory evidence that the scur phenotype generally occurs in animals that are heterozygous for the POLL allele.     

Characterization of the Russian beef cattle breed gene pools using inter simple sequence repeat DNA analysis (ISSR analysis)

The gene pools of beef cattle breeds bred in Russia were characterized on the basis of inter simple sequence repeat DNA analysis (ISSR analysis). Samples of Aberdeen Angus, Kalmyk, and Kazakh Whitehead breeds from Russia, as well as of Hereford breed, hybrids of Kazakh Whitehead and Hereford breeds, and Kazakh Whitehead breed from the Republic of Kazakhstan, were examined. In the examined breeds, 27 AG-ISSR fragments were identified, 25 of which were polymorphic. The examined breeds were different both in the fragment profiles (the presence/absence of individual ISSR fragments) and in their frequencies. It was demonstrated that the hybrid animals lacked some ISSR fragments that were present with high frequencies in parental forms, suggesting considerable genome rearrangement in the hybrid animals (at the regions of microsatellite localization) in crossings of the individuals from different breeds. The level of genetic diversity in Russian beef breeds was consistent with the values typical of farmed populations (breeds). The genetic diversity parameters assessed by applying Nei’s gene diversity index and the Shannon index varied from 0.0218 to 0.0605 and from 0.0225 to 0.0819, respectively. The highest Shannon index value was detected in the Kalmyk breed (0.0837) and Kazakh Whitehead breed from Russia (0.0819), and the highest level of Nei’s gene diversity index was found in the Kalmyk breed (0.0562) and in both populations of the Kazakh Whitehead breed (0.0509 and 0.0605). The high level of genetic similarity (according to Nei) was revealed between Russian beef cattle breeds and Hereford cattle: 0.839 (for the Kazakh Whitehead breed from Russia) and 0.769 (for the Kalmyk breed).     

Novel single nucleotide polymorphisms and haplotypes within the bovine<Emphasis Type="Italic"> CXCR2</Emphasis> gene

The objectives of this study were to identify single nucleotide polymorphisms (SNPs) and resulting haplotypes in the bovine CXCR2 gene. A 311-bp segment of the bovine CXCR2 gene was amplified and sequenced. Five SNPs at positions 612, 684, 777, 858, and 861 were expressed in both Holstein and Jersey dairy cattle. Four SNPs resulted in synonymous substitutions, while a non-synonymous switch at position 777 (GC) resulted in a glutamine to histidine substitution at amino acid residue 245. Strong linkage disequilibrium was exhibited for both breeds among all five loci (P<0.001). Both allele and genotype frequencies differed significantly with respect to breed at four of the five loci (P<0.001). The five polymorphisms generated ten distinct haplotypes. Six haplotypes were common between the two breeds, while Holsteins and Jerseys each uniquely expressed two haplotypes. Of the six common haplotypes, two represented 83% of the Jersey population; whereas four of these haplotypes represented 95% of the Holstein population.     

Breed differences in the distribution of BoLA-A locus antigens in American cattle

A total of 627 cattle representing seven breeds from south central Nebraska, USA were tested for 37 BoLA antigens which behave as products of 37 distinct alleles of the class I BoLA-A locus. Four antigens were absent from all breeds tested. The other antigens showed marked and statistically significant differences in breed distribution. There was no evidence for blank (null) alleles. The number of alleles in each breed ranged from 10 to 20. The Hereford and Simmental populations tested were less polymorphic than the Angus, Brown Swiss, Charolais, Gelbvieh and Limousin populations.     

Interactive response of the horn fly (Diptera: Muscidae) and selected breeds of beef cattle

Statistically significant differences were observed in the population density of the horn fly, Haematobia irritans irritans (L.), on different breeds of beef cattle. The European breed Chianina had a population density of horn flies generally less than or equal to 50% than that of the British cattle breeds (Angus, Hereford, Polled Hereford, and Red Poll) and another European breed (Charolais). Generally, no significant difference existed among numbers of horn flies on Hereford, Polled Hereford, and Red Poll cows in 1988 or among Angus, Hereford, Polled Hereford, and Red Poll cows in 1989. Factors other than color appeared to be involved in the selective process between the horn fly and its host. Population densities on two white European breeds (Charolais and Chianina) were significantly different on all weekly intervals except for 4 wk in both 1988 and 1989. No significant difference existed among Charolais and British breeds except during 4 wk in 1988 and 3 wk in 1989. When weaning weights of all calves were adjusted for the effects of age to 205 d, sex of calf, and age of dam, the indirect effect of the horn fly on weaning weight showed a significant linear regression. Each 100 flies per cow caused a reduction of 8.1 kg in calf weaning weight. Cows within each breed with low numbers of horn flies weaned significantly heavier calves than cows with higher numbers of horn flies.     

Geographic distribution of haplotype diversity at the bovine casein locus

The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A²-CSN3*A_I/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed.     

The Belt mutation in pigs is an allele at the Dominant white (I/KIT) locus

A white belt is a common coat color phenotype in pigs and is determined by a dominant allele (Be). Here we present the result of a genome scan performed using a Hampshire (Belt)/Pietrain (non-Belt) backcross segregating for the white belt trait. We demonstrate that Belt maps to the centromeric region of pig Chromosome (Chr) 8 harboring the Dominant white (I/KIT) locus. Complete cosegregation between Belt and a single nucleotide polymorphism in the KIT gene was observed. Another potential candidate gene, the endothelin receptor type A gene (EDNRA), was excluded as it was assigned to a different region (SSC8q21) by FISH analysis. We argue that Belt is a regulatory KIT mutation on the basis of comparative data on mouse KIT mutants and our previous sequence analysis of the KIT coding sequence from a Hampshire pig. Quantitative PCR analysis revealed that Belt is not associated with a KIT duplication, as is the case for the Patch and Dominant white alleles. Thus, Belt is a fourth allele at the Dominant white locus, and we suggest that it is denoted I ^Be . Received: 5 May 1999 / Accepted: 3 August 1999     

Genetic parameters for carcass weight,conformation and fat in five beef cattle breeds

Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879–19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h²=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h²=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h²=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r_G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r_P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r_G=0.28, s.e.=0.05) and Angus (r_G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r_G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r_P=0.11 to 0.15), but the respective genetic correlations were close to zero (r_G=−0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r_G=−0.18, s.e.=0.06, r_P=0.02; Limousin: r_G=−0.56, s.e.=0.04, r_P=−0.13). The results indicate genetic variation for the genetic improvement of the carcass traits, favorable correlations for the simultaneous improvement of carcass weight and conformation in all breeds, and breed differences in the correlations of carcass fat.     

Polledness in Argentinean Creole cattle,five centuries surviving

Polledness has been shown to have autosomal Mendelian inheritance, with the polled locus being dominant to the horned locus. This trait was mapped to the BTA1 centromeric end in several breeds. One of the distinctive attributes of Creole cattle, such as the Argentinean Creole, is the presence of long, lyre‐shaped horns. However, polled native animals were reported before the introduction of modern selected European breeds. Here, we studied the origin of the polled mutation, either independent or introgressed, in a Creole line from the Creole cattle founder group at the IIACS‐INTA Leales Experimental Station (northwest Argentina). The study sample (65 animals: 26 horned and 39 polled) was genotyped using high‐density SNP microarrays and three previously reported genetic markers (P_202ID, P_80kbID and P_G). A genome‐wide association study, selection signatures, linkage disequilibrium analysis and copy number variations were used to detect the responsible region and the segregating haplotypes/alleles. The interval mapped in the Leales herd (1.23–2.13 Mb) overlapped with the region previously reported in several European cattle breeds, suggesting that the same locus could be segregating in this population. The previously reported variants P_F and P_G 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 P_C 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.     

Novel SNPs of the mtDNA ND5 Gene and Their Associations with Several Growth Traits in the Nanyang Cattle Breed

Polymorphism of the mtDNA ND5 gene was detected by PCR-SSCP and DNA sequencing methods in 714 individuals from six Chinese cattle breeds. The results showed that at the P2 locus, two kinds of haplotypes, named A and B, with three SNPs (T12900C, A12923T, C12924T) were detected. The frequencies of haplotype A in six breeds were 0.041–0.167. Polymorphism of the ND5 gene was shown to be associated with growth in the Nanyang breed. Individuals with haplotype B had greater hucklebone width than those with haplotype A when 6 months old (P < 0.01), as well as better body height, body length, body weight, and average daily gain at 6 months (P < 0.05). Therefore, haplotype B of the ND5 gene was likely to have a positive effect on growth traits at 6 months in the Nanyang breed.     

Sequence and diversity of bovine T-cell receptor β-chain genes

The nucleotide sequences of 38 T-cell receptor (Tcr) -chain cDNA clones which were isolated from a cDNA library (2 × 10⁶ plaques) constructed from bovine peripheral blood lymphocytes were determined. Of 38 cDNA clones, 22 were rearranged and contained the functional variable (V) gene segments. These clones were tentatively divided into nine Tcrb-V gene families which correspond to the human Tcrb-V family. Among them, a Tcrb-V12 gene segment was isolated from 9 out of 22 clones, suggesting that this Tcrb-V family was expressed in the bovine peripheral blood lymphocytes. Two different constant (C) geen segments were found, and both C regions were composed of 178 amino residues. The amino acid sequences of bovine Tcrb-C regions are approximately 80%–82%, 78%, and 78% similar to those from human, mouse, and rabbit, respectively. To estimate Tcrb-V-associated restriction fragment length polymorphisms (RFLPs), Southern blot analysis was performed using liver DNAs from four bovine breeds, Holstein, Angus, Hereford, and Japanese Black. However, no significant difference was observed among genomic DNAs of Tcrb-V loci from these four breeds.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers D90121-40. Address correspondence and offprint requests to: N. Ishiguro.     

Nucleotide Substitution in 3' Arm of Bovine MIR-2467 in Five Cattle Breeds

The T > C single nucleotide polymorphism (SNP) in the MIR2467 gene was investigated in order to confirm its presence in cattle genome and to check for possible differences in its genotype distribution among different breeds. Additional purpose of the study was to investigate in silico potential effect of that substitution on the structure and stability of precursor mir-2467. The study involved 634 individuals of five cattle breeds: Angus, Hereford, Holstein-Friesian, Jersey, and Limousin, which were genotyped using PCR-RFLP assay. In this study, the presence of T > C polymorphism at position 24 was observed in all the cattle breeds excepting Hereford. In addition, the differences in the genotype distribution among analyzed breeds were indicated. On the basis of minimum free energy structure prediction, the C allele was indicated to have possible impact on decreasing the stability of the pre-mir-2467, thus altering its ability to regulate target genes expression.     

Restriction fragment length polymorphisms for growth hormone, prolactin, osteonectin, α crystallin, γ crystallin, fibronectin and 21-steroid hydroxylase in cattle

Summary. Genomic DNAs from animals representing six breeds of cattle (Angus, Brahman, Hereford, Holstein, Jersey and Texas Longhorn) were screened with cloned gene probes in a search for restriction fragment length polymorphisms (RFLPs). Eleven RFLPs were identified using seven different probes: growth hormone, prolactin, osteonectin, α A-crystallin, γ crystallin, fibronectin and 21-steroid hydroxylase. The frequencies of the alleles identified by each probe were calculated and compared in a limited sampling of the six bovine breeds. These polymorphisms greatly enhance the pool of immunogenetic, biochemical and molecular markers available in cattle for linkage analysis, testing of parentage, and distinction of breeds.