Estimates Of Average Heterozygosity Research Articles

Molecular characterization and core collection evaluation of Manihot esculenta Crantz

Cassava is one of the most important subsistence crops in tropical regions. It is necessary to preserve and to know the genetic diversity existent for the adequate use of genetic resources. The evaluation of genetic diversity among genotypes results in information about potential parents in breeding programs, allows duplicates identification, and facilitates germplasm exchange between research institutions. The objective of this study was to characterize the genetic diversity of cassava accessions of North Brazil region. A total of 106 accessions were analyzed using ten microsatellite markers. The genetic parameters estimated were: expected heterozygosity (HE), observed heterozygosity (HO) and polymorphic information content (PIC). Clustering was performed using the UPGMA and Neighbor-Joining (NJ) method. Bayesian analysis, analysis of principal coordinates and identification of a core collection were also used. The ten loci amplified 8,40 alleles on average. The average heterozygosity estimates were: HE = 0.71, HO = 0.58 and PIC = 0.72. Genetic distances ranged from 0.158 to 0.908. Six (5,66%) accesses were redundant. Clustering and dispersion analysis didn’t differentiate bitter from sweet cassava, and there wasn’t correlation between groups and collect origin. The core collection consisted of 22 individuals that represented 94% of total allelic diversity and 20,75% of the base collection. The results indicate high dissimilarity between the accessions and allowed the detection of redundant genotypes, showing the use of genetic markers as informative tools for the management of collections.

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data.

Simple SummaryIn this study, we estimated genetic diversity in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches, and detected regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome, which are still poorly characterized in the Maremmana breed. A sensitivity analysis on the parameters used to detect ROH and ROHet provided information which can be useful to guide studies on the detection of genomic runs in general, and in semi-feral cattle populations in particular. The average observed and expected heterozygosity were estimated at and , respectively. Pedigree-based average inbreeding (F) was estimated at . A total of ROH and ROHet were detected in the genomes of the 149 animals included in the study. Genes found to be within the identified ROH and ROHet islands (e.g., KCTD8, GNPDA2) point to phenotypic characteristics related to environmental adaptation and robustness of Maremmana cattle. These results are of important because they will help design and implement breeding and conservation strategies for Maremmana cattle, and provide guidelines for other local cattle breeds.Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches ( and ), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (, ). Pedigree-based average inbreeding (F) was estimated at . The correlation was low between F and genomic-based approaches ( with , with ), while it was higher between and (). The low correlation between F and coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.

Use of High Density Single Nucleotide Polymorphism (SNP) Arrays to Assess Genetic Diversity and Population Structure of Dairy Cattle in Smallholder Dairy Systems: The Case of Girinka Programme in Rwanda.

In most smallholder dairy programmes, farmers are not fully benefitting from the genetic potential of their dairy cows. This is in part due to the mismatch between the available genotypes and the environment, including management, in which the animals perform. With sparse performance and pedigree records in smallholder dairy farms, the true degree of baseline genetic variability and breed composition is not known and hence rendering any genetic improvement initiative difficult to implement. Using the Girinka programme of Rwanda as an exemplar, the current study was aimed at better understanding the genetic diversity and population structure of dairy cattle in the smallholder dairy farm set up. Further, the association between farmer self-reported cow genotypes and genetically determined genotypes was investigated. The average heterozygosity estimates were highest (0.38 ± 0.13) for Rwandan dairy cattle and lowest for Gir and N’Dama (0.18 ± 0.19 and 0.25 ± 0.20, respectively). Systematic characterization of the genetic variation and diversity available may inform the formulation of sustainable improvement strategies such as targeting and matching the genotype of cows to productivity goals and farmer profile and hence reducing the negative impact of genotype by environment interaction.

Genetic Structure and Variation of Van Cats

To determine the genetic structure and variation of Van cats and some other cats, seven enzyme loci were examined using horizontal starch gel electrophoresis. ME bands were observed for the first time in cats. For the enzyme loci CA ( 1 ), SOD, GPI, and GOT, neither the individual Van cats nor the specimens of other cat species exhibited any variation. These enzymes presented identical bands, all of which were homozygous. With respect to the PGD, ME, and ESD loci, however, genetic variation was observed in all of the cats. Hence, three of the seven gene-enzyme systems (43%) were polymorphic with two alleles, contributing to an estimate of average heterozygosity of 0.33-0.49 for the Van cats. PGD was the most discriminatory among the three polymorphic loci. The phylogenetic tree indicated that the Van, Persian, Turkish Angora, and Turkish Tekir cats are distinct from Siamese and Bombay cats.

An assessment of genetic diversity in wild and captive populations of endangered Japanese bitterling Tanakia tanago (Cyprinidae) using amplified fragment length polymorphism (AFLP) markers

The Japanese bitterling Tanakia tanago (Cyprinidae) is on the verge of extinction in the wild, placing great importance on captive breeding programs for current conservation of the species. However, the loss of genetic diversity during captive breeding is an ongoing matter of concern. Since some captive populations have been almost monomorphic in mitochondrial DNA (mtDNA), this hampers assessments of their genetic diversity during captive breeding. To more accurately assess their genetic diversity, one wild and three captive populations were examined using amplified fragment length polymorphism (AFLP) markers. Estimates of average heterozygosity and nucleotide diversity ranged 0.0479–0.1920 and 0.0023–0.0088, respectively, enabling comparison of genetic diversity among the wild and captive populations, and among year-classes of captive populations. Significant differences in numbers of amplified fragments and proportions of polymorphic fragments were observed among year-classes of all populations. The indices of genetic diversity calculated from AFLP seemed to be, however, less sensitive to weak bottlenecks. No continuous decrease in genetic diversity in nuclear DNA was detected in presently captive populations. This supports the possibility of re-introduction of the captive populations into the original habitats, although survival and reproductive ability in the wild must be taken into consideration.

The Investigation of Genetic Variation at Microsatellite Loci in Mazandaran Native Chickens

Blood samples of Mazandaran native chickens were collected. A total of 90 genomic DNAs were isolated through optimized and modified salting-out procedure. The samples were used in Polymerase Chain Reaction (PCR) with 20 micro satellite markers. Amplified PCR-products with the markers were separated on 8% denaturing polyacrylamide gel. One locus (MCW216) was monomorphic. According to allele frequencies of 20 micro satellite sites, mean heterozygosity (H) and Polymorphism Information Content (PIC) were calculated. The number of alleles varying from 1 to 6 and an estimate of average heterozygosity excluding the monomorphic data was calculated as 0.5872. The average heterozygosity and PIC value calculated from data on polymorphic and monomorphic loci was 0.5579 and 0.4939, respectively. The results of the heterozygosity were consistent with that of PIC. Diversity estimates in this study are lower than the observed frequencies of heterozygotes reported in other species using micro satellite markers. Other parameters for intrapopulation variation and Hardy-Weinberg proportions were also considered. All the loci except MCW222 and MCW165 showed deviations from Hardy-Weinberg equilibrium (p<0.005). Some of micro satellite sites were highly polymorphic, so they were effective markers for genetic diversity analysis. These results could provide basic molecular data for the research on the germplasm characteristics of Mazandaran native chickens.

Genetic Differences Between Two Wild and One Farmed Population of Atlantic Salmon (Salmo salar) Revealed by Three Classes of Genetic Markers

Mjelnerad, I. B., Refseth, U. H., Karlsen, E., Balstad, T., Jakobsen, K. S. and Hindar, K. 1997. Genetic differences between two wild and one farmed population of Atlantic salmon (Salmo salar) revealed by three classes of genetic markers. Hereditas 127: 239-248. Lund, Sweden. ISSN 0018-0661. Received April 7, 1997. Accepted August 21, 1997 Genetic diversity within and between two wild and one farmed population of Atlantic salmon was estimated by 12 variable enzyme loci, three single locus- and one multilocus DNA minisatellite probe. The farmed salmon were fifth-generation fish from one of the principal commercial strains in Norway and the wild salmon were from the rivers Numedalslagen and Tana, Norway. All three classes of markers detected significant differentiation between the populations, with the farmed population being genetically most divergent. The farmed fish showed less genetic variability than the wild populations, as all techniques revealed a lower (14 %-45 %) number of variable bands/alleles in this group. However, only multilocus DNA fingerprinting detected a significantly lower level of heterozygosity within the farmed population. Estimates of average heterozygosity within populations were almost identical for single locus and multilocus minisatellites (0.558 and 0.548, respectively), which were more than three times higher than for polymorphic allozymes (0.162). Estimates of interpopulation genetic differentiation, however, gave highly concordant results between the allozymes and minisatellites (Fst range: 0.106-0.135). Our results show that fifth generation farmed Atlantic salmon differ significantly from wild salmon in loci others than those chosen for selection in the breeding program. The study also suggests that the choice of genetic markers for studies of Atlantic salmon depends on the aim of the study (within- versus between-population variability).

Genetic Redundancy and Diversity among ‘Orange’ Accessions in the U.S. National Sorghum Collection as Assessed with Simple Sequence Repeat (SSR) Markers

Plant genetic resources conservation is a challenge based on the need to balance acquisition priorities with the constrained level of financial support that is dedicated to long‐term maintenance of collections. As such, understanding how variation is partitioned among accessions is essential for effective management. It is generally recognized that most large collections exhibit varying levels of genetic redundancy. To address this issue, all of the sorghum [Sorghum color (L.) Moench] accessions identified as ‘Orange’ presently maintained by the U.S. National Plant Germplasm System (NPGS) were assayed with 15 simple sequence repeat (SSR) markers. Genotyping was performed with fluorescent primers with five primer sets in each of three multiplex polymerase chain reactions (PCRs) and automated allele sizing. A total of 96 individuals were analyzed, five plants from each of 19 Orange accessions and one individual from an elite inbred line, ‘RTx430’. The SSR markers provided substantial genetic resolution among the Orange entries. Average heterozygosity estimates were low, and phenetic analyses (neighbor‐joining dendograms) were generally consistent with known historical relationships among accessions. Most accessions were genetically distinct, but two redundant groups (involving a total of five entries) were found among the 19 Orange accessions evaluated. The molecular variance analysis (AMOVA) showed that 90% of the total genetic variation was partitioned among accessions, while one‐tenth of the variation resulted from genetic differences between individual plants within accessions. The variance analysis also indicated that it should be possible to reduce the number of Orange accessions held by NPGS by almost half without seriously jeopardizing the overall amount of genetic variation contained in these holdings. This study demonstrated that a limited number of $SR markers can be used in a cost‐efficient manner to rapidly assess variation in accessions of Orange sorghum.

Simple sequence repeat (SSR) polymorphisms for colony management and population genetics in rhesus macaques (Macaca mulatta).

Cross-species amplification of 72 SSR (predominantly tetranucleotide) loci from the DNA of six rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Thirteen of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these six samples and which exhibited Mendelian properties, were also used to amplify SSR loci for 176 male rhesus macaques that are founders of six different captive breeding colonies. These include four groups of macaques originating in India and one group of macaques each that originated in China and Thailand. Gene diversity based on the SSR loci provided a reliable estimate of average heterozygosity but was between two and four times higher than that for 9 protein coding loci. Based on the SSR loci, Chinese rhesus were more genetically diverse and unique than were rhesus from India or Thailand, a conclusion not consistent with data based on protein coding loci. The six most informative SSR loci are unlinked and provide probabilities of single parent exclusion and genetic identity exceeding 0.99 and one in one million, respectively, both of which are reasonable standards for colony management purposes.

Temporal Stability of Nuclear Gene (Allozyme) and Mitochondrial DNA Genotypes among Red Drums from the Gulf of Mexico

Abstract Allelic variation in nine polymorphic nuclear genes and restriction-site variation in mitochondrial DNA (mtDNA) were assayed among 194 adult red drums Sciaenops ocellatus from the northern Gulf of Mexico, Data were combined with those of previous studies in order to examine patterns of temporal genetic variation among four year-classes (1984–1987) and individuals spawned prior to 1984, Tests of heterogeneity among year-classes in both nuclear gene allele frequencies and mtDNA haplotype frequencies were nonsignificant, and estimated fixation (F ST) values were 0.009 (nuclear genes) and 0.002 (mtDNA). Estimates of Nei's unbiased genetic distance (nuclear genes) and nucleotide sequence divergence (mtDNA) among year-classes also indicated the absence of temporal genetic differentiation, Estimates of average heterozygosity (nuclear genes) and nucleon and nucleotide sequence diversities (mtDNA) indicated that levels of genome-wide variation within and among year-classes of red drum are equivalent to (o...

Genetic evidence of population heterogeneity and cryptic speciation in the ommastrephid squid Martialia hyadesi from the Patagonian Shelf and Antarctic Polar Frontal Zone

Horizontal starch gel electrophoresis was used to investigate levels of genetic differentiation between four samples of the nominate squid species Martialia hyadesi Rochbrune and Mabille, 1889, obtained from regions of the Patagonian Shelf and Antarctic Polar Fron-tal Zone over 1000 km apart. M. hyadesi is an ecologically important South Atlantic ommastrephid squid and it is probable that, in the future, fishing effort will be increasingly directed towards this species. Details regarding the population structure of the species are therefore required. In comparison with the other three samples of M. hyadesi, one of the samples from the Patagonian Shelf (PAT 89II) exhibited fixed allelic differences at 16 of the 39 enzyme loci which were resolved (genetic identity, I=0.51). This high level of genetic differentiation contradicts the apparent morphological similarity between samples, indicating the presence of a cryptic or sibling congeneric species. Deviations from Hardy-Weinberg equilibrium and significant differences in allele distribution were also detected within and between the other three putative M. hyadesi samples, suggesting that the species fails to maintain effective panmixia across its geographical range. The occurrence of both temporal (1986 cf. 1989) and geographic structuring within the species complex is consequently indicated, caused possibly by an overlap of reproductively isolated stocks (stock mixing) outside their respective breeding areas. Low levels of genetic variability were detected throughout the samples examined, estimates of average heterozygosity per locus within the two species detected being in the order of 0.01 and 0.002. These values are discussed in relation to levels of genetic variability reported for other squid species, and in comparison with values typically expected for marine invertebrates.

Estimation of heterozygosity for single-probe multilocus DNA fingerprints.

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.

ESTIMATION OF AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE FROM A SMALL NUMBER OF INDIVIDUALS

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.