Number Of Different Alleles Research Articles

The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane

Little is known about the extent of allelic diversity of genes in the complex polyploid, sugarcane. Using sucrose phosphate synthase (SPS) Gene (SPS) Family III as an example, we have amplified and sequenced a 400 nt region from this gene from two sugarcane lines that are parents of a mapping population. Ten single nucleotide polymorphisms (SNPs) were identified within the 400 nt region of which seven were present in both lines. In the elite commercial cultivar Q165(A), 10 sequence haplotypes were identified, with four haplotypes recovered at 9% or greater frequency. Based on SNP presence, two clusters of haplotypes were observed. In IJ76-514, a Saccharum officinarum accession, 8 haplotypes were identified with 4 haplotypes recovered at 13% or greater frequency. Again, two clusters of haplotypes were observed. The results suggest that there may be two SPS Gene Family III genes per genome in sugarcane, each with different numbers of different alleles. This suggestion is supported by sequencing results in an elite parental sorghum line, 403463-2-1, in which 4 haplotypes, corresponding to two broad types, were also identified. Primers were designed to the sugarcane SNPs and screened over bulked DNA from high and low Sucrose-containing progeny from a cross between Q165(A) and IJ76-514. The SNP frequency did not vary in the two bulked DNA samples, suggesting that these SNPs from this SPS gene family are not associated with variation in sucrose content. Using an ecotilling approach, two of the SPS Gene Family III haplotypes were mapped to two different linkage groups in homology group 1 in Q165(A). Both haplotypes mapped near QTLs for increased sucrose content but were not themselves associated with any sugar-related trait.

Molecular Genotyping of Candida parapsilosis Group I Clinical Isolates by Analysis of Polymorphic Microsatellite Markers

Candida parapsilosis, a pathogenic yeast, is composed of three newly designated genomic species that are physiologically and morphologically indistinguishable. Nosocomial infections caused by group I C. parapsilosis are often associated with the breakdown of infection control practices and the contamination of medical devices, solutions, and indwelling catheters. Due to the low levels of nucleotide sequence variation that are observed, an investigation of the size polymorphisms in loci harboring microsatellite repeat sequences was applied for the typing of C. parapsilosis group I isolates. PCR primer sets that flank the microsatellite repeats for seven loci were designed. Following amplification by PCR, the size of each amplification product was determined automatically by capillary electrophoresis. A total of 42 C. parapsilosis group I isolates were typed by microsatellite analysis, and their profiles were compared to the hybridization profiles obtained by use of the Cp3-13 DNA probe. A high degree of discrimination (discriminatory power = 0.971) was observed by microsatellite analysis. The number of different alleles per locus ranged from 14 for locus B to 5 for locus C. Microsatellite analysis detected 30 different microsatellite genotypes, with 24 genotypes represented by a single isolate. Comparison of the genotypes obtained by microsatellite analysis and those obtained by analysis of the Cp3-13 hybridization profiles showed that they were similar, and these methods were able to identify related and unrelated isolates. Some discrepancies were observed between the methods and may be due to higher mutation rates and/or homoplasy by microsatellite markers. Identical results were observed between microsatellite analysis and Cp3-13 DNA hybridization profile analysis for C. parapsilosis isolates obtained from two patients, demonstrating the reproducibilities of the methods in vivo. Identical microsatellite profiles were observed for isolates displaying different phenotypic switching morphologies. Indistinguishable Cp3-13 DNA hybridization profiles were observed for six epidemiologically related isolates; however, only three of six primary isolates had identical microsatellite profiles. Size variation at a single locus was observed for three of six isolates obtained either after the outbreak period or from a different body site, suggesting the potential of the method to detect microevolutionary events. Interestingly, for most loci a single allele per strain was observed; in contrast, two alleles per locus were observed for some strains, and consistent with the findings for natural isolates, some isolates may be aneuploid. Due to the potential for high throughput, reproducibility, and discrimination, microsatellite analysis may provide a robust and efficient method for the genotyping of large numbers of C. parapsilosis group I isolates.

Genetic Diversity and Population Structure of Elytrigia pycnantha (Godr.) (Triticeae) in Mont Saint‐Michel Bay Using Microsatellite Markers

During the last decade, an invasive wheatgrass species (Elytrigia pycnantha) has colonized the low salt marshes of the Mont Saint Michel Bay resulting in an accelerated change in the vegetation. This study was conducted using microgeographical genetic diversity in order to understand the genetic structure of this invasive and clonal species. Genetic variation and population structure of fifteen populations collected in high and low marsh habitats around the Bay were analyzed using five microsatellite loci. Because E. pycnantha is an allohexaploid, the application of standard genetic diversity statistics was not possible; we chose to summarize genetic diversity using statistics calculated from banding phenotypes. The mean number of alleles per locus was 10.2, the mean number of different alleles per sample was 6.87. The mean number of allelic phenotypes across all populations was 7.21. The mean value of genetic diversity for the species, calculated as the average number of alleles by which pairs of individuals differ, was H's = 1.91 and H't = 2.04. Little genetic differentiation among populations was detected (0.067). The association between pairwise genetic differentiation and geographic distances exhibited no evidence for isolation by distance. A geographical pattern of population differentiation, where a single population GI was clearly separated from the remaining population groups (considered as a metapopulation), was revealed by principal component analysis (PCA), and we propose that this is because GI represents a new genotype.

Isolation of novel microsatellite loci in Orchesella villosa (Arthropoda, Collembola)

Summary An experimental procedure using biotin-labelled probes and streptavidin-bound magnetic beads (FIASCO) was used to produce a microsatellite-enriched library for the collembolan Orchesella villosa . PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. As a preliminary test of their variability, we investigated 15 individuals from 5 locations inside a dismissed mining area in southern Tuscany. All microsatellite loci showed high levels of polymorphism. The mean number of different alleles at each locus across populations was 10.1 and observed heterozygosity per locus was 0.13–0.86. Only 2 out of the 7 loci appeared to be in Hardy–Weinberg equilibrium. The potential application of these loci to test the effects of environmental contamination on the genetic structure of exposed populations is discussed.

Empirical Analysis of the STR Profiles Resulting from Conceptual Mixtures

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably deduce the number of contributors present in simulated mixtures of four or less contributors. The relatively small number of alleles detectable at most CODIS loci and the fact that some alleles are likely to be shared between individuals within a population can make the maximum number of different alleles observed at any tested loci an unreliable indicator of the maximum number of contributors to a mixed DNA sample. This analysis does not use other data available from the electropherograms (such as peak height or peak area) to estimate the number of contributors to each mixture. As a result, the study represents a worst case analysis of mixture characterization. Within this dataset, approximately 3% of three-person mixtures would be mischaracterized as two-person mixtures and more than 70% of four-person mixtures would be mischaracterized as two- or three-person mixtures using only the maximum number of alleles observed at any tested locus.

Characterization of nuclear 18S rRNA gene sequence diversity and expression in an individual lake sturgeon (Acipenser fulvescens)

The unexpected discovery of extensive intraindividual variation of the 18S rRNA gene in nine North American species of sturgeon (and its absence in the North American paddlefish) was described in a previous paper by Krieger and Fuerst (2002b). As part of the study, genomic 18S rRNA genes from a lake sturgeon (Acipenser fulvescens) individual were amplified by polymerase chain reaction (PCR), cloned and sequenced, resulting in the identification of at least 17 different sequence variants. Because of the number of variants detected and the improbability that such a large number of different alleles are required for survival, these sequence variants were subjected to further analyses (sequence comparison, phylogenetic and relative rate) to examine the possibility that some variants may be pseudogenes. The cDNA produced by reverse transcriptase (RT)-PCR amplification of 18S rRNA isolated from lake sturgeon liver tissue was also sequenced. The topology of the phylogenetic tree produced suggests a split of the sequence variants into two groups: paddlefish-like (PL) alleles and non-paddlefish-like (NPL) alleles. Relative rate comparisons of these two groups indicate that the alleles within the NPL allele group are evolving more quickly than those in the paddlefish-like (PL) group, and so are likely under relaxed functional constraints. Less than one-third of nucleotide changes in the non-paddlefish-like (NPL) alleles occur at positions that are considered to be highly conserved in a universal eukaryotic model of rRNA structure. No substitutions at eukaryotic universally conserved sites occur in the PL alleles. Analysis of the sequence of the RT-PCR product shows that a single lake sturgeon 18S rDNA sequence variant is expressed in major quantities in the liver, and that this single product is identical to the allele most similar in sequence to the paddlefish. These results provide support for the idea that many variants are unimportant for proper cellular function or are pseudogenes. Although concerted evolution has apparently failed to homogenize the many rDNA sequence variants found within sturgeon, the detection of a single major expressed sequence variant in lake sturgeon indicates that the expression of the variants is in fact under the control of selective factors.

Molecular evaluation of genetic diversity and S-allele composition of local Spanish sweet cherry (Prunus avium L.) cultivars

A group of 28 sweet cherry (Prunus avium L.) local cultivars from the Jerte Valley in Western Spain were fingerprinted using microsatellites and their self-incompatibility alleles determined using S-RNase conserved primers. A total of 12 microsatellite primer pairs revealed 42 informative alleles that allowed the unequivocal identification of 26 genotypes. UPGMA cluster analysis of the similarity data produced a clear separation between the old traditional cultivars and the most recent introductions. The S-allele analysis showed a low number of different alleles in the older cultivars studied and revealed the presence of three new S-alleles not described previously. The combined information obtained from SSR fingerprinting and S-allele identification will be useful to optimize the conservation of the cherry genetic resources present in the area. Moreover, this approach can be applied to optimize the conservation of local genetic resources of other fruit tree species.

Identification of NASH Quantitative Trait Loci (QTLs) using in silico mapping analysis in inbred mice

Aims: Non-alcoholic steatohepatitis (NASH) is a polygenic disease associated with the metabolic syndrome, however, the pathogenesis is poorly understood. The methionine-choline deficient (MCD) diet is an extensively utilized animal model for progressive steatohepatitis. Recently in silico QTL analysis has been developed as a novel method for chromosomal mapping of complex disease-related traits (1). The aims of this study are to define strain-specific differences of the MCD model of NASH and to utilize in silico mapping analysis to identify gene loci associated with steatohepatitis. Methods: A/J, AKR/J, BALB/c/J, C57BL/6J and DBA/2J inbred strains of mice were fed an MCD diet for up to 25 weeks. ALT, weight loss (WL), liver/body weight ratio (LW) and hepatic triglycerides (HT) were measured. The QTLs responsible for steatohepatitis in mice were mapped in silico, employing the Roche Mouse SNP Database and the Chesler algorithm. Using the SNP distributions across the inbred strains, the number of allelic differences between 2 strains was calculated at 30cM chromosomal intervals. Phenotypic and genotypic distance arrays (1 per 30cM window) were composed, and linear regression was used to calculate the correlation coefficients between the phenotypic and each of the genotypic arrays. Results: Strain specific phenotypic differences of ALT, WL, LW, and HT levels are identified in the 5 strains. By haplotype mapping with 109 SNPs, strong positive correlations (standardized correlation >1.5) are detected between HT concentrations and gene loci (QTLs) on chromosomes (Chr) 2, 5, and 14. QTLs that determine ALT activities map to Chr 1, 4, 7, 12, and 14, three of which co-localize with gene loci affecting WL. Gene loci associated with LW map to Chr 6, 7, 11, 14, and 19. Of note, a region on Chr 14 harbors QTLs for ALT, WL, LW, and HT. Conclusions: These data indicate that multiple gene loci (Nash genes) affect the development of steatohepatitis in the MCD model of NASH. Four distinct phenotypic QTLs co-localize on Chr 14, and several loci affecting ALT activities co-localize with loci affecting WL, LW or HT accumulation. We speculate that many distinct but interacting Nash loci modulate the pathophysiological mechanisms responsible for NASH.

Strategies to maximise the allelic diversity maintained in small conserved populations

One of the main objectives in conservation programmes is to maintain the highest levels of genetic variability, for the population to be able to face future environmental changes and to assure long-term response to selection, either natural or artificial (Oldenbroek, 1999, Barker, 2001). The classical measure of genetic diversity is the expected heterozygosity, or gene diversity (GD), but allelic diversity (AD), or the number of different alleles per locus, also has evolutionary importance. Most optimal strategies for conservation have aimed to maximise GD (e.g. Caballero and Toro 2000), but AD has received much less attention. The objective of the present study is to test the efficiency of the maintenance of allelic diversity of strategies based either on the allelic diversity itself or on the expected heterozygosity in a small population, using information from molecular markers.

Estimating the total number of alleles using a sample coverage method.

Previously reported methods for estimating the number of different alleles at a single locus in a population have not described a useful general result. Using the number of alleles observed in a sample gives an underestimate for the true number of alleles. The similar problem of estimating the number of species in a population was first investigated in 1943. In this article we use the sample coverage method proposed by Chao and Lee in 1992 to estimate the number of alleles in a population when there are unequal allele frequencies. Simulation studies under the recurrent mutation model show that, for reasonable sample sizes, a significantly better estimate of the true number can be obtained than that using only the observed alleles. Results under the stepwise mutation model and infinite-allele model are presented. Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles.

Construction of a genetic linkage map in tetraploid species using molecular markers.

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.

The Expected Number of Alleles in a Gene Conversion Model with Mutation

Gene conversions and mutations affect the number of different alleles in a population as it evolves. Here these effects are studied for a sample of r individuals represented by one chromosome, each with n loci. The long-term evolution of the sample is modelled with the coalescent. Gene conversions can only occur within a chromosome between a pair of loci. Recombination is not included in the model. Mutations occur according to the infinitely many alleles model. A new expression for the expected number of alleles is derived using the Backward time approach. It is then possible to simulate the expectation for various sample paths. The new estimator is computationally inexpensive and has a lower variance than the conventional, forward time, approximation by simulation.

Genetic variation in the green alga Caulerpataxifolia

Allozyme surveys of 12 populations of Caulerpa taxifolia collected from the central Great Barrier Reef (GBR) in north-east Australia, Moreton Bay in east Australia, and the western Mediterranean, including populations with fine and robust morphologies, revealed little overall genetic differentiation. Exceptions to the general rule were detected, nonetheless, among the allozymes of oxaloacetate-decarboxylating and non-oxaloacetate-decarboxylating malate dehydrogenase (ME and MDH, respectively). Variation in the allozymes of ME, in particular, indicated that populations with robust form in eastern Australia may be genetically more similar to populations with similar morphology in the Mediterranean than to populations with fine morphology in the central GBR. All Mediterranean populations, and the robust form from Australia were monomorphic for allele b, while the fine Australian populations had a number of different alleles, including allele b, but most commonly alleles c, d, g, and i. Comparative surveys of one eastern Mediterranean and two western Atlantic populations of Caulerpa mexicana demonstrated clear genetic differentiation from C. taxifolia, with fixed gene differences at several loci. There was little differentiation among populations of C. mexicana. These results suggest that allozyme markers could assist species identification of Caulerpa species on broad geographical scales, but also raises the question of whether there is high gene exchange today throughout the range of Caulerpa species.

Recovery of Superior Homozygous Progeny from Biparental Crosses and Backcrosses

Breeders of self‐pollinated species are often confronted with the question of how best to incorporate exotic germplasm into breeding populations. The objective of this work was to illustrate those situations in which a breeder might utilize one or more backcrosses to the better parent of a self‐pollinating population to increase the probability of recovery of desirable homozygous progeny from the population. The stochastic theory is presented along with probabilities associated with different conditions. The number of cycles of backcrossing needed to recover desirable progeny is a function of three variables specific to a particular pair of parents: the number of allelic differences between parents (N), the proportion (k) of desirable alleles in the better parent, and the number of loci homozygous for desirable alleles by which a progeny must exceed the number in the better parent to be selected (nd). In crosses between parents bearing equal or nearly equal numbers of desirable alleles (k close to 0.5), selfing provides the greatest probability of recovering the desired plants. As k approaches 1, the increased probability of recovering desirable alleles by backcrossing to the better parent outweighs the decreased probability of recovering desirable alleles from the worse parent, and backcrossing is indicated. With increasing N, or increasing nd, more cycles of backcrossing are needed to maximize the probability of recovery of desirable plants.

Using microsatellites, isozymes and AFLPs to evaluate genetic diversity and redundancy in the cassava core collection and to assess the usefulness of DNA-based markers to maintain germplasm collections

The cassava core collection was selected to represent, with minimum repetitiveness, the potential genetic diversity of the crop. The core (630 accessions) was chosen from the base collection (over 5500 accessions) on the basis of diversity of origin (country and geographic), morphology, isozyme patterns and specific agronomic criteria. To asses the genetic diversity of the core, 521 accessions were typed with four microsatellite loci. Allele diversity and frequency, and size variance of dinucleotide repeats (Rst statistic) were estimated. Microsatellite allele numbers and frequencies varied among countries: Colombia and Brazil had the largest number of different alleles across all loci. Mexico also had a high number, ranking fifth after Peru, Costa Rica and Venezuela (which tied). Unique alleles were present in accessions from Brazil, Colombia, Guatemala, Venezuela and Paraguay. A small number (1.34%) of potential duplicates were identified through isozyme and AFLP profiles. Thus, the present results indicated that traditional markers have been highly effective at selecting unique genotypes for the core. Future selections of cassava germplasm sets can be aided by DNA-based markers to ensure genetically representative, non-redundant samples.

Identifying Populations for Conservation on the Basis of Genetic Markers

To select candidate populations of wild species to be given priority for conservation, genetic criteria gained from the study of molecular markers may be useful. Traditionally, diversity measures such as expected heterozygosity or percentage of polymorphic loci have been considered. For conservation we propose instead that priority should be given to measures of allelic richness. To standardize the results of allelic richness across populations, we used the technique of rarefaction. This technique allows evaluation of the expected number of different alleles among equal‐sized samples drawn from several different populations. We also show how the contribution of each population to total diversity can be partitioned into two components. The first is related to the level of diversity of the population and the second to its divergence from the other populations. For conservation purposes the uniqueness of a population—in terms of its allelic composition—may be at least as important as its diversity level. These new descriptors are illustrated by means of isozyme and chloroplast DNA data obtained for an endangered tree species, the argan tree of Morocco (Argania spinosa(L.) Skeels). With these analyses the conservation value of the argan tree populations, especially those of two isolates present in the north of the country, can be better appreciated. The methods proposed to identify priority areas for conservation of the genetic resources of the argan tree are compared to those sometimes advocated in the case of reserve design, where one of the goals is to maximize species richness. Identificacón de Poblaciones para su Conservación en Base a Marcadores Genéticos Los criterios genéticos obtenidos del estudio de marcadores moleculares podrían ser útiles para seleccionar poblaciones de vida silvestre como candidatos con prioridad para su conservación. Tradicionalmente se consideran medidas de la diversidad como son la heterocigocidad esperada, o el porcentaje de loci polimórficos. Para medidas de conservación, nosotros proponemos en su lugar que la prioridad se enfoque en medidas de riqueza alélica. Para estandarizar los resultados de riqueza alélica entre problaciones, utilizamos una técnica de vacuidad. Esta técnica permite evaluar el número esperado de alelos entre muestras de igual tamaño obtenidas de diferentes poblaciones. Mostramos como la contribución de cada población a la diversidad total puede ser repartida en dos componentes; el primero esta relacionado con el nivel de diversidad de la población y el segundo con su divergencia de las otras poblaciones. Para propósitos de conservación, la singularidad de una población (en forma de composición alélica) puede ser por lo menos tan importante como lo es su nivel de diversidad, Estos nuevos elementos descriptivos son ilustrados mediante el uso de datos de DNA de isozima y cloroplasto para una especie de árbol en peligro, el árbol argan de Morocco (Argania spinosa(L.) Skeels). Con estos análisis, el valor de conservación de las poblaciones del árbol argan puede ser apreciado mejor, especialmente para aquellas provenientes de dos grupos aislados del norte del país. Los métodos propuestos para la identificación de áreas prioritarias para la conservación de los recursos genéticos del árbol argan son comparados con aquellos utilizados en el diseño de reservas, donde una de las metas es la maximización de la riqueza de especies.

Evolution of multigene families by gene duplication. A haploid model.

Evolution of multigene families by gene duplication and subsequent diversification is analyzed assuming a haploid model without interchromosomal crossing over. Chromosomes with more different genes are assumed to have higher fitness. Advantageous and deleterious mutations and duplication/deletion also affect the evolution, as in previous studies. In addition, negative selection on the total number of genes (copy number selection) is incorporated in the model. First, a Markov chain approximation is used to obtain formulas for the average numbers of different alleles, genes without pseudogene mutations, and pseudogenes assuming that mutation rates and duplication/deletion rates are all very small. Computer simulation shows that the approximation works well if the products of population size with mutation and duplication/deletion rates are all small compared to 1. However, as they become large, the approximation underestimates gene numbers, especially the number of pseudogenes. Based on the approximation, the following was found: (1) Gene redundancy measured by the average number of redundant genes decreases as advantageous selection becomes stronger. (2) The number of different genes can be approximately described by a linear pure-birth process and thus has a coefficient of variation around 1. (3) The birth rate is an increasing function of population size without copy number selection, but not necessarily so otherwise. (4) Copy number selection drastically decreases the number of pseudogenes. Available data of mutation rates and duplication/deletion rates suggest much faster increases of gene numbers than those observed in the evolution of currently existing multigene families. Various explanations for this discrepancy are discussed based on our approximate analysis.

A FISH cosmid 'cocktail' for detection of 13q deletions in chronic lymphocytic leukaemia--comparison with cytogenetics and Southern hybridization.

The most frequent structural chromosome abnormality in chronic lymphocytic leukaemia (CLL) is deletion at chromosome 13q14. Studies with Southern blot hybridisation have revealed deletions in the region located telomeric of the retinoblastoma gene in more than 40% of cases. The highest frequency of homozygous deletions has been found at the D13S319 locus and it is likely that a new tumour suppressor gene is located close to this region. We have analysed deletions in the D13S319 region in 20 selected CLL patients using conventional cytogenetic analysis, fluorescence in situ hybridisation (FISH) and Southern blot hybridisation. FISH and Southern hybridisation are equally efficient in detecting deleted clones in our study. However, FISH analysis indicate that subclones with different numbers of alleles in the D13S319 region can exist simultaneously. The cytogenetic analyses confirm that clones with different chromosomal abnormalities can occur in patients with CLL and that 13q14 deletions can be limited to one of these subclones. Furthermore, the FISH analyses show that trisomy 12 and deletion of 13q14 can occur in the same cell clone. Finally, our study confirms that mitogen stimulation of peripheral blood cells from CLL patients before FISH analysis may result in a sharp increase in normal appearing cells, which can hide leukaemic clones with deletions in the D13S319 region.

Application of the microsatellite technique for analyzing genetic diversity in shrimp breeding programs

The microsatellite technique was employed to demonstrate the use of genetic markers as a genetic analysis tool to manage breeding programs of cultured species. This technique was used on a total of 312 P. vannamei shrimp from Population 1 (Sinaloa, Mexico), Population 2 (Ecuador), Population 3 (hybrid of Population 1 X Population 2), Population 4 (Oaxaca, Mexico), a Guatemalan stock, and wild female broodstock from Salinas, Ecuador. Microsatellite 1, M1, was used to determine the allelic inheritance within 14 families from two populations and two groups from the Guatemalan stock. All of the offspring were shown to be genetic descendants of their presumed parents. All families showed Mendelian inheritance. A total of 47 different alleles were found at the M1 locus. The number of different alleles for each population ranged from four in Population 2 to 23 alleles in Population 4. Observed heterozygosities ranged from 45% to 100%. There were 23 population-specific markers, two of which were observed only in single families from Population 1. Microsatellite markers are useful for informing animal breeders of genetic diversity levels in populations of interest before implementing a breeding program.

Effect of total allelic relationship on accuracy of evaluation and response to selection.

Total allelic relationship (TA) as a possible alternative to the pedigree-derived additive genetic relationship (RA) is defined. The TA measures the actual allelic identity between individuals for loci segregating for the trait concerned. Its value was studied by simulation in populations of different family structure, different numbers of loci, different numbers of alleles per locus, and different heritability levels. The alternative types of relationship matrices were used in mixed model equations to derive best linear unbiased prediction estimates (EBV) of breeding values (BV). Accuracies of evaluations were calculated as correlations of EBV with true breeding values. In populations with random selection and mating, EBVTA derived using TA had higher accuracies than EBVRA derived using RA. In populations with selection, EBVTA was more accurate and resulted in higher responses than selection on EBVRA. We conclude that not accounting for variation in average measures of relationship and identity in state can be important sources of variance of prediction error, and taking account of them increases the accuracy of selection.