Unlinked Markers Research Articles

Marker-assisted introgression improves Striga resistance in an Eritrean Farmer-Preferred Sorghum Variety

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC3F2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC3F3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC3F3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement.

FDR and SDR processes in meiosis and diploid gamete formation in poplars (Populus L.) detected by centromere-associated microsatellite markers

Sexual polyploidisation is one of the appropriate approaches in poplar breeding. Controlled pollinations were carried out with spontaneously formed, as well as induced, 2n gametes. Among the offspring individuals, 36 triploid plants and 1 tetraploid individual were detected by flow cytometry. The parental clones and all polyploid offspring individuals were genotyped by 18 nuclear microsatellite markers. The allelic configurations, especially tri-allelic patterns, and dosage effects were used to recognise diploid contributions of the male or female gamete. Three out of 18 markers localised near the centromeres of linkage groups I, X and XV. They are assumed to be unaffected by crossing over events and, therefore, able to ascertain the mechanism of first division restitution (FDR) or second division restitution (SDR) to generate diploid gametes. The applied three unlinked centromere-associated microsatellite markers allow a very effective determination of FDR resp. SDR processes. Altogether, 21 diploid pollen (10 FDR and 11 SDR) and 13 diploid ovules (1 FDR and 12 SDR) as well as 2 cases of postmeiotic reconstitution were determined with no inconsistency for the three markers. A female hybrid aspen clone (Populus tremula × Populus tremuloides) was assured to be able to frequently spontaneously form diploid ovules by the SDR mechanism. The transferred average heterozygosity in FDR gametes was assessed to be remarkably higher than that in SDR gametes. However, a selective inducement to favour FDR gametes seems not to be feasible with the current thermo-treatment techniques.

The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

The degree of admixture in Brazil between historically isolated populations is complex and geographically variable. Studies differ as to what the genetic and phenotypic consequences of this mixing have been. In Northeastern Brazil, we enrolled 522 residents of Salvador and 620 of Fortaleza whose distributions of self-declared color were comparable to those in the national census. Using the program Structure and principal components analysis there was a clear correlation between biogeographic ancestry and categories of skin color. This correlation with African ancestry was stronger in Salvador (r=0.585; P<0.001) than in Fortaleza (r=0.236; P<0.001). In Fortaleza, although self-declared blacks had a greater proportion of European ancestry, they had more African ancestry than the other categories. When the populations were analyzed without pseudoancestors, as in some studies, the relationship of 'race' to genetic ancestry tended to diffuse or disappear. The inclusion of different African populations also influenced ancestry estimates. The percentage of unlinked ancestry informative markers in linkage disequilibrium, a measure of population structure, was 3-5 times higher in both Brazilian populations than expected by chance. We propose that certain methods, ascertainment bias and population history of the specific populations surveyed can result in failure to demonstrate a correlation between skin color and genetic ancestry. Population structure in Brazil has important implications for genetic studies, but genetic ancestry is irrelevant for how individuals are treated in society, their health, their income or their inclusion. These track more closely with perceived skin color than genetic ancestry.

Extension of the generalized disequilibrium test to polytomous phenotypes and two-locus models.

We extend the usual logistic model between a dichotomous phenotype and an allele count in two ways: a polytomous phenotype with K > 2 levels, and modeling of allele counts at two unlinked marker loci. Inference is based on within-family information to guard against potential bias due to population genetic structure. Score tests of the model coefficients taking into account the correlation between relatives in entire pedigrees are derived as an extension of the Generalized Disequilibrium Test (GDT). Simulations confirm that the tests have the expected statistical properties, and that their power exceeds that of the GDT under a favorable scenario. The score tests are illustrated with candidate genetic markers, a major psychosis phenotype and a cognitive endophenotype in large kindreds from Eastern Quebec.

Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II

Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany.

Multiplex genome editing by natural transformation.

Editing bacterial genomes is an essential tool in research and synthetic biology applications. Here, we describe multiplex genome editing by natural transformation (MuGENT), a method for accelerated evolution based on the cotransformation of unlinked genetic markers in naturally competent microorganisms. We found that natural cotransformation allows scarless genome editing at unprecedented frequencies of ∼50%. Using DNA substrates with randomized nucleotides, we found no evidence for bias during natural cotransformation, indicating that this method can be used for directed evolution studies. Furthermore, we found that natural cotransformation is an effective method for multiplex genome editing. Because MuGENT does not require selection at edited loci in cis, output mutant pools are highly complex, and strains may have any number and combination of the multiplexed genome edits. We demonstrate the utility of this technique in metabolic and phenotypic engineering by optimizing natural transformation in Vibrio cholerae. This was accomplished by combinatorially editing the genome via gene deletions and promoter replacements and by tuning translation initiation of five genes involved in the process of natural competence and transformation. MuGENT allowed for the generation of a complex mutant pool in 1 wk and resulted in the selection of a genetically edited strain with a 30-fold improvement in natural transformation. We also demonstrate the efficacy of this technique in Streptococcus pneumoniae and highlight the potential for MuGENT to be used in multiplex genetic interaction analysis. Thus, MuGENT is a broadly applicable platform for accelerated evolution and genetic interaction studies in diverse naturally competent species.

Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis.

BackgroundGrain size and shape greatly influence grain weight which ultimately enhances grain yield in wheat. Digital imaging (DI) based phenomic characterization can capture the three dimensional variation in grain size and shape than has hitherto been possible. In this study, we report the results from using digital imaging of grain size and shape to understand the relationship among different components of this trait, their contribution to enhance grain weight, and to identify genomic regions (QTLs) controlling grain morphology using genome wide association mapping with high density diversity array technology (DArT) and allele-specific markers.ResultsSignificant positive correlations were observed between grain weight and grain size measurements such as grain length (r = 0.43), width, thickness (r = 0.64) and factor from density (FFD) (r = 0.69). A total of 231 synthetic hexaploid wheats (SHWs) were grouped into five different sub-clusters by Bayesian structure analysis using unlinked DArT markers. Linkage disequilibrium (LD) decay was observed among DArT loci > 10 cM distance and approximately 28% marker pairs were in significant LD. In total, 197 loci over 60 chromosomal regions and 79 loci over 31 chromosomal regions were associated with grain morphology by genome wide analysis using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. They were mainly distributed on homoeologous group 2, 3, 6 and 7 chromosomes. Twenty eight marker-trait associations (MTAs) on the D genome chromosomes 2D, 3D and 6D may carry novel alleles with potential to enhance grain weight due to the use of untapped wild accessions of Aegilops tauschii. Statistical simulations showed that favorable alleles for thousand kernel weight (TKW), grain length, width and thickness have additive genetic effects. Allelic variations for known genes controlling grain size and weight, viz. TaCwi-2A, TaSus-2B, TaCKX6-3D and TaGw2-6A, were also associated with TKW, grain width and thickness. In silico functional analysis predicted a range of biological functions for 32 DArT loci and receptor like kinase, known to affect plant development, appeared to be common protein family encoded by several loci responsible for grain size and shape.ConclusionConclusively, we demonstrated the application and integration of multiple approaches including high throughput phenotyping using DI, genome wide association studies (GWAS) and in silico functional analysis of candidate loci to analyze target traits, and identify candidate genomic regions underlying these traits. These approaches provided great opportunity to understand the breeding value of SHWs for improving grain weight and enhanced our deep understanding on molecular genetics of grain weight in wheat.

Identifying large sets of unrelated individuals and unrelated markers

BackgroundGenetic Analyses in large sample populations are important for a better understanding of the variation between populations, for designing conservation programs, for detecting rare mutations which may be risk factors for a variety of diseases, among other reasons. However these analyses frequently assume that the participating individuals or animals are mutually unrelated which may not be the case in large samples, leading to erroneous conclusions. In order to retain as much data as possible while minimizing the risk of false positives it is useful to identify a large subset of relatively unrelated individuals in the population. This can be done using a heuristic for finding a large set of independent of nodes in an undirected graph. We describe a fast randomized heuristic for this purpose. The same methodology can also be used for identifying a suitable set of markers for analyzing population stratification, and other instances where a rapid heuristic for maximal independent sets in large graphs is needed.ResultsWe present FastIndep, a fast random heuristic algorithm for finding a maximal independent set of nodes in an arbitrary undirected graph along with an efficient implementation in C++. On a 64 bit Linux or MacOS platform the execution time is a few minutes, even with a graph of several thousand nodes. The algorithm can discover multiple solutions of the same cardinality. FastIndep can be used to discover unlinked markers, and unrelated individuals in populations.ConclusionsThe methods presented here provide a quick and efficient method for identifying sets of unrelated individuals in large populations and unlinked markers in marker panels. The C++ source code and instructions along with utilities for generating the input files in the appropriate format are available at http://taurus.ansci.iastate.edu/wiki/people/jabr/Joseph_Abraham.html

Association mapping identifies QTLS on wheat chromosome 3A for yield related traits

A panel of 94 diverse hexaploid wheat accessions was used to map quantitative trait loci (QTL) underlying the yield related traits on chromosome 3A. Population structure and kinships were estimated using unlinked SSR markers from all 21 chromosomes. Analysis of variance revealed significant difference among accessions; however, genotype × year interaction was non-significant for majority of yield related traits. A mixed linear model (MLM) approach identified six QTLs for four traits that individually accounted for 10.7 to 17.3% phenotypic variability. All QTLs were consistently observed for both study years. New putative QTLs for the maximum fertile florets per spike and spike length were identified. This report on QTLs for yield related traits on chromosome 3A will extend the existing knowledge and may prove useful in marker-assisted selection (MAS) for development of high yielding cultivars.

Validation of 58 autosomal individual identification SNPs in three Chinese populations

AimTo genotype and evaluate a panel of single-nucleotide polymorphisms for individual identification (IISNPs) in three Chinese populations: Chinese Han, Uyghur, and Tibetan.MethodsTwo previously identified panels of IISNPs, 86 unlinked IISNPs and SNPforID 52-plex markers, were pooled and analyzed. Four SNPs were included in both panels. In total, 132 SNPs were typed on Sequenom MassARRAY® platform in 330 individuals from Han Chinese, Uyghur, and Tibetan populations. Population genetic indices and forensic parameters were determined for all studied markers.ResultsNo significant deviation from Hardy-Weinberg equilibrium was observed for any of the SNPs in 3 populations. Expected heterozygosity (He) ranged from 0.144 to 0.500 in Han Chinese, from 0.197 to 0.500 in Uyghur, and from 0.018 to 0.500 in Tibetan population. Wright's Fst values ranged from 0.0001 to 0.1613. Pairwise linkage disequilibrium (LD) calculations for all 132 SNPs showed no significant LD across the populations (r2<0.147). A subset of 58 unlinked IISNPs (r2<0.094) with He>0.450 and Fst values from 0.0002 to 0.0536 gave match probabilities of 10−25 and a cumulative probability of exclusion of 0.999992.ConclusionThe 58 unlinked IISNPs with high heterozygosity have low allele frequency variation among 3 Chinese populations, which makes them excellent candidates for the development of multiplex assays for individual identification and paternity testing.

Genetic Structure, Linkage Disequilibrium and Association Mapping of Verticillium Wilt Resistance in Elite Cotton (Gossypium hirsutum L.) Germplasm Population

Understanding the population structure and linkage disequilibrium in an association panel can effectively avoid spurious associations and improve the accuracy in association mapping. In this study, one hundred and fifty eight elite cotton (Gossypium hirsutum L.) germplasm from all over the world, which were genotyped with 212 whole genome-wide marker loci and phenotyped with an disease nursery and greenhouse screening method, were assayed for population structure, linkage disequilibrium, and association mapping of Verticillium wilt resistance. A total of 480 alleles ranging from 2 to 4 per locus were identified from all collections. Model-based analysis identified two groups (G1 and G2) and seven subgroups (G1a–c, G2a–d), and differentiation analysis showed that subgroup having a single origin or pedigree was apt to differentiate with those having a mixed origin. Only 8.12% linked marker pairs showed significant LD (P<0.001) in this association panel. The LD level for linked markers is significantly higher than that for unlinked markers, suggesting that physical linkage strongly influences LD in this panel, and LD level was elevated when the panel was classified into groups and subgroups. The LD decay analysis for several chromosomes showed that different chromosomes showed a notable change in LD decay distances for the same gene pool. Based on the disease nursery and greenhouse environment, 42 marker loci associated with Verticillium wilt resistance were identified through association mapping, which widely were distributed among 15 chromosomes. Among which 10 marker loci were found to be consistent with previously identified QTLs and 32 were new unreported marker loci, and QTL clusters for Verticillium wilt resistanc on Chr.16 were also proved in our study, which was consistent with the strong linkage in this chromosome. Our results would contribute to association mapping and supply the marker candidates for marker-assisted selection of Verticillium wilt resistance in cotton.

Genetic Structure in FCV Tobacco Population as Assessed by Multi-locus Genotyping Using SSR Markers

Association mapping studies largely depend on the genetic nature of the population. An understanding of genetic structure of population assists in designing apt studies that accounts the dynamics of variability in population. Current study is aimed at analyzing genetic structure of tobacco (Nicotiana tabacum L.) population consisted of 135 FCV (Flue Cured Virginia) genotypes using multi-locus genotyping with mapped Simple Sequence Repeat (SSR) markers. 25 unlinked SSR markers delineated 135 genotypes revealing a total of 85 alleles with an average of 3.4 alleles per locus. Contrasting allelic frequencies were observed in most of the loci studied. Bayesian method of inference employed the genotyping data to derive genetic structure information from the population. High FST measures in the subpopulations (0.44, 0.09 and 0.29 at population level K=3) indicated high inbreeding coefficient signifying a strongly structured population. Evolutionary dissimilarity estimate using DARwin also supported the finding of resilient structure in the population. These findings were found highly useful in designing appropriate mapping strategies for tobacco breeding.

Pure hereditary spastic paraplegia due to ade novomutation in theNIPA1gene

Hereditary spastic paraplegia (HSP) is a group of diseases with heterogeneous mode of inheritance and is characterized primarily by progressive spasticity of the lower limbs due to degeneration of long pyramidal tract. HSP type 6 (SPG6) is caused by mutations in the NIPA1 gene [1] (OMIM #600363) and accounts for less than 1% of autosomal dominant cases among Caucasians patients [2]. Traditionally, SPG6 was considered a pure (uncomplicated) form of HSP. Recent observations, however, expanded the phenotypic spectrum and linked NIPA1 mutations to some cases of more complex forms of HSP [3, 4]. We report here a family with a pure form of HSP due to a de novo transition mutation in the NIPA1 gene. The three affected members of the family were a 46 year-old parent and two children, aged 21 and 15 years of age. They all developed slowly progressive spastic gait that started during the first half of their second decade of life. Medical history was absent except for mild delayed speech development and attention deficit in the younger child and a single questionable generalized seizure in the older child that was not documented on electroencephalogram. This episode included a sudden loss of consciousness, lasted only few seconds and was associated with tongue biting and twitching of the left fingers but without clear postictal period. The proband, 36 years after symptom onset, had difficulty ambulating and was assisted by a walker. Both children had spastic gait but walked without assistance. Neurological examination of the affected family members was significant for marked spasticity, mild weakness of hip extensors, bilateral ankle clonus, globally hyperactive deep tendon reflexes that were more prominent in the lower extremities and extensor plantar responses. Cognition, ocular movements and cerebellar functions were all normal. Sequencing of the NIPA1 gene (Athena Diagnostics, Inc) revealed in all the affected family members a point mutation causing transition from adenine to guanine (G→A) at position 316. This mutation led to an amino acid change, from glycine to arginine, in codon 106. This specific mutation has been previously reported as pathogenic [3, 5] of a pure form of HSP, although cases of complicated HSP with epilepsy have been also documented [3]. Other ancillary tests included brain MRI studies, genetic testing for other autosomal dominant HSPs (SPG3A, SPG4 and SPG31) and extensive metabolic work-up were all normal. An MRI study of the proband’s thoracic spine showed spinal cord atrophy. Lack of symptoms or clinical signs in the parents of the proband led us to test them for a mutation in the NIPA1 gene (after they signed an informed consent for a research protocol approved by Columbia University IRB). The mutation was not present in the non-manifesting parents of the proband. True parenthood was confirmed using a panel of six highly informative unlinked microsatellite markers. To ensure specificity of this method, genetic polymorphism was also tested by three CEPH (1331-1, 1332-12, 1347-1) and showed perfect concordance. This finding supports the hypothesis that this was a de novo mutation. According to our knowledge, de novo mutations were never documented to cause SPG6 although such mutations were sparsely documented in other HSPs [6]. This finding strengths the assumption that this is a pathogenic mutation and emphasizes the need to consider autosomal dominant HSP even in the absence of family history.

Allelic diversity and its implications for the rate of adaptation.

Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.

Genomic Consequences of Ecological Speciation in Astyanax Cavefish

The cave environment is consistently radically different than the surface environment because it lacks light, and animals adapting to cave life are subject to strong selective forces much different than those experienced by their ancestors who evolved in the presence of light. As such, their divergence from surface ancestors and eventual speciation is likely to be driven by the shift in ecology. We report here that hybrids between cave and surface Astyanax mexicanus fishes produce offspring with allelic frequencies that differ significantly from Mendelian expectations both for transmission ratios and for independent assortment of unlinked markers. Comparison of allelic content of DNA from fin clips and sperm pools show that the transmission ratio distortion likely occurs during spermatogenesis. Departures from expectations of independent assortment are essentially epistatic phenomena generating linkage disequilibrium. A novel analysis of the epistatic interactions reveals an apparent network of interactions among genes known or suspected to be involved in cave adaptation, implying that the epistasis arose as a “by product” of the divergence due to cave adaptation.

Genetic analysis of population differentiation and adaptation in Leuciscus waleckii

Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.

Integrative taxonomy of the freshwater worm Rhyacodrilus falciformis s.l. (Clitellata: Naididae), with the description of a new species

The genetic and morphological variation within Rhyacodrilus falciformis Bretscher, 1901 (Clitellata: Naididae) in Europe was explored using an integrative approach, with three unlinked genetic markers [the mitochondrial cytochrome c oxidase subunit I (COI), the nuclear histone 3 (H3) and internal transcribed spacer region (ITS)] combined with morphology, to investigate whether this taxon constitutes a single or several species. Using Automatic Barcode Gap Discovery on the COI data set, the specimens were divided into seven clusters, used as hypothetical species that were further tested with the other data sources. Single‐gene trees were estimated for all three markers, using coalescence analysis and they were in many parts incongruent with each other. Only one of the clusters was supported by all trees; it was also morphologically differentiated from the other clusters by the shape of its modified penial chaetae. This group consists of two specimens from the Crotot Cave in south‐eastern France, and morphologically they fit a previously described but invalid variety, ‘pigueti’, which is here described as a new species, Rhyacodrilus pigueti Achurra &amp; Martinsson sp. n. The study highlights the fact that a single data source (e.g. COI barcodes) seldom provides a sufficient basis for taxonomic decisions such as species delimitation.

Modelling wild-domestic interbreeding: How selection on a quantitative trait affects gene flow at a neutral locus

Interbreeding between domesticated individuals and their wild conspecifics occurs in a range of species. The rate of gene flow into the wild population, estimated using genetic markers, is often smaller than the fraction of immigrants, as immigrants and their descendants generally have lower relative fitness. Here the difference between one-way migration rate and gene flow (effective migration rate) is explored using quantitative genetic simulations. We model a trait undergoing stabilizing selection in the recipient population, influenced by an infinite number of loci, each with small effect. Immigrants have suboptimal trait values, and differ in allele frequency at an unlinked neutral marker locus. We derive an analytical approximation for the effective migration rate, and show that in the limiting case of low migration rates, the ratio between effective and actual migration rate approximately equals the ratio between mean fitness of immigrants and in the admixed population. This ignores indirect selection on the marker locus within the admixed population due to covariance with the trait value, which may be substantial when the genetic difference between the populations is large. For higher migration rates, the gene flow/migration ratio rises with increasing migration rate, inflating the rate of gene flow.

DNA barcoding of COI gene in some medicinal animals of Lacertilia

To identify some medicinal animals of Lacertilia, in total 59 individuals belonging to 12 species 7 genera 3 families, we used the universal barcoding primers to sequence these species, compared with other homologous sequences (564 bp) obtaining from the GenBank and finally constructed phylogenetic trees using Neighbor-joining, Maximum parsimony and Bayesian inference, respectively. As a result, the mean content of G + C (46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the whole individuals mean distance for interspecies and intraspecies was 35. 5% and 1.7%, respectively. The mean distance for interspecies was 21 times as much as that for intraspecies. The mean distance for intraspecies of Gekko swinhonis, Hemidactylus frenatus and G. gecko was greater than 2%, respectively. Further analyses suggested that geographical groups of the three species might be of different subSpecies, even species. Of course, incorporating morphological characters and other unlinked genetic markers in future studies will offer further insights into the divergence. On the basis of phylogenetic trees constructed by COI, our results indicated that the taxonomy of the category (family, genus, and species) by DNA barcoding is consistent with morphological characters. Therefore, DNA barcoding is a useful tool for both identification and phylogeny of medicinal animals of Lacertilia, particularly for nonprofessor identifying authentication of Chinese crude drugs of these species.

Improved estimation of inbreeding and kinship in pigs using optimized SNP panels

BackgroundTraditional breeding programs consider an average pairwise kinship between sibs. Based on pedigree information, the relationship matrix is used for genetic evaluations disregarding variation due to Mendelian sampling. Therefore, inbreeding and kinship coefficients are either over or underestimated resulting in reduction of accuracy of genetic evaluations and genetic progress. Single nucleotide polymorphism (SNPs) can be used to estimate pairwise kinship and individual inbreeding more accurately. The aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship and inbreeding.ResultsA total of 1,565 animals from three commercial pig populations were analyzed for 28,740 SNPs from the PorcineSNP60 Beadchip. Mean genomic inbreeding was higher than pedigree-based estimates in lines 2 and 3, but lower in line 1. As expected, a larger variation of genomic kinship estimates was observed for half and full sibs than for pedigree-based kinship reflecting Mendelian sampling. Genomic kinship between father-offspring pairs was lower (0.23) than the estimate based on pedigree (0.26). Bootstrap analyses using six reduced SNP panels (n = 500, 1000, 1500, 2000, 2500 and 3000) showed that 2,000 SNPs were able to reproduce the results very close to those obtained using the full set of unlinked markers (n = 7,984-10,235) with high correlations (inbreeding r > 0.82 and kinship r > 0.96) and low variation between different sets with the same number of SNPs.ConclusionsVariation of kinship between sibs due to Mendelian sampling is better captured using genomic information than the pedigree-based method. Therefore, the reduced sets of SNPs could generate more accurate kinship coefficients between sibs than the pedigree-based method. Variation of genomic kinship of father-offspring pairs is recommended as a parameter to determine accuracy of the method rather than correlation with pedigree-based estimates. Inbreeding and kinship coefficients can be estimated with high accuracy using ≥2,000 unlinked SNPs within all three commercial pig lines evaluated. However, a larger number of SNPs might be necessary in other populations or across lines.