Percentage Of Genetic Variance Research Articles

Morphological differences yet genetic similarity among seasonal cohorts of Japanese anchovy during the early life stages in the Kii Channel

Abstract Species in the genus Engraulis show extensive intraspecific as well as interspecific morphological and genetic diversity. Since morphological differences do not necessarily correspond to genetic differences, it is necessary to clarify the relationship between morphological differences and genetic differences for a better understanding of the population structure. Fish morphology at a given standard length differs between cohorts of Japanese anchovy Engraulis japonicus during the early life stages in the Kii Channel, but it is unknown whether the differences are caused by genetic differences or not. The Kii Channel includes the boundary between the Pacific (southern side of the Kii Channel) and the Seto Inland Sea stocks (northern side), but stock separation is based primarily on demographic characteristics. In the present study, genetic analyses were conducted to examine the genetic differences among samples (month and area) based on mitochondrial DNA cytochrome b region (Cyt b), control region (CR) and microsatellite markers. AMOVA revealed that the percentage of genetic variation among samples was low at 0.11% for Cyt b, 0.30% for CR and 0.00% for microsatellite, and no significant genetic variation was observed among samples. Although two clades were identified in the unrooted neighbour-joining tree for Cyt b and CR, both Cyt b and CR sequences were similar between months and between areas. Accordingly, the morphological differences among cohorts can be attributed to phenotypic plasticity. Additionally, there were no genetic differences between samples from the southern side and the northern side of the Kii Channel, suggesting strong genetic connectivity in these areas.

Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species.

Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

GENETIC DIVERSITY ESTIMATION AMONG THIRTEEN LATE MATURING MANGO VARIETIES USING SSR MARKERS

Genetic diversity estimation of 13 varieties of mango was assessed using 28 microsatellite markers. Mean values of 3.9231, 0.4455, 0.5407 and 0.4952 were observed for alleles, minor alleles frequency, gene diversity and polymorphic information content respectively. The observed heterozygosity value of YY implies that spontaneous hybridization may have contributed to the ancestry of some genotypes and that improvement by farmers may have possibly been by selection of somatic mutants. The dendrogram of the cluster analysis revealed three groups. Findings demonstrated the efficiency of SSR markers in distinguishing closely related mango varieties due to their high specificity. The study contributes to the understanding of the genetic organization of the mango germplasm. Nonetheless, fifteen SSR markers were used in thirteen exotic mango varieties to calculate polymorphism percentage, genetic diversity, frequency based genetic distances, genetic diversity percentage, allelic frequencies and PIC values. Polymorphism percentage recorded was 76.48%. Moreover, varietal similarity index of genome helped to construct phylogenetic tree that divided all varieties into three clusters according to their genetic similarities. First cluster that exhibited similarity in genetic consonance included varieties viz. Collector, Haden, Zill, Early gold and Pope. Two varieties i.e. Momi-k and Spring Fells were similar to each other genetically. Similarly, third cluster encapsulated Kensington Pride, Tomi-Atkin, Keitt, Maya and Sensation cultivars in genetic harmony.

Genetic diversity of redclaw crayfish Cherax quadricarinatus von Martens 1868 using 16S mitochondrial DNA marker

There have been reported around 11 aquatic invasive alien species (IAS) found in Malaysian waters. Cherax quadricarinatus, or commonly known as Australian redclaw crayfish, is one of the invasive species. C. quadricarinatus has the potential of causing negative impacts ecologically and economically in the local environment as it has reported in several countries if they get established and not monitored properly. Habitat alteration, native species depletion and spreading of diseases are among the reported negative impacts of C. quadricarinatus. This study was conducted with the aim to assess the genetic diversity of C. quadricarinatus from 4 different populations. Uncovering the diversity and population structure of the redclaw crayfish will help in enhancing the understanding of adaptation and survival of C. quadricarinatus. Thus, the information can be used in monitoring and management of this invasive crayfish in future. DNA of C. quadricarinatus was successfully extracted from its tissue and amplified via polymerase chain reaction (PCR) using mitochondrial DNA (mtDNA) 16S gene then proceeded for sequencing and analysed using several genetic analysis software to understand the diversity, phylogeny and population structure of this invasive crayfish species. A total of 493 bp fragments of 32 samples from four sampling sites were obtained. Four haplotypes were observed which Hap-1 was the most common haplotype. The highest genetic variation is Selangor (Pi = 0.00248, Hd = 0.694). However, low levels of both haplotype and nucleotide diversity indicates the loss of genetic diversity. Analysis of molecular variance (AMOVA) results revealed that the percentage of genetic variation within the population was 69.58% while among populations was 30.42%, indicating significant genetic differentiation among population (P < 0.05). The maximum likelihood tree showed that all haplotypes were clustered and grouped together with United States, Czech Republic, China and Australia.

Characterization of yeast population from unstudied natural sources in La Mancha region.

This study aims to identify the yeast species and strains which entitled an unstudied area of Spain and evaluate the yeast species diversity richness and the genetic variety. A total of 702 yeasts were isolated from different environments in a central Spanish region (La Mancha) with diverse sources of origin (food, animals, flowers and environmental sources) during spring season. Thanks to the analysis carried out by the PCR-RFLP technique and sequencing, 35 species were identified. A neighbour-joining phylogenetic tree was created based on D1/D2 sequences. Moreover 330 strains were determined by PCR-RAPD and their profiles were analysed using the bioinformatics programme BioNumerics 7·6. The Simpson's index (D) and the genetic diversity percentage were calculated with the aim of studying the richness of the species in each environment and the genetic variety in each species. This study has permitted to know that the majority of the species found was Diutina rugosa while the most ubiquitous was Rhodotorula mucilaginosa which expose the dispersion capability of this species. The diversity parameters has revealed that the highest species richness was associated to environmental samples and the highest genetic variety was presented in those species with better dispersion capability or a smaller number of isolates. This study permits to better understand the yeast communities in La Mancha region which gives a value the microbial potential of this region.

Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms

BackgroundIt becomes clear that the increase in the density of marker panels and even the use of sequence data didn’t result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (RM) or variance component (VC) approaches. This is in part due to the limitations of current methods. Association model are well over-parameterized and suffer from severe co-linearity and lack of statistical power. Even when the variant effects are not directly estimated using VC based approaches, the genomic relationships didn’t improve after the marker density exceeded a certain threshold. SNP prioritization-based fixation index (FST) scores were used to track the majority of significant QTL and to reduce the dimensionality of the association model.ResultsTwo populations with average LD between adjacent markers of 0.3 (P1) and 0.7 (P2) were simulated. In both populations, the genomic data consisted of 400 K SNP markers distributed on 10 chromosomes. The density of simulated genomic data mimics roughly 1.2 million SNP markers in the bovine genome. The genomic relationship matrix (G) was calculated for each set of selected SNPs based on their FST score and similar numbers of SNPs were selected randomly for comparison. Using all 400 K SNPs, 46% of the off-diagonal elements (OD) were between − 0.01 and 0.01. The same portion was 31, 23 and 16% when 80 K, 40 K and 20 K SNPs were selected based on FST scores. For randomly selected 20 K SNP subsets, around 33% of the OD fell within the same range. Genomic similarity computed using SNPs selected based on FST scores was always higher than using the same number of SNPs selected randomly. Maximum accuracies of 0.741 and 0.828 were achieved when 20 and 10 K SNPs were selected based on FST scores in P1 and P2, respectively.ConclusionsGenomic similarity could be maximized by the decrease in the number of selected SNPs, but it also leads to a decrease in the percentage of genetic variation explained by the selected markers. Finding the balance between these two parameters could optimize the accuracy of GS in the presence of high density marker panels.

Genome Association Study for Visual Scores in Nellore Cattle Measured at Weaning

BackgroundGenome-wide association studies (GWAS) are utilized in cattle to identify regions or genetic variants associated with phenotypes of interest, and thus, to identify design strategies that allow for the increase of the frequency of favorable alleles. Visual scores are important traits of cattle production in Brazil because they are utilized as selection criteria, helping to choose more harmonious animals. Despite its importance, there are still no studies on the genome association for these traits. This study aimed to identify genome regions associated with the traits of conformation, precocity and muscling, based on a visual score measured at weaning.ResultsBayesian approaches with BayesC and Bayesian LASSO were utilized with 2873 phenotypes of Nellore cattle for a GWAS. The animals were genotyped with Illumina BovineHD BeadChip, and a total of 309,865 SNPs were utilized after quality control. In the analyses, phenotype and deregressed breeding values were utilized as dependent variables; a threshold model was utilized for the former and a linear model for the latter. The association criterion was the percentage of genetic variance explained by SNPs found in 1 Mb-long windows. The Bayesian approach BayesC was better adjusted to the data because it could explain a larger phenotypic variance for both dependent variables.ConclusionsThere were no large effects for the visual scores, indicating that they have a polygenic nature; however, regions in chromosomes 1, 3, 5, 7, 14, 15, 16, 19, 20 and 23 were identified and explained a large part of the genetic variance.

Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation

Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria’s largest Berber groups.Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria.Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups.Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity.Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.

Population structure, morphological and genetic diversity within and among melon (Cucumis melo L.) landraces in Iran.

ISSR markers were applied to evaluate the genetic diversity and differentiation of 270 individuals of 27 Iranian C. melo landraces of various varietal groups include vars. inodorous, cantalupensis, reticulatus, ameri, dudaim. Genetic diversity among the studied genotypes obtained by GeneAlex analysis (H = 0.08, I = 0.12, Na = 0.77, PPL = 22.6%). Cluster analysis divided Iranian melon landraces into two main cluster. Non-sweet genotype (dudaim group) was well separated from sweet genotypes (inodorous, ameri, reticulatus, cantalupensis). The most similar genotypes were BANI and TONI (0.95) and the most dissimilar ones were GER and TS (0.58). AMOVA result showed that the percentage of genetic variation among and within Iranian melon is 69% and 31%, respectively. All landraces evaluated based on 10 morphological traits which revealed the diversity of melon varietal groups. Bayesian analysis assigned ten landraces to Pop 1, eight landraces to Pop 2 and nine melon landraces to Pop 3. Bayesian and UPGMA cluster analyses demonstrated the almost related results. Our results indicated that ISSR markers technique alongside polyacrylamide gel analysis could be helpful to discriminate varieties of melon.

Assessment of genetic diversity for quantitative traits in sunflower germplasm

Evaluating genetic diversity in germplasm resources is a prerequisite for any effective breeding program. In this context, an investigation was carried out for analyzing genetic diversity in a set of 18 sunflower lines, which were grown at Oilseeds Section, Agriculture Research Institute, Tandojam, Sindh, Pakistan. Results demonstrated that mean squares were highly significantly different (P< 0.01) for days to flowering, days to maturity, plant height, head diameter, seeds head-1, seed index and grain yield plant-1. It represents that studied sunflower germplasm tend to have useful genetic resources for further breeding programs. In respect to genetic distance, a number of pairs were identified, which possess wide as well as narrow genetic distance; hence these pairs may be utilized for heterosis and backcross breeding purpose, respectively. Principal component analysis depicted that first three components showed a very high percentage of genetic variance (91.60%), indicating a great amount of genetic diversity in studied germplasm. Considering cluster analysis, diverse parents have also been identified through different clusters, signifying their importance for upcoming hybridization programs in sunflower. Keywords: Genetic diversity; Sunflower; Cluster analysis; Quantitative traits http://dx.doi.org/10.19045/bspab.2017.60022

Interspecific genetic analysis of orchids in Brazil using molecular markers

Several species of Orchidaceae, one of the largest plant families, are considered endangered throughout South America and legal protection policies are needed so they can be preserved. Inter simple sequence repeats (ISSRs) markers are a potential tool to be used in the phylogenetic reconstruction of closely related species. In this study, we evaluate the polymorphic information content (PIC) and optimum number of ISSR markers (ONM) for five Laeliinae orchids in order to assess genetic diversity. The phylogenetic relationships between Cattleya granulosa, an endangered Brazilian orchid, and four other native Brazilian species (Brassavola tuberculata, Cattleya bicolor, Cattleya labiata and Cattleya schofieldiana) were analyzed for genetic diversity and differentiation. The 11 selected primers generated 166 unambiguous loci (PIC = 0.354; ONM = 156). Of the five studied species, C. bicolor exhibited the highest level of genetic diversity (H E = 0.219), while C. labiata exhibited the lowest level (H E = 0.132). The percentage of genetic variation among species (analysis of molecular variance) was 23.26 %. The principal component analysis (PCA) of ISSR data showed that unifoliate and bifoliolate species are genetically divergent. Additionally, PCA indicated a close relation between C. granulosa and C. schofieldiana, a species considered to be a variety of C. granulosa by many researchers. Thus, we conclude that ISSR genetic markers are effective in detecting genetic differentiation among orchid species.

Genomewide Selection when Major Genes Are Known

ABSTRACTCurrent methods for genomewide selection do not distinguish between known major genes and random genomewide markers. My objectives were to determine if explicitly modeling the effects of known major genes affects the response to genomewide selection, and to identify situations in which considering major genes as having fixed effects is helpful. Simulation experiments showed that having a fixed effect for a major gene became more advantageous as the percentage of genetic variance (VG) explained by a major gene (R2) increased and as the heritability on an entry‐mean basis (h2) increased. With R2 = 50% and h2 = 0.80, the relative efficiency (based on selection gains in Cycle 4) with a major gene having a fixed versus random effect was 112–121%. Specifying a fixed effect for a single major gene was never disadvantageous except with R2 &lt; 10%. With h2 ≥ 0.50, specifying a fixed versus random effect for a single major gene had little effect on prediction accuracy in Cycle 0. However, prediction accuracy in later cycles declined more rapidly when a major gene had a random effect instead of a fixed effect. The results with L = 2 or 3 major genes were similar to those with one major gene. In contrast, the usefulness of gene information was low with L = 10 major genes. Overall, major genes should be fitted as having fixed effects in genomewide selection when only a few major genes are present and each major gene accounts for ≥10% of VG.

Variasi Genetik Spesies Mangrove Ceriops tagal berdasarkan Marka RAPD

Ceriops tagal are found at Segara Anakan Cilacap, Baluran National Park and Karimunjawa National Park. Information on the genetic diversity can be used for conservation policy. Genetic variation of C. tagal were analysed by using Random Amplified Polymorphic DNA (RAPD). This study aims to determine the genetic variation in each population and between populations C. tagal based on RAPD markers. The total DNA was extracted with CTAB extraction method. Amplification was performed using 10 primer (OPA-3, OPA-10, OPB-1, OPB-6, OPB-7, OPB-8, OPB-10, OPB-12, OPB-17 and OPB-18). Amplification includes pradenaturation at 94°C for 5 min, followed by 45 cycles of denaturation at 94°C for min, primer annealing at 37°C for min, and primer elongation on 72°C for min 30 sec, final extension at 72°C for 5 min and ends with holding at 4°C for min. The analysis was done by changing the pattern of fragments to binary data (for bands appear = 1 and for bands do not appear = 0). It is done using a program GenAlEx 2.1 and NTSYS-PC 6.1. A population that has the highest genetic variation ( h ) was Segara Anakan (0.308), followed by Baluran (0.295) and Karimunjawa (0.123). Baluran has the highest polymorphism (75.00%), Segara Anakan 69.23%, while Karimunjawa was 30.77%. The results of AMOVA, showed that the percentage of genetic variation within populations is greater (77%) than among populations (23%). The results of PCA analysis showed a similar pattern of genetic distance and UPGMA. Samples of Karimunjawa clustered with samples of the population, SA1 and SA3 likely close to the sample of Karimunjawa and SA2 are likely not one group with another sample of the Segara Anakan. Results of mantel test, the value of r = 0.347 and p = 0.02.

Analysis of genetic diversity among wild bermudagrass germplasm from southwest China using SSR markers

Fifty-five wild accessions of bermudagrass (Cynodon dactylon) were collected from southwest China (Sichuan, Chongqing, Yunnan, Guizhou, and Tibet), and their genetic diversity was analyzed using simple sequence repeat markers. A total of 267 polymorphic bands were detected with 18 primer combinations. The genetic similarity among the accessions ranged from 0.688 to 0.894 with an average of 0.797. All 55 wild accessions were clustered into 7 eco-geographic groups. Our data showed that the dendrogram was almost in accordance with geographic distribution, and accessions from the same collection sites tended to be clustered into the same group. A genetic differentiation analysis revealed that the percentage of genetic variance was 70.07 and 29.93% within and among groups, respectively. Finally, we discuss the implications of these results for C. dactylon in southwest China.

Genetic variability and differentiation of Caragana microphylla populations as revealed by RAPD markers

Genetic variability in random amplified polymorphic DNA (RAPD) was studied in 90 individuals of Caragana microphylla, an outcrossing perennial shrub species, from five natural populations sampled in Inner Mongolia steppe of China on a small scale. Nineteen selected primers were used to amplify DNA samples, and totally 225 bands were detected. The percentage of polymorphic bands within populations ranged form 58.22% to 63.56%, with an average of 60% at the population level and 71.11% at the species level, indicating relatively high genetic variations in C. microphylla species. Shannon's information index (I) and Nei's gene diversity (h) showed the similar trend with each other. According to the analysis of Nei's gene diversity, the percentage of genetic variation among populations was 7.13%, indicating a low level of genetic differentiation among populations. There existed a strong gene flow (Nm = 3.26) among populations. Although AMOVA analysis also revealed most variation was within populations (phi(ST) = 4.1%), a significant proportion was observed among populations (P<0.001) in the present study, suggesting genetic differentiation occurred among populations at a certain extent. Based on Mantel's tests and the results of previous studies, the genetic structure pattern of C. microphylla accorded with the isolation-by-distance model on a very large scale, however, on a small scale, the significant genetic differentiation among populations might be enhanced by the micro-environmental divergence among the sampling sites, rather than by geographic factors. Analysis of the genetic variations of C. microphylla populations provided useful information for the adaptive strategy of Caragana species.

Analysis of genetic factors that control shoot mineral concentrations in rapeseed (Brassica napus) in different boron environments

Mineral nutrients are essential for plant cell function, and understanding the genetic and physiological basis of mineral concentration is therefore important for the development of nutrient-efficient crop varieties that can cope with a shortage of mineral resources. In the present study, we investigated the profiles of B, Ca, Fe, Cu, Mg, P and Zn concentrations in shoots and analyzed the genetic variation in a rapeseed (Brassica napus) double haploid population at normal and deficient boron (B) levels in hydroponic conditions. Significant correlations between the concentrations of different minerals, such as Ca and Mg, Ca and P, and Cu and Fe, existed in both B environments. A total of 35 quantitative trait loci (QTL) and 74 epistatic interaction pairs for mineral concentrations were identified by whole genome analysis of QTL and epistatic interactions. The individual phenotypic contributions of the QTL ranged from 4.4% to 19.0%, and the total percentage of genetic variance that was due to QTL and epistatic interactions varied from 10.4% to 82.4%. Most of these QTL corresponded specifically to one of the two B conditions except for one stable main-effect P-QTL across the B environments. Three QTL for Ca and Mg were found to co-localize under normal B condition. These results revealed that genetic factors control mineral homeostasis in plants and multigenes involving ion transport are required to regulate mineral balance in plants under conditions of diverse nutrient stress. In addition, 26 genes involved in ion uptake and transport in Arabidopsis thaliana were in silico mapped onto the QTL intervals of B. napus by comparative genomic analysis. These candidate orthologous genes in B. napus allowed the selection of genes involved in the controlling mineral concentration that may account for the identified QTL.

Utilisation of genetic variation by marker assisted selection in commercial dairy cattle populations

Potential genetic benefits of marker assisted selection (MAS) were evaluated by calculating selection response resulting from four pathways of selection. Genetic variation was partitioned into polygenic and loci that were in linkage disequilibrium with marker loci or haplotypes. The percentage of genetic variation that was marked was varied from 0 to 100%. These assumptions describe the degree of genetic knowledge that may be available in 10 years. Three breeding strategies with markers were evaluated: progeny test scheme (BMARK); progeny test scheme but unproven bulls allowed on the bull to bull selection path (YBULL); and a breeding programme where cows without lactation information and bulls without progeny information were eligible for selection (OPEN). Rates of genetic gain (per year) with no marked genetic variance were 0.26 σ G for the BMARK and YBULL schemes and 0.28 σ G for the OPEN scheme. On average, an increase of 1% marked genetic variance resulted in an increase in genetic gain of ∼0.25% for the BMARK scheme, 0.5% for the YBULL scheme and 1% for the OPEN scheme. Maximum genetic response (100% marked genetic variance) for the BMARK scheme was 1.24 times that achieved with no marked genetic variance, 1.52 times for the YBULL scheme, and 2.05 times for the OPEN scheme. Changes in the structure of the breeding scheme are needed to fully gain the benefits of identified loci especially for medium to large proportions of marked genetic variance.