Low FST Values Research Articles

Genetic variability in populations of the southern chinch bug, Blissus insularis, assessed using AFLP analysis.

Southern chinch bug, Blissus insularis Barber (Heteroptera: Blissidae), is the most destructive insect pest of St. Augustine grass, Stenotaphrum secundatum Waltz (Kuntze), in the southern United States. The present study is focused on assessing genetic variability in five populations of B. insularis collected from Texas and Florida where St. Augustine grass is widely grown. The amplified fragment length polymorphism technique was used to DNA fingerprint individuals from each population (a total of 46 individuals) using five primer combinations (EcoRI/MSeI). Analysis of molecular variance results show no evidence to support significant genetic variability among Texas and Florida populations of B. insularis. Nearly all genetic variation was found to reside within populations (95%), with only approximately 3% residing among populations between regions. Low GST values obtained from POPGENE and low FST values obtained from the analysis of molecular variance both support the conclusion for high levels of gene flow resulting from interbreeding and/or migratory events among the populations. A Mantel test of Euclidean squared distances showed no correlation between the genetic distance and geographic distance matrices of tested populations of B. insularis. The results of the present study suggests that gene flow is occurring among populations of B. insularis and, therefore, breeders need to be aware that this resistance will most likely not remain localized, and it has the potential to spread as a result of migratory events.

Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST-based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among-clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low FST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.

Genetic structure of the common terrestrial pulmonate snail, Cryptozona siamensis (Pfeiffer, 1856), in Thailand

Abstract Allozyme variation was examined in 432 specimens of the pulmonate snail, Cryptozona siamensis, from 24 localities across three regions of Thailand plus an additional population from Malaysia. Although this snail is a cosmopolitan species it was predicted that C. siamensis should exhibit a large degree of genetic subdivision across these regions due to a low level of inter-population gene flow. To test this hypothesis, 10 enzyme systems were screened using horizontal starch gel electrophoresis, from which 14 presumed allozyme loci were scored and 13 found to be polymorphic. For these 13 polymorphic loci the expected heterozygosity levels were moderate (Hexp = 0.036–0.183, mean = 0.101). Genetic differentiation among the samples was low, with a low FST value (0.254) and genetic distance (D = 0.000–0.124, mean = 0.034) and no significant isolation by distance (IBD) across the whole sampled range of Thailand or Thailand plus Malaysia. However, an IBD pattern in the population substructure in the central Thailand region was detected. The low FST and moderate Hexp values in various populations of C. siamensis suggests a high degree of gene flow/migration between populations across the three geographic regions of Thailand (northern, central and southern) as well as the sampled population in Malaysia, perhaps associated with the anthropochoric effect of snail dispersal. The apparent IBD in the central Thailand region could be the consequence of local dynamics though this region.

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

In many mammals social organization promotes genetic structuring, which can be influenced by the dispersal pattern of the species. We analyzed the population genetic structure and dispersal of white-lipped peccaries (Tayassu pecari) from the Pantanal, Brazil. We genotyped 100 individuals at 7 microsatellite loci from 2 adjacent locations with no obvious geographic barrier between them. We found a significant but low FST value, and the Bayesian analysis indicated a unique cluster. No significant differences were observed between mean assignment indices of resident males and females from both locations, and the probability of being born at the location sampled of .30% of the individuals analyzed was lower than average. Mean relatedness between resident female, male, and opposite-sex pairs was not statistically different in both locations. These results suggest a low degree of genetic differentiation between the locations analyzed, and dispersal by both sexes (contrary to the predicted male-biased dispersal of most mammalian species).

Abstract 3883: Multiplexed formats for detection of SNPs for cell line authentication and cancer related mutations

Abstract Rapid and accurate identification of SNPs and mutations are useful in ensuring that the correctly identified cell lines are being used in cancer research studies and for accurate identification of SNPs and indels in cancer cells. In this study we report on a method that uses nucleic acid isolation methods, multiplexed PCR to amplify up to 48 regions within the human genome followed by an oligonucleotide ligation assay that can detect SNPs, mutations and indels. The protocol takes about 4 hrs to complete and uses panels optimized for human cell identification and detection of mutations in EGFR and KRAS genes. We typed the NCI-60 panel and several cell lines from the ATCC using two panels. One is a panel of SNPs that has been tested with samples from over 46 human populations to identify a set of SNPs that would discriminate globally. This SNP set has 48 markers with high heterozygosity (>0.4) and low Fst values (<0.06) across multiple human populations. The panel has a high power of discrimination. (Hum Genet; 127 (3) 315-324; 2010) comparable to that obtained with STR kits. A panel of 31 samples from closely related individuals within families was typed to test the power of discrimination. In another study, we applied this system to a cancer mutation study, in which an assay for detecting 29 EGFR and 5 KRAS gene mutations was developed. These mutations are frequently found in human cancers. DNA preparations from 48 ATCC and 60 NCI tumor cell lines were genotyped by this assay. These SNPs and mutations were further confirmed by the Sanger sequencing chemistry, showing 100% concordance between two technologies. The information generated from this study will be definitely useful when these cell lines are used as models for cancer study and cancer drug screening. In conclusion, we have developed a sensitive, highly accurate, high throughput genotyping system. Studies have demonstrated its effectiveness for successful SNP/InDel detection and mutation screening. This system has been successfully used for oncogen mutation studies in cancer cell lines. Overall, the system can become a valuable tool for molecular and clinical diagnostics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3883. doi:10.1158/1538-7445.AM2011-3883

Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean

Simple sequence repeat (SSR) markers were used to classify 116 isolates of Phakopsora pachyrhizi, the cause of soyabean rust, collected from infected soyabean leaves in four agroecological zones in Nigeria. A high degree of genetic variation was observed within the sampled populations of P. pachyrhizi. Eighty‐four distinct genotypes were identified among three of the four agroecological zones. Nei’s average genetic diversity across geographical regions was 0·22. Hierarchical analysis of molecular variance showed low genetic differentiation among all populations of P. pachyrhizi. The majority (> 90%) of the genetic diversity was distributed within each soyabean field, while approximately 6% of the genetic diversity was distributed among fields within geographic regions. Low population differentiation was indicated by the low FST values among populations, suggesting a wide dispersal of identical genotypes on a regional scale. Phylogenetic analysis indicated a strictly clonal structure of the populations and five main groups were observed, with group II accounting for 30% of the entire population. Because of the asexual reproduction of P. pachyrhizi, single‐step mutations in SSR genotypes are likely to account for the genetic differences within each group.

Genetic characterization and structure of the Italian Podolian cattle breed and its relationship with some major European breeds

The Italian Podolian is an autochthonous breed belonging to the grey steppe cattle group. In the past, the Podolian was present throughout all of the Adriatic and the southern part of Italy, but now it is restricted to four regions and displays morphological differences according to the region. It is thought that the Podolian contributed heavily to the genetic make-up of the Chianina and Romagnola breeds, while contrasting opinions exist regarding the relationship between the Podolian and the Piemontese. This paper aimed at characterizing genetic variability and structure by means of microsatellite loci to assess the relationship between the Podolian and the most relevant European breeds, and to detect evidence of selection in the considered breeds by investigating the existence of outlier loci. The DNA of 134 Italian Podolian individuals from 14 different herds in 4 breeding areas were collected, genotyped at 30 microsatellite loci and compared to 13 Italian and European breeds, including the grey type ones and using N’dama as the outgroup. The Podolian showed the highest values of observed heterozygosity and polymorphism content. Moreover in a subset of 50 samples (chosen according to geographic origin), polymorphism data analysis evidenced the absence of a geographically determined genetic structure. The hierarchical population clustering evidenced a Podolian cluster at K=5 and the phylogenetic tree based on Reynold’s distances confirmed the genetic links between the Podolian breeds. Two loci presented significantly low FST values, suggesting that they could be under the effect of balancing selection. It can be concluded that Italian Podolian has no genetic subdivision, contains a notable amount of genetic variability and is closely related to the other Podolian type breeds.

Genotype Shifts Along One Generation of the Blue ButterflyPolyommatus coridonwithout Changes in Allele Frequencies

Evolutionary and ecological effects of DNA and protein polymorphisms are controversially discussed, since the raising of molecular approaches. Functional differences among different genotypes of allozymes might strongly influence evolutionary processes and spatial distributions. Therefore, we analysed nine polymorphic allozyme loci for 127 individuals sampled from one population of the chalk-hill blue Polyommatus coridon during one flight season. We observed fluctuations in the genotype frequencies during this flight season, but only two enzyme loci showed significant changes. The percentage of observed heterozygosity was decreasing in more than three quarters of all loci over time (e.g. Mdh2 decreasing from 72.7% to 36.4%). These changes might be due to different adaptations of heterozygotic individuals if compared with homozygotic ones. In contrast to genotypes, no changes in allele frequencies were observed (e.g. low FST value for Mdh2). Therefore, allozyme data represent a suitable tool for studying e...

Surfing Snails: Population Genetics of the Land SnailVentridens ligera(Stylommatophora: Zonitidae) in the Potomac Gorge*

The population structure of the land snail Ventridens ligera (Say, 1821) was investigated in the Potomac River Basin (Virginia, Maryland, U.S.A.). Animals were collected from two islands and the adjacent riverbanks along an 8.8-km stretch of the river. Four landlocked populations in Illinois and Maryland were also sampled to provide a comparison to the river populations. A total of 246 individuals were genotyped with five newly designed species-specific microsatellite primers. Low pairwise FST values (<0.0477) among the Potomac River sites suggest high levels of gene flow between the populations. In contrast, the landlocked populations had high FST values (0.0738 to 0.6004) which suggest genetic structuring, most likely due to physical isolation, because FST values >0.2 indicate population structuring. Low-level isolation by distance was found among the Potomac River populations, and the low FST suggests that the river is facilitating gene flow rather than acting as a barrier.

Multiplexed SNP detection panels for human identification

SNP profiling is a very powerful tool for human identification. Two panels of 49 and 41 SNPs were selected based on high average heterozygosity (>0.4) and low global Fst values (<0.06) as a set of highly discriminative SNPs suitable for human identification in all geographic populations. SNPs were selected based on testing samples from 44 populations across the globe using TaqMan ® allelic discrimination formats. Coding SNPs, and SNPs with known functional or phenotypic manifestations were excluded. To test the performance characteristics of the two panels of SNPs and to compare their utility to STR analysis for human identification and paternity testing, we genotyped a panel of 41 individuals from three different CEPH families spanning three generations. The test samples were genotyped using the two SNP panels and a 15-loci STR kit. Further, utility of the SNP panels in human ID testing and related applications was demonstrated using degraded DNA and DNA from blood, semen and saliva samples. The development of highly multiplexed SNP detection systems enabling lower cost and higher throughput via automation will result in increased use of SNP profiling in applications like human identification, cell line authentication, species identification and bacterial strain typing.

Detecting loci under selection in a hierarchically structured population

Patterns of genetic diversity between populations are often used to detect loci under selection in genome scans. Indeed, loci involved in local adaptations should show high F(ST) values, whereas loci under balancing selection should rather show low F(ST) values. Most tests of selection based on F(ST) use a null distribution generated under a simple island model of population differentiation. Although this model has been shown to be robust, many species have a more complex genetic structure, with some populations sharing a recent ancestry or due to the presence of barriers to gene flow between different parts of a species range. In this paper, we propose the use of a hierarchical island model, in which demes exchange more migrants within groups than between groups, to generate the joint distribution of genetic diversity within and between populations. We show that tests not accounting for a hierarchical structure, when it exists, do generate a large excess of false positive loci, whereas the hierarchical island model is robust to uncertainties about the exact number of groups and demes per group in the system. Our approach also explicitly takes into account the mutational process, and does not just rely on allele frequencies, which is important for short tandem repeat (STR) data. An application to human and stickleback STR data sets reveals a much lower number of significant loci than previously obtained under a non-hierarchical model. The elimination of false positive loci from genome scans should allow us to better determine on which specific class of genes selection is operating.

Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene

The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the ∼730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428 bp of mitochondrial cytochrome c oxidase subunit I ( COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst = 0.70, P < 0.00001; Nm = 0.21) and Minjiang River (Fst = 0.73, P < 0.00001; Nm = 0.18) groups, while low Fst value (Fst = 0.018, P > 0.05) and high rate of migration (Nm = 28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (≤0.12) and high Nm values (>3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst ≥ 0.59; Nm < 1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage.

Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

Genetic relationships among lake whitefish ( Coregonus clupeaformis ) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island – Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low Fstvalues suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fstvalues potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.

Song dialects do not restrict gene flow in an urban population of the orange-tufted sunbird, Nectarinia osea

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. In this study, we test the hypothesis that song dialect, a culturally transmitted trait, is related to the population genetic structure of the orange-tufted sunbird, Nectarinia osea. To address this, we compared mitochondrial DNA (mtDNA) sequence variation together with allele frequencies at five microsatellite loci from an urban population of sunbirds exhibiting two distinct song dialects on a microgeographic scale. Our findings reveal no association between dialect membership and genetic composition. All genetic measures, from both mitochondrial and nuclear DNA, indicate high levels of gene flow between both dialect populations. The low F ST values obtained from mtDNA and microsatellite analysis imply that the variation among dialects does not account for more than 2%, at best, of the overall genetic variation found in the entire population. These measures fall well within the range of similar measures obtained in other studies of species exhibiting vocal dialects, most of which fail to detect any dialect-based genetic differentiation. The persistence of dialects in the orange-tufted sunbird may thus best be explained by dispersal of individuals across dialect boundaries and possibly from surrounding areas, followed by postdispersal vocal matching. Because genetic structuring appears weaker than cultural structure in this species, we discuss the behavioral mechanisms underlying dialect maintenance in the presence of apparent gene flow.

Selective versus stochastic processes in the genetic differentiation of populations of the butterfly Erebia embla (Thnbg) (Lepidoptera, Satyridae)

Four populations of the butterfly Erebia embla were studied by allozyme electrophoresis. Three populations were isolated by distance and the fourth by distance and time (flying in different years). Populations differed significantly in allele frequencies at five polymorphic loci, but the difference between the odd year population and the even year populations was not larger than the differences among the latter. Monte Carlo simulations showed that the genetic differentiation was lower than expected if caused by drift and gene flow only, whereas strong heterotic selection could explain the low FST value (0.02). We therefore conclude that the genetic variation of the populations is stabilized by selective forces permitting stochastic processes to operate within narrow limits only.

Stock enhancement program for black sea bream (Acanthopagrus schlegelii) in Hiroshima Bay: Monitoring the genetic effects

Black sea bream have been intensively stocked in Hiroshima Bay since 1982. However, no information regarding the long-term effects resulting from the release of large numbers of juveniles on the wild population has been reported. We investigated the fate of black sea bream juveniles released at the sampling site from 2000 to 2001 using six microsatellite DNA markers. In 2003 and 2004 respectively, 12.5 and 13.5% of captured black sea bream were identified as hatchery reared. Variation in total length by age between the released and native stocks was not statistically significant. Low FST values confirmed high genetic similarity between wild and hatchery stocks. Pedigree reconstruction confirmed a small loss of genetic variability, with a final inbreeding rate for recaptured fish of around 3% per year, rising to 4% when both years were combined. There was high survival of released black sea bream juveniles. Some of these specimens reached maturity and may have hybridized with their wild counterparts, highlighting the need to monitor the genetic effects of releasing large number of juveniles.

The Application of Microsatellites for Stock Identification of Yukon River Chinook Salmon

AbstractIn a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (FST) values, but loci with lower FST values also tended to provide more‐accurate estimates of stock composition. The observed number of alleles was related to the power of the locus for providing accurate estimates of stock composition of simulated single‐population samples. Mean estimated stock compositions for these mixtures ranged from 38.9% for simulations of single loci with fewer than 10 alleles to 85.5% for simulated loci with more than 60 alleles. Reliable population‐specific estimation of stock composition was obtained with a minimum of five loci. Comparison of microsatellite stock identification power with an existing nine‐locus single‐nucleotide polymorphism (SNP) baseline indicated that nine SNPs or a single microsatellite locus can provide accurate and reasonably precise estimates of stock composition to country of origin. In comparisons of population‐specific estimation, the nine‐SNP baseline was approximately equivalent to a single microsatellite locus with 17–22 alleles. Mixed‐stock analysis applying the microsatellite baseline outlined in this study can accurately and precisely allocate Chinook salmon to units useful for management, such as region or major drainage, providing managers with a powerful tool for assessing and regulating fisheries.

Genetic characterization of Italian honeybees,Apis mellifera ligustica, based on microsatellite DNA polymorphisms

The genetic variability of Apis mellifera ligustica was screened throughout the Italian peninsula and Sardinia with eight polymorphic microsatellite loci. Samples of Apis mellifera mellifera, Apis mellifera carnica and from the Buckfast breeding line were genotyped for comparison. Low Fis and Fst values suggest the absence of genetic structure within and among A. m. ligustica populations, although the high number of alleles detected and heterozygosity. Phylogenetic and individual analyses confirmed that A. m. ligustica has come to resemble one large population, probably as a result of intensive beekeeping practices such as migratory beekeeping and large-scale commercial queen trading. Since the introgression of foreign alleles into both endemic natural and commercial A. m. ligustica populations, can be detected and monitored by microsatellite analysis, the results provide a reference data set for future local biodiversity conservation and other controlled breeding programs.

Allozyme Variation in the Camaenid Tree Snails Amphidromus atricallosus (Gould, 1843) and A. inversus (Müller, 1774)

We examined allozyme variation in two camaenid tree snails, Amphidromus atricallosus and A. inversus, across two principal regions of Thailand and from Singapore, plus for A. inversus, one site in peninsular Malaysia. Using horizontal starch gel electrophoresis, 13 allozyme loci (11 polymorphic) were screened for A. atricallosus and 18 (5 polymorphic) for A. inversus. Heterozygosity was higher in A. atricallosus (Hexp=0.018-0.201, mean=0.085) than in A. inversus (Hexp=0-0.023, mean= 0.002). Genetic heterogeneity among samples was higher in A. inversus (Fst=0.965) than in A. atricallosus (Fst=0.781). Within A. atricallosus, populations were more differentiated in southern Thailand (Fst=0.551) than in eastern Thailand (Fst=0.144). The high Fst and low Hexp in populations of A. inversus suggest that this species is likely to have experienced a series of strong bottlenecks, perhaps occurring chiefly on offshore continental-shelf islands. The low Fst values of A. atricallosus in eastern Thailand suggest frequent gene flows among populations in this region. The southern and eastern samples of A. atricallosus exhibited fixed allele differences at four loci and great genetic distance (Nei's D=0.485-0.946), suggesting that these two samples may actually represent, or else be evolving into, separate species.

κ-casein gene (CSN3) allelic polymorphism in Russian cattle breeds and its information value as a genetic marker

The frequencies of the κ-casein gene (CSN3) alleles and genotypes have been determined in five Russian cattle breeds (Bestuzhev, Kalmyk, Russian Black Pied, Yaroslavl, and Yakut breeds) by means of PCR-RFLP analysis using two independent restriction nucleases (HinfI and TaqI) and by allele-specific PCR. Typing alleles A and B of CSN3 is of practical importance, because allele B is correlated with commercially valuable parameters of milk productivity (protein content and milk yield) and improves the cheese yielding capacity. The frequencies of the B allele of CSN3 in the breeds studied vary from 0.16 to 0.50; and those of the AB and BB genotypes, from 0.27 to 0.60 and from 0.02 to 0.23, respectively. The Yaroslavl breed had the highest frequencies of CSN3 allele B and genotype BB (0.50 and 0.23, respectively). The frequencies of the B allele and BB genotype in other breeds studied varied from 0.25 to 0.32 and from 0.03 to 0.09, respectively. In none of the breeds studied have the observed and expected heterozygosities been found to differ from each other significantly. However, the observed genotype distributions significantly differ from the expected one in some herds (in most such cases, an excess of heterozygotes is observed). Two herds of the Yaroslavl breed dramatically differ from each other in the heterozygosity level: a deficit (D = −0.14) and an excess (D = 0.20) of heterozygotes have been observed at the Mikhailovskoe and Gorshikha farms, respectively. In general, however, the heterozygosity of the Yaroslavl breed corresponds to the expected level (D = 0.04). Analysis of breeds for homogeneity with the use of Kulback’s test has shown that all cattle breeds studied are heterogeneous, the CSN3 diversity within breeds being higher than that among different breeds, which is confirmed by low Fst values (0.0025–0.0431). Thus, a DNA marker based on CSN3 gene polymorphism is extremely important for breeding practice as a marker of milk quality; however, it is inapplicable to marking differences between breeds or phylogenetic relationships between cattle breeds because of the high diversity with respect to this locus within breeds.