Measures Of Genetic Similarity Research Articles

Comparison of measures for haplotype similarity

Measuring the association of haplotype similarities with phenotype similarities has been used to develop statistical tests of genetic association. Previously, we applied the general approach of Mantel statistics to correlate genetic and phenotype similarity, where genetic similarity was defined by the number of intervals flanked by markers identical by state for pairs of haplotypes. Here we investigated in the case-control study design the effect on power of the Mantel statistics for five different measures of genetic similarity based on haplotypes: 1) the number of shared intervals, 2) the physical length of the shared intervals, 3) the genetic length of the shared intervals in centimorgans, 4) the genetic length of the shared intervals in linkage disequilibrium units (LDU) and 5) Yu's measure that attaches more weight to the sharing of rare than common alleles. With prior knowledge of the answers of Genetic Analysis Workshop 15 Problem 3, we analyzed the simulated data sets in two genomic regions surrounding the disease loci on chromosomes 6 and 18. For the dense map on chromosome 6, all methods showed a very high power of comparable magnitude. For chromosome 18, we observed a power between 19% and 99% at the pointwise 5% significance level using 1000 cases and 1000 controls for all methods except Yu's measure. While it yielded a much lower power, Yu's measure had 80% power around the disease locus.

Support vector machine regression for the prediction of maize hybrid performance

Accurate prediction of the phenotypical performance of untested single-cross hybrids allows for a faster genetic progress of the breeding pool at a reduced cost. We propose a prediction method based on epsilon-insensitive support vector machine regression (epsilon-SVR). A brief overview of the theoretical background of this fairly new technique and the use of specific kernel functions based on commonly applied genetic similarity measures for dominant and co-dominant markers are presented. These different marker types can be integrated into a single regression model by means of simple kernel operations. Field trial data from the grain maize breeding programme of the private company RAGT R2n are used to assess the predictive capabilities of the proposed methodology. Prediction accuracies are compared to those of one of today's best performing prediction methods based on best linear unbiased prediction. Results on our data indicate that both methods match each other's prediction accuracies for several combinations of marker types and traits. The epsilon-SVR framework, however, allows for a greater flexibility in combining different kinds of predictor variables.

Genetic Diversity in the Highbush Blueberry Evaluated with Microsatellite Markers

Sixty-nine accessions representing wild and domesticated highbush blueberry (Vaccinium corymbosum L.) germplasm were genotyped using 28 simple sequence repeats (SSRs). A total of 627 alleles was detected and unique fingerprints were generated for all accessions. Suspected duplicate accessions of `Coville' and `Ivanhoe' had DNA fingerprints that were identical to `Coville' and `Ivanhoe', respectively. Genetic similarity measures placed wild and cultivated blueberries in separate groups. Northern highbush blueberries grouped among ancestral clones that were used extensively in blueberry breeding such as `Rubel' and `Stanley'. Southern highbush blueberries formed a separate group from northern highbush blueberries. The microsatellite markers used here show excellent promise for further use in germplasm identification, in genetic studies of wild Vaccinium L. populations, and for constructing linkage maps.

Correlations between heterozygosity and measures of genetic similarity: implications for understanding mate choice

There is currently considerable interest in testing the effects of genetic compatibility and heterozygosity on animal mate preferences. Evidence for either effect is rapidly accumulating, although results are not always clear-cut. However, correlations between mating preferences and either genetic similarity or heterozygosity are usually tested independently, and the possibility that similarity and heterozygosity may be confounded has rarely been taken into account. Here we show that measures of genetic similarity (allele sharing, relatedness) may be correlated with heterozygosity, using data from 441 human individuals genotyped at major loci in the major histocompatibility complex, and 281 peafowl (Pavo cristatus) individuals genotyped at 13 microsatellite loci. We show that average levels of allele sharing and relatedness are each significantly associated with heterozygosity in both humans and peafowl, that these relationships are influenced by the level of polymorphism, and that these similarity measures may correlate with heterozygosity in qualitatively different ways. We discuss the implications of these inter-relationships for interpretation of mate choice studies. It has recently become apparent that mating preferences for 'good genes' and 'compatible genes' may introduce discordant choice amongst individuals, since the optimal mate for one trait may not be optimal for the other, and our results are consistent with this idea. The inter-relationship between these measures of genetic quality also carries implications for the way in which mate choice studies are designed and interpreted, and generates predictions that can be tested in future research.

Population variation and phylogeny in the endangered Chamaesyce skottsbergii (Euphorbiaceae) based on RAPD and ITS analyses

Chamaesyce skottsbergii var. skottsbergii is federally listed as an endangered taxon, and is found in small and isolated populations restricted to calcareous soils in dry shrubland habitats on the Hawaiian islands of Oahu and Molokai. Concern over the genetic relationship among these disjunct populations arose as a result of threats to the habitat of the Oahu population. The populations were examined using random amplified polymorphic DNA (RAPD) markers and sequence analysis of the internal transcribed spacer (ITS) region of the rDNA cistron. Chamaesyce skottsbergii var. vaccinioides, a closely related variety found in several small populations on Molokai, was used for baseline comparison of the genetic divergence among populations. RAPD analysis demonstrated that variation within and among populations is the highest for any Hawaiian species examined. Polymorphism was greater than 95% within populations and was 99.4% at the species level. Similarly, measures of genetic similarity indicate that differentiation among these populations is higher than is known for some species. Both RAPD and ITS sequence analysis indicate that populations of C. skottsbergii var. skottsbergii on Oahu and Molokai are genetically distinct, and the extent of this genetic differentiation supports the recognition of these populations as distinct varieties. The Molokai population is in fact much more closely related to var. vaccinioides than to var. skottsbergii on Oahu, and thus should be recognized by the previously used variety name, C. skottsbergii var. audens. Further conservation measures for each of the varieties are addressed.

Haplotypes and haplotype-tagging single-nucleotide polymorphism: Presentation Group 8 of Genetic Analysis Workshop 14

Moderately dense maps of single-nucleotide polymorphism (SNP) markers across the human genome for both the simulated data set and data from the Collaborative Study of the Genetics of Alcoholism were available at Genetic Analysis Workshop 14 for the first time. This allowed examination of various novel and existing methods for haplotype analyses. Three contributors applied Mantel statistics in different ways for both linkage and association analysis by using the shared length between two haplotypes at a marker locus as a measure of genetic similarity. The results indicate that haplotype-sharing based on Mantel statistics can be a powerful approach and needs further methodological evaluation. Four contributors investigated haplotype-tagging SNP (htSNP) selection procedures, two contributors examined the use of multilocus haplotypes compared to single loci in association tests, and two contributors compared the accuracy of various methods for reconstructing haplotypes and estimating haplotype frequencies for both pedigree data and data from unrelated individuals. For all three different tasks, software packages and procedures gave similar results in regions of high linkage disequilibrium (LD). However, they were not as consistent in regions of moderate to low LD. One coalescence-based approach for estimating haplotype frequencies, coupled with a Markov chain Monte Carlo technique, outperformed the other haplotype frequency estimation methods in regions of low LD. In conclusion, regardless of the task, results were similar in chromosomal regions of high LD. However, based on the differing results observed here, methodological improvements are required for chromosomal regions of low to moderate LD.

Diversity of Mycobacterium tuberculosis isolates in an immigrant population: evidence against a founder effect.

Population-based studies have used DNA typing of Mycobacterium tuberculosis organisms to estimate the extent of ongoing tuberculosis transmission in various communities and to characterize associated risk factors. The finding of matched DNA "fingerprints" among isolates from an immigrant subgroup may reflect transmission in the adopted country but could also reflect limited diversity among M. tuberculosis organisms within that immigrant community. The authors sought to determine which hypothesis is more likely to explain the high frequency of matched isolates among Haitian-born tuberculosis patients in Montreal, Quebec, Canada. The authors determined the number of different bacterial genotypes in this community as compared with other foreign-born tuberculosis patients and applied a recently described measure of genetic similarity between M. tuberculosis organisms ("genetic distance"). Among 76 Haitian-born tuberculosis patients diagnosed during 1996-1998, the authors identified 47 distinct genotypes on the basis of standard IS6110 DNA typing and categorical analysis. In genetic distance analysis, these 47 genotypes showed as great a genetic diversity as that observed among the 191 distinct genotypes identified in 216 other foreign-born tuberculosis patients. A mycobacterial "founder effect" is unlikely to account for the high proportion of shared isolates among Haitian-born Montrealers. Recent transmission remains the most likely explanation.

Genetics and geography of wild cereal domestication in the near east.

About 12,000 years ago, humans began the transition from hunter-gathering to a sedentary, agriculture-based society. From its origins in the Near East, farming expanded throughout Europe, Asia and Africa, together with various domesticated plants and animals. Where, how and why agriculture originated is still debated. But newer findings, on the basis of genome-wide measures of genetic similarity, have traced the origins of some domesticated cereals to wild populations of naturally occurring grasses that persist in the Near East. A better understanding of the genetic differences between wild grasses and domesticated crops adds important facets to the continuing debate on the origin of Western agriculture and the societies to which it gave rise.

Polymorphism in Indigenous Poultry Germplasm Detected through Randomly Amplified Polymorphic DNA

Sharma. D., Singh, D.P. and Singh, R.V. 2000. Polymorphism in indigenous poultry germplasm detected through randomly amplified polymorphic DNA. J. Appl. Anim. Res., 18: 115–120. This study involved the use of randomly amplified polymorphic DNA (RAPD) markers in detecting the polymorphism between two important native chicken breeds viz. Aseel and Kadaknath and to estimate the genetic variability between them. Out of 30 primers screened, 24 could generate distinct and reproducible RAPD patterns and only 7 of these, detected the polymorphism between these two native breeds. Thirteen of the 63 amplicons generated from the 7 selected primers, were found to be polymorphic. The Aseel population (WS = 0.91 to 0.96) showed higher within breed genetic similarity in comparison to the Kadaknath (WS = 0.81 to 0.82) from either measure of genetic similarity. Both the breeds showed moderate genetic distances (0.108) between them. Some selected primers could detect polymorphism between two varities of Aseel i.e. Peela and Kala

Population genetics of Glossina morsitans submorsitans (Diptera: Glossinidae).

Breeding structure of Glossina morsitans submorsitans Newstead was evaluated by using genetic markers in mitochondrial DNA where diversity was scored at two loci in five natural populations from The Gambia and two populations in Ethiopia (form ugandensis Vanderplank), countries separated by c. 5450 km. Twenty six haplotype combinations were found, of which 17 were shared among two or more populations. Nine haplotypes were found in The Gambia and 23 haplotypes in Ethiopia. There were 12 unique haplotypes. Only six haplotypes were shared between the two countries. Populations in The Gambia (he = 0.26 +/- 0.04) showed less than a third of the diversity of populations in Ethiopia (he = 0.84 +/- 0.03). This suggests recovery from an earlier reduction in population. In a nested analysis of molecular variance of haplotype frequencies, 65% of the variance was due to differences within populations, 34% to differences between populations grouped by country, and only 1% was due to differences among populations within countries. In terms of gene flow, the fixation index FST = 0.35, which leads to an estimate by Wright's island model of less than one reproducing migrant per generation exchanged between the eastern and western submorsitans populations. Nei's genetic similarity measure showed a deep division between Gambian and Ethiopian populations.

POPDIST, version 1.1.1: a program to calculate population genetic distance and identity measures.

In this note we announce the release of POPDIST version 1.1.1. This is a program to calculate genetic distance and identity measures, including the measure of Tomiuk and Loeschcke, which also allows calculation of genetic similarity measures for comparisons involving polyploid and parthenogenetic populations. The program is available for free from the Internet as C source code, or compiled for the Macintosh, MS Windows 95, and various brands of UNIX.

Changes in genetic diversity during seven cycles of recurrent selection for grainyield in oat, Avena sativa L.

AbstractVariability for desirable alleles within elite breeding populations is a requirement for long‐term genetic improvement. Changes in genetic diversity were evaluated in a recurrent selection programme for enhanced grain yield in oat, Avena sativa L., using coefficient of parentage (rp) and restriction fragment length polymorphism (RFLP) based genetic similarity (S) estimates. Both rp and s increased during seven cycles of recurrent selection, indicating a reduction in the level of genetic diversity within the population. The relationship between genetic diversity and agronomic performance was also examined. Genetic similarity measures were poor predictors of the near‐homozygous progeny performance and general and specific combining ability effects for three agronomic traits in the recurrent selection programme. In addition, there was no apparent trend for preferential selection of progeny from either more similar or more diverse parents within a given cycle of selection. The overall reduction in genetic diversity in this population has not affected selection response for grain yield. Variability remaining at important loci or de novo variation are possible explanations for the continued selection progress.

Genetic Similarities among Winter Wheat Cultivars Determined on the Basis of RFLPs, AFLPs, and SSRs and Their Use for Predicting Progeny Variance

The efficiency of breeding programs could be increased by predicting the prospects of crosses for line development before producing and testing lines derived from them. In this study, we (i) assessed the level of genetic diversity among German and Austrian winter wheat (Triticum aestivum L.) cultivars using 117 restriction fragment length polymorphism (RFLP) probes, 16 amplified fragment length polymorphism (AFLP) primer combinations, and 21 simple sequence repeat (SSR) primer pairs, (ii) investigated the correlation between coancestry (f) and genetic similarity (GS) estimated from molecular markers, and (iii) evaluated the use of f and GS for predicting the genetic variance (σ2g) within sets of 22 F4n (n = 7 or 8) lines derived from 30 crosses between these winter wheat cultivars. The average polymorphic information content (PIC) for polymorphic bands was not significantly different between the three marker systems (0.30 ≤ PIC ≤ 0.33), whereas the marker index was low for RFLPs and SSRs but high for AFLPs. Estimates of f between all 55 cultivar combinations ranged from 0.01 to 0.53. ‐values varied between 0.52 and 0.89 for RFLPs, between 0.40 and 0.83 for AFLPs, and between 0.16 and 0.91 for SSRs. The Mantel Z test statistic revealed no common pattern between the four dendrograms obtained by cluster analyses. Significant (P < 0.05) correlations among f̂, ‐RFLP, ‐AFLP, and ‐SSR were detected only for related parent combinations (f̂≥ 0.10). For all seven traits analyzed, estimates of σ2g were not significantly associated with any measure of GS between parents. On the basis of these results, we recommend AFLPs for fingerprinting wheat cultivars. However, predicting the progeny variance (σ2g) remains an unsolved problem.

Estimation of genetic variation and relationship in potato (Solanum Tuberosum L.) cultivars using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to distinguish commercial cultivars and to assess the level of polymorphism in potato. AFLP analysis templates were made using Eco RI and Mse I as described in the Gibco BRL AFLP kit protocol. Seven primer combinations with three selective nucleotides on both primers were screened individually with 12 potato cultivars. Multiple polymorphisms could be detected in a single reaction to the extent that all 12 commercial potatoes tested could be distinguished using any one primer combination. Up to 84 polymorphic bands were detected with a single primer combination among 12 accessions. The seven primer combinations generated a total of 466 bands, of which 409 (88%) were clearly polymorphic among the cultivars. The presence or absence of each AFLP markers was scored and then phylogenetic and genetic distance analyses were used to generate dendrograms showing genetic relationships among the cultivars evaluated. The analyses based on amplified DNA fragments did not always reflect the known genetic relationships among the cultivars. These results demonstrate that AFLP DNA markers can be of great value in identification and measurement of variation, but should be treated with caution for purposes of estimating true measures of genetic similarity in potato.

Heterosis in Soybean and Its Prediction by Genetic Similarity Measures

Coefficient of parentage (CP) and restriction fragment length polymorphism‐based genetic similarity estimates (RFLP‐GS) have been proposed as measures of genetic distance in crop species. If these measures are to have application in practical breeding, it is important to validate their utility in predicting genetic traits of interest such as heterosis. The objectives of this paper were to (i) estimate heterosis for yield in soybean [Glycine max (L.) Merr.] adapted to the southern USA, and (ii) predict heterosis by means of CP and RFLP‐GS as genetic distance measures. Twenty‐four F2 populations were developed by crossing three testers (‘Young’, ‘Centennial’, and ‘Tracy’) eight contrasting parents, representing a wide range of CP and RFLPGS. The experimental material was divided into three sets representing the testers above, and was evaluated in eight replications at Clayton and Plymouth, NC, in 1994. Midparent heterosis for yield was 7.9, 4.5, and 7.9% for Sets 1, 2, and 3, respectively. Heterosis was 3.5, 1.6, and 3.0% for 100‐seed weight, and 4.1, 5.4, and 13.2% for plant height. The CP and RFLP‐GS were highly correlated (r = 0.80, 0.92 and 0.95 for Sets 1, 2, and 3, respectively, P = 0.01), but neither predicted heterosis well for yield averaged across locations because of a large genotype × environment (G × E) interaction. In contrast, CP and RFLP‐GS predicted heterosis well for 100‐seed weight and plant height in two of the three sets averaged over locations. Our estimates of high parent heterosis for yield (as high as 11% over locations), may justify soybean hybrids as a breeding objective. However, the limited predictive value of CP and RFLP‐GS in our study indicates that the identification of favorable heterotic combinations may require extensive field testing.

RFLP Genetic Similarity Estimates and Coefficient of Parentage as Genetic Variance Predictors for Soybean Yield

RFLP genetic‐similarity estimates (RFLP‐GS) and coefficient of parentage (CP) have been used as measures of genetic similarity within crop species. However, practical application of these measures in plant breeding remains uncertain. This study was designed to probe the utility of RFLP‐GS and CP in predicting genetic variance (GV) for seed yield among inbred soybean [Glycine max (L.) Merr.] lines. achieve this goal, five single seed descent populations were studied, representing a range of RFLP‐GS and CP between the parents from 57 to 75% and 0.06 to 0.5, respectively. The GV for yield was estimated for each population through field evaluation of 30 inbred lines per population, in two North Carolina field locations during 1994. Both RFLP‐GS and CP correctly identified the population with the highest GV; however, CP predicted GV for yield more efficiently (rCP.RFLP‐GS = 0.91*; rCP.GV = −0.81*; and rRFLP‐GS.GV = −0,58). The GV was near zero when the CP between parents was larger than 0.27 or when RFLP‐GS was larger than 75%. Neither genotype × environment interaction nor low field precision were factors for the lower predictive value of RFLP‐GS. Expected gains from selection agreed partially with RFLP‐GS results but closely matched CP and the actual fate of populations in a USDA breeding program. These results indicated that caution should be taken in an applied soybean breeding program when crossing parents with a relationship larger than half‐sib or when the RFLP‐GS is larger than 75% when yield improvement is the main breeding objective.

RAPD and isozyme analysis of genetic relationships between Carica papaya and wild relatives

The genetic origin of cultivated papaya is not clear. Wild relatives of papaya (Carica papaya) from central southern America were investigated using isozyme and RAPD analysis. Seven other species (including six from the genus Carica) were found to be relatively distant from papaya providing no indication of the genetic origin of papaya. Isozyme and RAPD data gave similar measures of genetic similarity within this group. C. papaya was about 70% dissimilar to the other Carica species by both methods. The other Carica species had average dissimilarities around 50%. Two species, C. pubescens and C. stipulata were much closer to each other with similarities of 87% by isozyme analysis and 82% by RAPD analysis. Although both methods gave similar measures for genetic distance the large number of RAPD markers available made RAPD analysis more reliable for analysis of the extremes (e.g. closely related taxa may show no isozyme differences and distant taxa may show no isozyme similarities).

The Use of DNA Fingerprinting in Ecological Studies of Phragmites australis (Cav.) Trin. ex Steudel

SummaryA number of reed populations (Phragmites australis) from natural locations on the shore of Lake Ammersee in the south of Bavaria as well as artificially grown reed plants were analyzed for restriction fragment length polymorphisms (RFLPs) in order to evaluate for further ecological studies the dynamics of the restriction pattern within the genome of plants which propagate themselves asexually. The artificially grown reed plants were raised in four ponds supplemented with different phosphate concentrations (8 μg, 16 μg, 50 μg, and 200 μg/l) from rhizomes taken from a neighbouring fish pond. The genomic DNA of 25 of these plants and the DNA from 37 plants out of 18 stands from the lakeshore was isolated and restricted with the enzyme EcoRI, EcoRV, XbaI and HindIII and hybridized to three probes from a shot‐gun cloned reed plasmid library. The probes gave between 15 and 26 bands (DNA fingerprints) of high polymorphic frequency (68% − 100%) after hybridization with repetitive sequences of restricted DNA. A cluster analysis based on the banding pattern as a measure of genetic similarity (GS) was performed with the two sets of reed plants. The plants from the lakeshore exhibited a clear formation of clusters with GS up to 100%; the 20 plants grown from rhizomes, in contrast, did not show any clear correlation among themselves, neither to the phosphate concentration they grew in, nor to the five plants tested from the pond their rhizomes came from. The value of genetical investigations of the plant genome in context with environmental impact on plants is being discussed.

RFLP variation and genealogical distance, multivariate distance, heterosis, and genetic variance in oats

Patterns of restriction fragment length polymorphisms (RFLPs) have been proposed as estimators of genetic diversity among breeding lines and as predictors of heterosis and genetic variance. We evaluated these proposals by using a set of nine elite oat lines crossed in a diallel mating design without reciprocals. RFLP analysis was conducted using HindIII-digested DNA and a total of 107 probes from three different sources: 14 heterologous wheat cDNA clones, 17 oat genomic clones, and 76 oat cDNA clones. Of the 77 probes that produced high-quality autoradiographs, 26 detected polymorphisms among this set of lines, with an average of 2.6 variants per probe. RFLP-based genetic distance (FD) was calculated from these data by using Nei and Li's measure of genetic similarity, and was compared with two other measures of genetic divergence. Genealogical distance (GD (*)) was obtained from the coefficients of parentage based on known parental pedigrees, and multivariate distance (DI) was calculated by using the first five principal components of the parental correlation matrix for 12 agronomic traits. FD was significantly correlated with GD (*) (r=0.63, P<0.01), but not with DI (r=-0.05). Cluster analysis based on these three distance estimates did not produce equivalent groupings, but the FD and GD (*) clusters were more similar to each other than to the DI clusters. These results indicate that: (1) sufficient variation exists for further application of RFLP technologyto oats, (2) RFLPs could provide accurate estimates of genetic divergence among elite oat lines, and (3) it is unlikely that dispersed markers can predict heterosis or population genetic variance in oats. Further investigations will require more parental lines, a larger set of markers, and more information on the linkage relationships between RFLP markers and loci controlling the trait of interest.

Subject: Methods

Oological material from two Kharkov Region colonies, Zmiyov and Chuguyev, of the black-headed gull Larus ridibundus were studied with the purpose to estimate population variability for the following traits: egg length (EL), egg width (EW), egg shape index (ESI), asymmetry value (AV), egg mass (EM) and egg shell background optical density (ESBOD). There were no significant differences between the two colonies for the characters studied, average character values in Kharkov population were respectively 52.4 mm, 37.0 mm, 0.707, 22.1 mm, 37.3 g, 84.1 cB, the corresponding coefficients of character variation being 3.82, 2.76, 3.90, 3.71, 7.24 and 15.70%. By using starch gel electrophoresis of egg whites, the polymorphism of an autosomal ovoglobulin locus G3 was revealed both in the Zmiyov and Chuguyev subpopulations with the frequencies of allele G3A 0.567 and 0.543, and of allele G3B 0.433 and 0.457, respectively. In the Zmiyov subpopulation, the polymorphism of an autosomal ovalbumin locus Ov was observed with the frequencies of allele OvA 0.896 and of allele OvB 0.104. Polymorphic types of egg white transferrin (locus Tf) were not found in the both subpopulations. With regard to values of population similarity and diversity (1), genetic similarity measure, r, was found to be 0.973 with identity criterion, I, 4.7 (P > .05) that testified to the insignificant differences between two subpopulations studied. Significant differences (P < .001) between the Zmiyov and Chuguyev subpopulations were observed by using values of population diversity, mean allele number, h (1.80 vs 1.50), and rare allele share (0.100 vs 0.012).