Proportion Of Heterozygosity Research Articles

Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers

BackgroundGinseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. MethodsWe developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. ResultsMost of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (He) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. ConclusionGinseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.

Effects of heterozygosity on performance of purebred and crossbred pigs

BackgroundIn pigs, crossbreeding aims at exploiting heterosis, but heterosis is difficult to quantify. Heterozygosity at genetic markers is easier to measure and could potentially be used as an indicator of heterosis. The objective of this study was to investigate the effect of heterozygosity on various maternal and production traits in purebred and crossbred pigs. The proportion of heterozygosity at genetic markers across the genome for each individual was included in the prediction model as a fixed regression across or within breeds.ResultsEstimates of regression coefficients of heterozygosity showed large effects for some traits. For maternal traits, regression coefficient estimates were always in a favourable direction, while for production, meat and slaughter quality traits, they were both favourable and unfavourable. Traits with the largest estimated effects of heterozygosity were total number born, litter weight at 3 weeks, weight at 150 days, and age at 40 kg. Estimates of regression coefficients on heterozygosity differed between breeds. Traits with the largest effect of heterozygosity also showed a significant (P < 0.05) increase in prediction accuracy when heterozygosity was included in the model compared to the model without heterozygosity.ConclusionsFor traits with the largest estimates of regression coefficients on heterozygosity, the inclusion of heterozygosity in the model improved prediction accuracy. Using models that include heterozygosity would result in selecting different animals for breeding, which has the potential to improve genetic gain for these traits. This is most beneficial when crossbreds or several breeds are included in the estimation of breeding values and is relevant to all species, not only pigs. Thus, our results show that including heterozygosity in the model is beneficial for some traits, likely due to dominant gene action.

Genetic variation of the striped hamster (Cricetulus barabensis) and the impact of population density and environmental factors

The striped hamster (Cricetulus barabensis) is a dominant rodent species in the North China Plain and has suffered a continuous decline of population size in the last 17 years. However, little is known about the population genetic structure of this species and how it is influenced by geographical and environmental factors. In the present study, we investigated the genetic diversity and genetic differentiation of the striped hamsters in four geographical populations of different environmental features. The genetic variability for a sample of 158 animals from the four populations was estimated using data from 10 microsatellite loci. Genetic diversity exists in the striped hamster. The number of alleles and the proportion of heterozygosity indicate moderate variability. A total of 46 alleles were detected, with a moderate mean number of alleles. Significant genetic differentiation (p < 0.01) exists among all four examined geographical populations. Population-specific alleles and variable allelic richness were detected in all populations regardless of the geographical distances. The genetic diversity positively correlates with the population density, while the genetic distance is partially affected by the geographical distances. Moreover, the habitat environment is also an important factor influencing the genetic differentiation of the species. The genetic diversity of the striped hamster is mainly impacted by population density, while partially influenced by geographical distances. The results of our study and other studies collectively suggest that a minimum geographical distance is required to prevent gene flow between different populations and for genetic differentiation to be pronounced.

Genetic structure of three Croatian horse breeds: implications for their conservation strategy

The genetic variability for a sample of 107 animals from three autochthonous Croatian horse breeds was estimated using 20 microsatellites. The average number of alleles per locus (6.3) and proportion of heterozygosity (0.732) indicated a moderate variability. The expected heterozygosity was similar among all breeds and ranged between 0.724 in the Posavina horse, and 0.737 in the Croatian Coldblood and Murinsulaner horse. The inbreeding coefficient Fis was low and non-significant over the three populations. The genetic differentiation among the three populations was low (Fst=0.026), suggesting that only 2.6% of the total genetic variability was due to differences between the breeds, and 97% to individual differences.The results of pairwise genetic differentiation suggest that the Posavina horse and the Croatian Coldblood were the most closely related populations (Fst=0.016). These results are confirmed by Nei’s genetic distances with the highest value observed between the Posavina horse and the Murinsulaner (0.082) and the lowest between the Posavina horse and the Croatian Coldblood (0.044). An assignment test correctly assigned 82% of individuals to the correct breed. Strategies for preserving the original native genes in the Croatian native horse breeds should be considered in order to prevent these breeds from becoming extinct and include them in the future breeding programmes.

Effect of Quantitative Trait Loci for Milk Protein Percentage on Milk Protein Yield and Milk Yield in Israeli Holstein Dairy Cattle

Although numerous quantitative trait loci (QTL) mapping studies involving milk protein percent (PP), milk yield (MY), and protein yield (PY) have been carried out, there has not been any systematic evaluation of the effects of individual QTL on these 3 interrelated traits. Consequently, the aim of the present study was to investigate the effects on MY and PY of QTL for PP previously mapped in various laboratories. The study, based on selective DNA pooling of milk samples, included 10 Israeli Holstein artificial insemination bulls, each the sire of 1,800 or more milk-recorded daughters. For each sire-trait combination across the 10 sires, milk samples of the highest and lowest daughters with respect to estimated breeding values for PP, PY, and MY were collected for pooling. A total of 134 dinucleotide microsatellites distributed over 25 bovine autosomes were used. An empirical standard error for marker-QTL linkage testing was calculated based on the variation among split samples within the same tail. Threshold comparison-wise error rate P-values were set to control proportion of false positives at P=0.10 level for declaring significant effects at the marker-trait level. Estimates of the number of true null hypotheses for each trait were obtained from the histogram of marker comparison-wise error rate P-values. Based on these estimates, effective power of the experiment at the marker-trait level was estimated as 0.75, 0.41, and 0.73 for PP, PY, and MY. The proportion of heterozygosity at the QTL was estimated as 0.46, 0.39, and 0.40, respectively. After correcting for incomplete power and proportion of false positives, it was estimated that 38.7 and 37.5% of the markers affecting PP and MY, respectively, also affected PY. Of the markers affecting PY, 68.9 and 76.5%, respectively, also affected PP and MY. Apparently, none of the significant markers affected PY exclusively, and only 6.5 and 16.0%, respectively, affected PP or MY exclusively. Thus, almost all significant markers, and by inference almost all QTL, had effects on at least 2 of the 3 traits.

Genetic diversity in the Pantaneiro horse breed assessed using microsatellite DNA markers

The genetic variability for a sample of 227 animals from three populations of Pantaneiro horses was estimated using data from 10 microsatellite loci. The number of alleles and the proportion of heterozygosity indicated high variability. A total of 91 alleles were found, with a significantly high mean number of alleles. The mean polymorphic information content was 0.7 and the paternity exclusion probability was 99.3%. The inbreeding coefficient (F(IS)) was low for the three populations: Ipiranga (F(IS) = 0.147), Nova Esperança (F(IS) = 0.094) and Promissão (F(IS) = 0.108). Genetic differentiation among all three populations was low (F(ST) = 0.008 to 0.064). Three methods were used to test for a recent bottleneck effect. The graphical method and the Wilcoxon test using the stepwise mutation model showed no bottleneck pattern for any of the populations. The test by two-phase mutation model showed genetic signatures of bottleneck for Ipiranga and Promissão. When we consider standard deviation value for Nova Esperança, the M-statistic detected a bottleneck pattern, but this result could be explained by a sample size effect. Therefore, there is no immediate cause for concern regarding loss of variation within the breed.

Identification and frequency of tetraploid progeny from 2x–4x and 4x–2x crosses in Dactylis

The utilization of diploid germ plasm in the improvement of tetraploid orchard grass (Dactylis glomerata L. ssp. glomerata Hayek) requires some means of polyploidization. Studies in several different crop species have shown that sexual polyploidization has the advantage of transmitting a large proportion of heterozygosity from the parent to the offspring. In tetrasomic tetraploids, maximum heterozygosity is a necessary requirement for maximum heterosis. The objective of this research was to investigate the occurrence of 2n eggs and 2n pollen in several sources of wild diploid germ plasm, by quantifying the frequency of 4x genotypes among the progeny of interploidy crosses. Pollen diameter was determined in 110 diploid genotypes. These genotypes were then ranked for five descriptive statistics based on diameter (maximum, 75th percentile, median, arithmetic mean, mode). The eight top-ranking genotypes in four of the five categories were crossed to male-sterile 4x seed parents. Randomly selected diploid genotypes were also crossed as seed parents to 4x genotypes. Tetraploid progeny were recovered from both types of crosses. Of 57 2x genotypes, 15 produced 2n eggs. Of the 8 large pollen diameter genotypes, 6 produced 4x progeny in relative frequencies of 3–100%. The success of recovery was dependent on the genotype of the pollen parent as well as the seed parent. Of the 6 genotypes producing 2n pollen, 2 also produced 2n eggs, resulting in the recovery of tetraploids from selfed progeny.Key words: germ-plasm utilization, interploidy crosses, forage grasses, plant introductions.

Polymorphism of polytene chromosomes in Bilobella aurantiaca (Insecta: Collembola)

Polytene chromosomes in the salivary glands of Bilobella aurantiaca are analysed in a population from Sierra de Gredos (Central Spain). They display a high degree of heterozygosity. Only a short part of the total length of the seven pairs of homologous chromosomes, examined in a single favourable specimen, was homozygous. Concerning the short arm of chromosomes III and IV, the respective proportion of heterozygosity for the whole population was 38.6% and 92.9%. Some hypotheses are formulated to account for these results: differential funtioning of homologous chromosomes, generalisation of minute duplications and deficiencies, complex inversions (which cannot be specified owing to the asynapsis of homologous chromosomes), and possibly local large deletions.

Genetic structure and climatic correlates of desert landsnails.

Allozymic variation in proteins encoded by 20 loci was analyzed electrophoretically in 126 adult specimens representing 4 populations and 2 species of the desert landsnail Trochoidea, subgenus Xerocrassa, in a variable desert climatic back-ground of temperature and water factors. In addition, geographic variation in 3 morphological body variables of these snails was also studied. The results indicate that: (i) Most loci (55%) were strongly polymorphic; (ii) A large proportion of the polymorphic loci (55%) displayed fixation of alternative alleles either within or between species; (iii) Most of the variant alleles (75%) were not widespread, indicating sharp local and regional geographic differentiation; (iv) Southward progressive trends were found in genic diversity, some allele frequencies, shell banding and body characters. (v) The mean estimates of genetic indices are: not of alleles per locus, A=1.69; proportion of polymorphism per population P=0.41, and proportion of heterozygosity per individual, H=0.07; (vi) The level of P increases and that of H decreases southward; (vii) The amount of variation in different functional elasses of enzymes follows the Gillespie-Kojima and partly the Johnson hypotheses; (viii) Coefficients of genetic disfance, D, between populations are high, [Formula: see text], range 0.05-0.26. D's within species may be higher than between species. Likewise, D's from the northernmost population increase progressively southwards; (ix) Significant gametic phase disequilibria occur in several populations in both species; (x) Deviations from Hardy-Weinberg equilibria were found in several loci in some populations in both species; (xi) A statistically significant (P<0.001) amount of morphological variation of all 3 body variables occurs within and between species. Body diameter decreases with evaporation. (xii) P, H, and allozymic variation in several gene loci are significantly correlated with climatic variable, primarily related to some water factors and secondarily to temperature; (xiii) Shell banding was negatively correlated with solar radiation; and (xiv) Few correlations between allozymic and morphological variations were revealed.The pattern of genetic variation of Trochoidea (Xerocrassa) vetzenii and T. (X) erkelii suggests that (a) climatic selection plays a major role in allozymic (and morphological) population structure and differentiation; (b) variation in allozyme and visual polymorphisms may provide the genetic basis for the complex physiological adaptations of landsnails enabling them to survive in hostile, hot and dry deserts, and is therefore partly adaptive rather than neutral.