S. L. Kacirek
K. M. Irvin1
P. I. Dimsoski
M. E. Davis
H. C. Hines
The Ohio State University
Department of Animal Sciences
1 For more information, contact at: 2029 Fyffe Road, 110F Animal Science Building, Columbus, OH 43210, (614)292-6407, (614)292-2929 FAX, e-mail: irvin.3@osu.edu.
This study utilizes 17 highly polymorphic microsatellites to study the relationship between the Large White and Yorkshire breeds. These breeds originally developed from a single breed in England, where it was called the Large White breed. This breed was brought to the United States during the 19th century, where the name was changed to Yorkshire. Until recent years, the U.S. and English lines have had limited contact. Because of their history, it is questioned whether these two breeds represent different gene pools, as they concurrently developed from differing selection schemes and in varying environments. The Hampshire breed was included in the analysis because it serves as a potentially unrelated reference breed which could be used to more clearly define the relationship between the Large White and Yorkshire breeds. Calculations such as heterozygosity levels, Fst values, and Nei's genetic identity and distance were made from the allele frequencies in each breed. Fst values indicated that differentiation between the Large White and Yorkshire breeds was moderate. Genetic distances indicated the breeds were related in the following order (from most to least): Yorkshire, Large White, and Hampshire. The distance between the Large White and Yorkshire population was smaller than the distances between other breed pairs. Therefore, the study concluded that the Large White and Yorkshire breeds are highly similar but represent separate populations that have evolved from one another over the last 100 years.
Microsatellites are tandem repeats of short nucleotide repeats, usually between one and six base pairs in length. Prior studies have used microsatellites as genetic markers for mapping purposes to estimate gene flow, effective population size, and inbreeding, as well as in parentage determination and forensics. The purpose of this study was to utilize the highly polymorphic nature of microsatellites in order to examine the variation among the Large White, Yorkshire, and Hampshire breeds. With the development of the Yorkshire breed in the United States, it is expected that the Large White and Yorkshire breeds may represent two gene pools. The microsatellite variation in the Hampshire breed was used as a reference family to help define the relationship between the Large White and Yorkshire breeds.
Thirty individuals of each breed were chosen according to least relatedness criteria. Seventeen dinucleotide microsatellites were randomly chosen for analysis. DNA was extracted from blood or semen samples and amplified by the Polymerase Chain Reaction (PCR). The PCR products were loaded into 6% polyacrylamide sequencing gels. The gels were silver stained so allele frequencies could be counted. The gels from the Large White and Yorkshire breeds were run and genotyped in a prior study (Dimsoski, 1996). These gels were genotyped a second time, along with the gels from the Hampshire breed in order to provide uniformity in the analysis. In all three populations, the same calculations were made: allele frequencies, percent heterozygosities, observed and expected heterozygosities, exact Hardy-Weinberg tests for Hardy-Weinberg equilibrium and heterozygote deficiency, fixation indices including Fst values, and Nei's genetic identity and distances (Nei 1972).
Microsatellite primers were examined for polymorphism in a total of 89 unrelated animals in the Large White, Yorkshire, and Hampshire breeds. All of the microsatellites examined were polymorphic in the Hampshire and Large White breeds, while 94% were polymorphic in the Yorkshire breed. There were 58, 59, and 69 total alleles in the Yorkshire, Large White, and Hampshire populations, with an average number of allele per locus being 3.4, 3.7, and 4.0, respectively. Number of alleles ranged from two to seven. Some alleles were present in the Hampshire population, but not in the Large White or Yorkshire populations. Alleles were of the same size in all three populations at six loci. Allele frequencies were measured by direct counting and ranged from 0.0 to 0.983 in the Hampshire population, 0.0 to 0.900 in the Yorkshire population, and 0.017 to 0.867 in the Large White population. There were fewer microsatellite loci having similar allele frequencies in the Large White and Yorkshire population than when compared to either of the two populations with the Hampshire breed. Quantification of allele frequencies was fundamental to this study because genetic changes in a population are most often described by changes in gene frequency (Nei 1987).
Levels of heterozygosity, which reflect the fraction of individuals with two different alleles, were calculated in all three populations for each microsatellite. The mean heterozygosity levels of the Large White and Yorkshire populations were 52% and 51%, respectively, while 42% of the Hampshire population was heterozygous. This result indicates the genetic basis of the Hampshire breed is less broad than that of the other two breeds. Observed versus expected number of heterozygotes in each population were calculated. Mean observed heterozygosity over all populations was 0.567, while mean expected heterozygosity was 0.635.
An Exact test for Hardy-Weinberg equilibrium was performed. There were 10, eight, and eight microsatellite loci found to be in disequilibrium in the Hampshire, Large White, and Yorkshire populations respectively (P < 0.05). Another Exact test was performed with the alternative hypothesis being heterozygote deficiency. There were eight, seven, and six microsatellite loci where a heterozygote deficiency existed (P < 0.05). The average fixation index over all three populations was 0.109. This value also indicates a heterozygosity deficiency. There are many probable causes for such deviations. Selection, inbreeding, and assortive mating, all popular practices in swine breeding, act by increasing the frequency of homozygotes. There are other theoretical explanations as to why deviations exist. The first reason is the presence of null alleles in which only one of the two alleles is amplified. This result causes heterozygotes to be falsely typed as homozygotes. Also, the close association of a microsatellite with a gene of interest or some other selectable sequence increases the amount of homozygosity in the vicinity of the locus for which selection is made. Finally, with the limited number of subject samples, a bias may have been introduced into the parameters studied.
Fst values were calculated for all breed combinations to assess the genetic subdivisions in the three populations. Qualitatively, an Fst value with in the range of 0.05 to 0.15 indicates moderate differentiation, within 0.15 to 0.25 great differentiation, and greater than 0.25 indicates very great differentiation (Wright 1978). Average Fst values were 0.0593 for the Large White x Yorkshire comparison, 0.1829 for the Large White x Hampshire comparison, and 0.2135 for the Yorkshire x Hampshire comparison. Only three loci in the Large White and Yorkshire comparison demonstrated great differentiation, while three had moderate differentiation. When examining the Fst values between the Yorkshire and Large White populations versus the Hampshire populations, many loci were found to have great differentiation. In the Large White x Hampshire comparison four loci showed great differentiation, whereas seven showed very great differentiation in the Yorkshire x Hampshire comparison. The Fst values can also be interpreted in the following way. The average Fst value for the Large White x Yorkshire comparison was 0.059. This value indicates that of the total genetic variation found between the two breeds, 6% was due to differences in allele frequencies and 94% was found within the breeds themselves (Neel 1978). The lower Fst value found between the Large White and Yorkshire breeds indicates the two breeds can be considered highly similar. However, they have maintained enough differences in selection over the last 100 years to be considered as two separate populations.
Nei's genetic identity and distance were calculated for all possible pairs. Genetic distance between the Hampshire and Large White populations was 0.4368, between the Hampshire and Yorkshire populations was 0.4992, and between the Large White and Yorkshire populations was 0.1065. These distances measured the accumulated allele differences per locus between populations. The genetic distance between the Large White and Yorkshire populations was smaller than any other comparison. Values for Nei's genetic identity were 0.899 (Large White x Yorkshire), 0.646 (Large White x Hampshire), and 0.607 (Hampshire x Yorkshire). The calculation for genetic identity describes the proportion of alleles or genes that are alike between two populations. Therefore, nearly 90% of the alleles found in the Large White and Yorkshire populations were alike, whereas only 60% of the alleles were alike in the other two comparisons.
ConclusionThe genetic distances, along with the Fst values, indicate the order of relatedness from most to least related is: Yorkshire, Large White, and Hampshire. We conclude that the Yorkshire and Large White breeds, as a result of many generations of selection, diverged sufficiently that their differences are large enough to be measured by microsatellite variation. Further, we can conclude that the Yorkshire and Large White breeds represent two distinct populations.
ReferencesDimsoski, P. I. 1996. Variation in microsatellite loci and trait differences in Yorkshire and Large White. Ph.D. Dissertation. The Ohio State University, Columbus.
Neel, J. V. and E. A. Thompson. 1978. Founder effect and the number of private polymorphisms observed in Amerindian tribes. Proc. Natl. Acad. Sci. U.S.A. 75: 1904-1908.
Nei, M. 1972. Genetic distance between populations. The American Naturalist 106:283-292.
Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Wright, S. 1969-1978. Evolution and the genetics of populations. 4 Vols. University of Chicago Press., Chicago.