Quantification Of Genetic Variation Research Articles

Preface: Functional biogeography in Japanese cedar

Preface: Functional biogeography in Japanese cedar

EMPLOYMENT OF DIGITAL PHENOTYPING IN THE SELECTION OF FULLSIBLING FAMILIES OF PASSION FRUIT THROUGH REML/BLUP

Digital phenotyping has been used to measure seed morphological traits, which are applied efficiently in the quantification of genetic diversity. The objective of this work was to estimate the genetic parameters to predict the genetic gain via indexes of selection of the REML/BLUP methodology using morphophysiological traits of seeds of sour passion fruit. Seeds from 98 full sibling families (FSF) were evaluated in a randomized block design with three replications and three plants per plot. Thirteen morphophysiological traits of the seeds were evaluated, and the morphological traits were measured through digital image analysis. The genetic parameters were estimated using the REML/BLUP methodology and the classic, multiplicative and Mulamba and Mock selection indexes were used to rank all individuals, where the 30 best FSFs per index were selected. Genetic variability was observed for the morphophysiological traits of the seeds of complete sibling families of passion fruit, with narrow-sense heritability of high magnitude for the traits of greatest morphophysiological interest tested. All selection indexes provided genetic gains, and the classic index had the greatest gains for the main traits of morphophysiological interest of the seed.

Community genomics: a community-wide perspective on within-species genetic diversity.

Community genomics: a community-wide perspective on within-species genetic diversity.

Parental selection and descriptor evaluation in the identification of superior cowpea genotypes

The objective of this study was to evaluate and quantify the genetic divergence between accessions of cowpea, aiming to identify the characters that most contribute to diversity and select superior parents. Seventy-six cowpea accessions were evaluated using 19 descriptors that were also utilized to estimate genetic diversity using the Shannon-Weaver index. Phenology and production data were analyzed using descriptive statistics and were subjected to Pearson’s correlation test. The descriptors flower color, pod color, and seed brightness showed greater variability in the quantification of genetic diversity. The genotypes Das Almas, Galanjão, selected from CE-13, 7907-Purple Hull and Caupi Branco should be incorporated into cowpea breeding programs as they exhibit desirable agronomic characters. Crossings involving the genotype 7907-Purple Hull with Das Almas and Galanjão are indicated, which could result in obtaining superior genotypes in terms of precocity and grain yield.

Development of microsatellite markers for the predatory mite Phytoseiulus macropilis and cross-amplification in three otherspecies of phytoseiid mites.

Phytoseiid mites are efficient predators of mites and small pest insects. Understanding the dispersion and distribution pattern of phytoseiid mites is essential to promote the conservation of these natural enemies and support their use in biological control. Population genetic studies using molecular markers such as microsatellites have proved to be extremely informative to address questions about population structure and dispersion patterns of predatory mites. The objective of this work was to develop specific microsatellite markers for the predatory mite Phytoseiulus macropilis, aiming at improving field dispersion studies. For this purpose, the genomic DNA was extracted from the whole body of a pool of 260 adult females and used to build the genomic microsatellites-enriched library, using biotinylated probes (CT)8 and (GT)8. In total 26 pairs of primers were synthesized and screened across 30 adult females of P. macropilis for characterization. Seven loci were polymorphic, revealing from two to six alleles per locus. Cross amplifications were successfully obtained in the species Phytoseiulus persimilis, Amblyseius swirskii and Proprioseiopsis sp. The molecular markers obtained are the first developed for P. macropilis-they are effective for the detection and quantification of genetic variation, and show high transferability, thus can be used in genetic and molecular studies of this and other species of the same genus and also of close genera.

RH genotyping by nonspecific quantitative next‐generation sequencing

Conventional sequencing uses gene-specific primers to determine the location of RH variants and permits a qualitative assessment of zygosity. Whole-genome and whole-exome sequencing determine the genetic location of variants and enable a quantitative assessment of zygosity. Nonspecific sequencing uses RH-consensus primers to detect variants and sequencing-read ratios to quantify their copy number. Two hundred seventy eight samples with diverse genotypes were analyzed by next-generation sequencing with RH- consensus primers. Custom-developed data analysis software was used to detect individual variants and infer the RH genotype. The method was evaluated for its quantitative nature, its ability to discriminate similar genotypes, its accuracy to detect variants, and its accuracy to assign them to RHD or RHCE. As a measure of balanced amplification of RHD and RHCE sequences, observed ratio medians deviate from expected ratios by 3% or less of the ratio range. As a measure of discriminatory power, contiguous RHCE / [RHD + RHCE] ratio averages are separated by 4 or more standard deviations of the mean. Variants are detected with a sensitivity and specificity greater than 99%, and variants at consensus positions are correctly assigned to RHD vs RHCE with a sensitivity greater than 72% and a specificity greater than 99%. The method is successful in the identification of genotypes with large conversion events and in the detection of copy number variation. Nonspecific sequencing of homologous gene sets combines detection and quantification of genetic variation in a single assay. Evidence is provided for the quantitative nature of the method, its sensitivity and specificity, and its ability to identify complex RH genotypes.

The genetic characterization of fall armyworm populations in Ecuador and its implications to migration and pest management in the northern regions of South America.

The fall armyworm (Spodoptera frugiperda) is a moth pest native to the Western Hemisphere that has recently become a global problem, invading Africa, Asia, and Australia. The species has a broad host range, long-distance migration capability, and a propensity for the generation of pesticide resistance traits that make it a formidable invasive threat and a difficult pest to control. While fall armyworm migration has been extensively studied in North America, where annual migrations of thousands of kilometers are the norm, migration patterns in South America are less understood. As a first step to address this issue we have been genetically characterizing fall armyworm populations in Ecuador, a country in the northern portion of South America that has not been extensively surveyed for this pest. These studies confirm and extend past findings indicating similarities in the fall armyworm populations from Ecuador, Trinidad-Tobago, Peru, and Bolivia that suggest substantial migratory interactions. Specifically, we found that populations throughout Ecuador are genetically homogeneous, indicating that the Andes mountain range is not a long-term barrier to fall armyworm migration. Quantification of genetic variation in an intron sequence describe patterns of similarity between fall armyworm from different locations in South America with implications for how migration might be occurring. In addition, we unexpectedly found these observations only apply to one subset of fall armyworm (the C-strain), as the other group (R-strain) was not present in Ecuador. The results suggest differences in migration behavior between fall armyworm groups in South America that appear to be related to differences in host plant preferences.

Single‐Nucleotide Polymorphism Discovery and Genetic Variation in YY‐Male and Mixed‐Sex Strains of Nile Tilapia Available in the United States

AbstractThe present study was focused on the discovery of single‐nucleotide polymorphisms (SNPs) and measuring genetic variation in three YY‐male and five mixed‐sex Nile Tilapia Oreochromis niloticus strains, which are available in the United States. We performed restriction site‐associated DNA sequencing for SNP discovery and genotyping. Overall, 31,813 SNPs were identified and used to measure both intra‐ and interstrain genetic variation. Mean expected heterozygosity (He) ranged from a low of 0.084 in the Miami YY strain to a high of 0.222 in the Miami mixed‐sex strain. Two of the three YY groups (Miami YY and Fishgen YY Red) had the lowest He values (0.084 and 0.085, respectively) and the second‐ and third‐lowest observed heterozygosity (Ho) values (both Ho = 0.107). The number of private alleles varied from 90 to 3,795 in different strains and tended to increase with increasing He. Inbreeding, as measured by FIS, was found to be low in all populations, ranging from −0.060 ± 0.004 (mean ± SE) in the Fishgen YY Dark strain to 0.04 ± 0.0093 in the GIFT (Genetically Improved Farmed Tilapia) strain; this indicates that the analyzed strains are currently being maintained with approximately random mating of individuals. Genetic differentiation between populations, as measured by pairwise FST, ranged from little differentiation (FST = 0.06 for the Ismailia Canal and GIFT strains) to strong differentiation (FST = 0.32 for the Miami YY and Lake Manzala strains). The discovered SNPs and quantification of genetic variation can be used for parentage determination and high‐throughput pedigree reconstruction as well as for determining the optimal interstrain crosses to achieve heterosis.

Somatic hybridization provides segregating populations for the identification of causative mutations in sterile mutants of the moss Physcomitrella patens.

Forward genetics is now straightforward in the moss Physcomitrella patens, and large mutant populations can be screened relatively easily. However, perturbation of development before the formation of gametes currently leaves no route to gene discovery. Somatic hybridization has previously been used to rescue sterile mutants and to assign P.patens mutations to complementation groups, but the cellular basis of the fusion process could not be monitored, and there was no tractable way to identify causative mutations. Here we use fluorescently tagged lines to generate somatic hybrids between Gransden (Gd) and Villersexel (Vx) strains of P.patens, and show that hybridization produces fertile diploid gametophytes that form phenotypically normal tetraploid sporophytes. Quantification of genetic variation between the two parental strains reveals single nucleotide polymorphisms at a frequency of 1/286bp. Given that the genetic distinction between Gd and Vx strains exceeds that found between pairs of strains that are commonly used for genetic mapping in other plant species, the spore populations derived from hybrid sporophytes provide suitable material for bulk segregant analysis and gene identification by genome sequencing.

First microsatellite markers for Paspalum plicatulum (Poaceae) characterization and cross-amplification in different Paspalum species of the Plicatula group.

Background Paspalum plicatulum is a perennial rhizomatous grass with natural diploid and polyploid cytotypes. It is a member of Plicatula, which has historically been recognized as a highly complex group containing species of ecological, ornamental and forage importance. The complex nature of the P. plicatulum genome makes it a challenging species for genetic research. This study aimed to develop and characterize microsatellite molecular markers in P. plicatulum and to evaluate their transferability to other Plicatula group species.FindingsMicrosatellite sequences were identified from three enriched libraries from P. plicatulum. Specific primers were designed, and 25 displayed polymorphism when screened across 48 polyploid Paspalum spp. genotypes. The number of bands per locus ranged from 2 to 17, with a mean of 8.65. Private bands for each species were identified; the highest number of private bands was observed for P. plicatulum in 52% of the loci analyzed. The mean polymorphism information content of all loci was 0.69, and the mean discriminatory power was 0.82. Microsatellite markers were satisfactorily cross-amplified for the eight tested Plicatula-group Paspalum species, with P. atratum exhibiting the highest transferability rate (89.86%). STRUCTURE and Discriminant Analysis of Principal Components separated accessions into three groups but did not reveal separation of the accessions according to species.ConclusionsThis study describes the first microsatellite markers in P. plicatulum, which are polymorphic, efficient for the detection and quantification of genetic variation, and show high transferability into other species of the Plicatula group. This set of markers can be used in future genetic and molecular studies necessary for the proper development of conservation and breeding programs. Private bands within the markers can be used to assist in species identification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2312-z) contains supplementary material, which is available to authorized users.

Diversity and spatial genetic structure of a natural population of Theobroma speciosum (Malvaceae) in the Brazilian Amazon

The quantification of genetic diversity and intrapopulation spatial genetic structure (SGS) of tree species are important aspects for in and ex situ conservation practices. In this study we seek to understand the importance of conservation areas by quantifying the genetic diversity and the spatial genetic structure of a natural population of Theobroma speciosum. Within this population, 49 adults and 51 subadults were genotyped for five microsatellite loci. The results showed that adults and subadults have similar levels of genetic diversity and inbreeding (adults: A= 10.4, Ae = 10.3, F= 0.68, subadults: A= 10.6, Ae= 10.6, F= 0.57). Genetic diversity was spatially structured within the population, and the results suggest that near-neighbor trees up to a distance of 70 m are likely related. SGS is likely the result of short-distance seed dispersal, the short-distance range of pollinators, and infrequent breaches of the self-incompatible mating system. Considering the high demographic density of the species and size of the study area, as well as the high average number of alleles per locus and the presence of rare alleles, we believe that the study population is an excellent resource for in situ genetic conservation of T. speciosum. The study area is also a useful resource for collecting germplasm for ex situ conservation and seed collection, either for breeding programs used in the restoration of degraded areas or forest improvement.

Using Whole Exome Sequencing to Identify Genetic Variation and Polymorphisms Associated with Graft Versus Host Disease in Allogeneic Stem Cell Transplant Recipients

Objective: Allogeneic stem cell transplant (ASCT) is a potentially curative treatment for many hematologic malignancies. HLA match is the principal factor in donor selection but the total antigenic landscape as seen by the donor immune cells extends beyond the HLA and minor HLA antigens. Thus, despite "perfect" HLA match graft versus host disease (GVHD) caused by alloreactive donor immune cells reacting to disparate antigens in the recipient, remains a significant cause of morbidity and mortality. Whole exome sequencing (WES) which assays all the protein coding nucleotide sequences provides a powerful means to assess the entire antigenic makeup of the individual. We examined the WES of sibling donor-recipient pairs undergoing BMT to assess the influence of the extent of genetic disparity and specific gene polymorphisms on GVHD.Methods: Sixteen matched sibling donor-recipient pairs receiving allogeneic stem cell transplants between June 2008 and April 2013 had samples available for retrospective WES. Transplant data including conditioning regimen, age of donor and recipient at the time of transplant, development and type of GVHD and cause of death were recorded. The sequencing was performed using Illumina HiSeq2000 and the single nucleotide variants (SNVs) and small insertions and deletions (INDELs) were identified using the haplotype caller within the Genome Analysis Toolkit GATK v2.7. Functional variants including non-synonymous, frame-shift, truncating, and splice site SNVs and INDELs identified were compared between donor and recipient and among those with GVHD and those without GVHD (non-GVHD). One-sided Fisher's exact test was used to determine the statistical significance of the SNPs in GVHD and non-GVHD. Candidate genes with a p value of <0.05 were further evaluated for their biochemical pathway and possible role in inflammatory or immune responses.Results: Nine of 16 patients had a diagnosis of AML or high grade myelodysplastic syndrome, 3 had a diagnosis of non- Hodgkin lymphoma, 1 had Hodgkin lymphoma, 1 had multiple myeloma, and 2 had CML. Six patients were conditioned with a myeloablative regimen, others with a reduced intensity conditioning regimen. Eight of 16 patients were female and 7 of 16 donors were female. Nine of 16 patients developed stage II-IV acute and/or chronic GVHD with 7 of them developing GVHD of the skin. A total of 12,623 genes with 43,670 functional variants were identified using WES. 134 genes had a p value < 0.05 and enrichment analysis was performed on these genes. 12 out of 134 genes were associated with gene ontology (GO) term "immune system development" with an unadjusted enrichment p-value 0.0015. Three (IL31RA, OSMR, SIRPA) out of 134 genes were associated with "inflammation_Jak-STAT pathway" with an adjusted enrichment p-value 0.07. Variants of IL31RA, OSMR, and PTX3 were identified as genes with polymorphisms associated with GVHD (p= 0.003, 0.01, and 0.01, respectively) with 5 variants identified in IL31RA, 7 variants in OSMR, and 2 variants in PTX3. Further investigation of these three genes revealed their role in inflammatory or immune responses.Discussion: GVHD is a cytokine mediated immune-inflammatory process that can occur despite "perfect" HLA matching. WES identified the extensive genetic variability between donors and recipients implying large allo-reactivity potential that can lead to GVHD. Quantification of genetic variation may allow for more precise determination of GVHD risk and better selection of donors. In our cohort, WES identified polymorphisms in IL31RA, OSMR, and PTX3 as statistically significantly associated with development of GVHD. The protein products of these three genes have each been shown to be involved in inflammatory processes and are influenced by other cytokines. IL31RA and OSMR are found in many tissues including the skin and lungs. They function both independently and as a heterodimer receptor capable of binding multiple cytokines including IL-31, IL-6, and TNF-α. PTX3 is a reactive protein that increases in response to cytokine release related to systemic inflammation. Levels of this protein have been used as a prognostic marker in many disease processes with high levels correlating with poor outcomes. The small sample size of our cohort precludes any firm conclusions but provides promising hypotheses for further evaluation in larger studies. DisclosuresNo relevant conflicts of interest to declare.

Wheat in the Mediterranean revisited--tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers.

BackgroundSingle Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat.ResultsWe genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspecies, except for durum and rivet that are not separable. A more detailed population structure of durum landraces could be obtained than with SSR markers. The results also suggest an emmer, rather than durum, ancestry of bread wheat and with gene flow from wild emmer.ConclusionsSNP markers developed for elite cultivars show great potential for inferring population structure and can address evolutionary questions in landrace wheat. Issues of marker genome specificity and mapping need, however, to be addressed. Ascertainment bias does not seem to interfere with the ability of a SNP marker system developed for elite bread wheat accessions to detect population structure in other types of wheat.

Landscape genetics in mammals

AbstractThe focus of this review is on landscape genetics (LG), a relatively new discipline that arose approximately 10 years ago. LG spans the interface between population genetics and landscape ecology and thus incorporates the concepts, methods, and tools from both disciplines. On the basis of an understanding of the spatial distribution of genetic diversity, LG aims to explain how landscape and environmental characteristics influence microevolutionary processes and metapopulation dynamics, including gene flow (i.e., connectivity) and selection (i.e., local adaptations). LG is concerned with events that occurred during the recent time scale, and the individual is the operational unit. As a discipline that combines spatial genetic diversity with ecological features, LG is able to address questions relating to different evolutionary processes. We illustrate some of these here using examples taken from mammals: population structure; gene flow and the identification of barriers; fragmentation, connectivity, and corridors; local adaptation and selection; there are two different questions: applications in conservation genetics; and future developments in LG. We will then present the methods and tools commonly used in the different steps of LG analyses: the genetic and landscape sampling, the quantification of genetic variation, the characterization of spatial landscape structures, and finally, the correlation between genetic patterns and landscape features.

Isolation and characterization of polymorphic microsatellite loci in the mahseer Neolissochilus soroides (Teleostei: Cyprinidae) from Khao Soi Dao population in Thailand

Habitat fragmentation and anthropogenic activities have caused changes to many fishes, such as Neolissochilus soroides in protected areas despite of its abundance. Therefore, it would be interesting to observe the changes in behavior and genetics of this species at fine scale. Quantification of genetic diversity in N. soroides using primers from related species was not successful. Therefore, new microsatellite loci were developed. The number of alleles per locus ranged from 3 to 17 with an average of 8.21 alleles per locus. Significant linkage disequilibrium was not observed. Deviation from Hardy–Weinberg equilibrium was observed at several loci, which coincided with the detection of recent bottleneck of this population.

AFLP analysis of genetic diversity within and between populations of perennial ryegrass (Lolium perenne L.)

Amplified fragment length polymorphism (AFLP) analysis has been used to measure genetic diversity in perennial ryegrass (Lolium perenne L.) and to relate intra- and interpopulation variation to breeding history. Cluster analysis of AFLP data from contrasting populations showed features consistent with the origins of these varieties. Significant differences in intrapopulation diversity were detected and partial separation of different cultivars was observed. Restricted base cultivars, derived from small numbers of foundation clones, were suitable for this type of study, allowing near complete discrimination of closely related cultivars. Analysis of bulked samples was based on the pooling of genomic DNA from 20 individuals from 6 selected populations. Cluster analysis of AFLP data from bulked samples produced a phenogram showing relationships consistent with the results of individual analysis. AFLP profiling provides an important tool for the detection and quantification of genetic variation in perennial ryegrass.

Quantification of genetic diversity at allozyme loci

L'electrophorese sur gel d'amidon constitue une methode puissante et economiquement abordable pour estimer la variabilite genetique des especes vegetales et de leurs populations. Les loci d'alloenzymes representent des caracteres typiquement monogeniques, qui se recombinent de facon independante et affichent des alleles co-dominants. Des tailles d'echantillon variant de 30-50 individus analyses pour 10-20 loci polymorphes s'averent suffisantes pour caracteriser de facon adequate la diversite genetique d'une population et evaluer comment la diversite genetique se repartit parmi les populations. Les parametres qui devraient etre utilises sont le pourcentage de loci polymorphes (P), le nombre moyen d'alleles par locus polymorphe (AP), l'heterozygotie theorique (diversite genetique, H c ), la valeur G ST de Nei, l'identite genetique (I) et la distance genetique (D). Les auteurs presentent des exemples, en plus de faire un sommaire des tests qui permettent d'evaluer la confiance statistique des estimations de parametres.

Quantification of genetic diversity at allozyme loci

Quantification of genetic diversity at allozyme loci