Showing papers in "Journal of Heredity in 2008"
TL;DR: An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.
Abstract: Ever since its first release in 1999, the free software package for visualization of molecular marker data, graphical genotype (GGT), has been constantly adapted and improved. The GGT package was developed in a plant-breeding context and thus focuses on plant genetic data but was not intended to be limited to plants only. The current version has many options for genetic analysis of populations including diversity analyses and simple association studies. A second release of the GGT package, GGT 2.0 (available through http://www.plantbreeding.wur.nl), is therefore presented in this paper. An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT 2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.
329 citations
TL;DR: Data presented here, based on simulations, show that the percentage of correctly assigned individuals in model-based clustering and Bayesian assignment methods were slightly reduced and the presence of null alleles caused a small, however, significant overestimation of F(ST).
Abstract: Microsatellite null alleles are found to a varying degree across all taxa. They are problematic as they may inflate measures of genetic differentiation and create false homozygotes. Although there are several methods for correcting allele frequencies for null alleles and enable estimations of FST, much less is known about how null alleles affect assignment testing. Data presented here, based on simulations, show that the percentage of correctly assigned individuals in model-based clustering and Bayesian assignment methods were slightly, though significantly, reduced in the presence of null alleles (frequency range from 0.000 to 0.913). The bias in assignment tests caused by null alleles lead to a slight reduction in the power to correctly assigned individuals (0.2 and 1.0 percent units for STRUCTURE- and 2.4 percent units for GENECLASS-based assignment tests). Further, the presence of null alleles caused a small, however, significant overestimation of FST. Consequently, microsatellite loci affected by null alleles would probably not alter the overall outcome of assignment testing and could therefore be included in these types of studies. Nevertheless, loci prone to null alleles should be used with caution as they lower the power of assignment tests and alter the accuracy of FST, and loci less prone to null alleles should always be preferred.
315 citations
TL;DR: Results indicate that geographic distance alone may not be a barrier to dispersal, but rather the combined effects of distance, depth, and the polar front act to prevent gene flow between A. agassizii populations in the Southern Ocean.
Abstract: Studies examining population structure and genetic diversity of benthic marine invertebrates in the Southern Ocean have emerged in recent years. However, many taxonomic groups remain largely unstudied, echinoderms being one conspicuous example. The brittle star Astrotoma agassizii is distributed widely throughout Antarctica and southern South America. This species is a brooding echinoderm and therefore may have limited dispersal capacity. In order to determine the effect of hypothesized isolating barriers in the Southern Ocean, such as depth, geographic distance, and the polar front, 2 mitochondrial DNA markers were used to compare populations from the South American and Antarctic continental shelves. Astrotoma agassizii was shown to be genetically discontinuous across the polar front. In fact, populations previously assumed to be panmictic instead represent 3 separate lineages that lack morphological distinction. However, within lineages, genetic continuity was displayed across a large geographic range (>500 km). Therefore, despite lacking a pelagic larval stage, A. agassizii can disperse across substantial geographic distance within continental shelf regions. These results indicate that geographic distance alone may not be a barrier to dispersal, but rather the combined effects of distance, depth, and the polar front act to prevent gene flow between A. agassizii populations in the Southern Ocean.
178 citations
TL;DR: Nucleotide sequence diversity in domesticated avocados ranged between 80% and 90% of that observed for the same loci in wild avocado, depending on the diversity statistic used for comparison.
Abstract: It has been difficult to infer the genetic history of avocado breeding, owing to the role of hybridization in the origin of contemporary avocado cultivars. To address this difficulty, we used the model-based clustering program, STRUCTURE, and nucleotide polymorphism in 5960 bp of sequence from 4 nuclear loci to examine population structure in 21 wild avocado accessions. The origins of 33 cultivars were inferred relative to the wild sample. Nucleotide sequence diversity in domesticated avocados ranged between 80% and 90% of that observed for the same loci in wild avocado, depending on the diversity statistic used for comparison. Substantial genetic differentiation among 3 geographic groups of wild germplasm corresponded to the classically defined horticultural races of avocado. Previously undetected genetic differentiation was revealed in wild populations from Central Mexico, where 2 subpopulations were distinguished based on elevation and latitude.
148 citations
TL;DR: High-performance liquid chromatography and mass spectrometry analysis of violet and black fruit tissue identified a single anthocyanin that was determined to be delphinidin-3-p-coumaroyl-rutinoside-5-glucoside that produced the characteristic black pigmentation observed in fruits and leaves of selected genotypes.
Abstract: Shades ranging from violet to black pigmentation in pepper (Capsicum annuum L.) are attributed to anthocyanin accumulation. High-performance liquid chromatography and mass spectrometry analysis of violet and black fruit tissue identified a single anthocyanin that was determined to be delphinidin-3-p-coumaroyl-rutinoside-5-glucoside. Leaf tissue of a black-pigmented foliage genotype contained the same anthocyanin found in fruit but at a considerably higher concentration in comparison to violet and black fruit tissue. Fruit chlorophyll concentration was approximately 14-fold higher in black fruit in comparison to violet fruit that contained relatively little chlorophyll. b-carotene, lutein, violaxanthin, and neoxanthin carotenoid concentrations in black fruit were also significantly greater in comparison to violet fruit. High concentrations of delphinidin in combination with chlorophyll and accessory carotenoid pigments produced the characteristic black pigmentation observed in fruits and leaves of selected genotypes. Anthocyanins were accumulated in the outer mesocarp of violet and black fruit and in the palisade and mesophyll cells of black leaves. Consistent with chlorophyll content of respective genotypes, chloroplast density was greater in cells of black fruits. Utilizing Capsicum pigment variants, we determine the biochemical factors responsible for violet versus black-pigmented pepper tissue in the context of described pepper color genes.
99 citations
TL;DR: This study attempted to identify Phaseolus vulgaris homologues of 12 Arabidopsis genes that are involved in meristem identity determination and the photoperiod-dependent and autonomous flowering pathways and identified 7 of which could be mapped onto the common bean-linkage map using the BAT93 x Jalo EEP 558 and Midas x G12873 recombinant inbred populations.
Abstract: Determinacy and photoperiod insensitivity are agronomically important traits, selected during or after domestication in common bean. Determinacy reduces aboveground plant biomass and accelerates and synchronizes flowering. Photoperiod insensitivity allows common bean to be grown at higher latitudes under long days. In this study, we attempted to identify Phaseolus vulgaris homologues of 12 Arabidopsis genes that are involved in meristem identity determination and the photoperiod-dependent and autonomous flowering pathways. Amplification products with homology to the original Arabidopsis gene were obtained for 8 genes, 7 of which could be mapped onto the common bean-linkage map using the
96 citations
TL;DR: The results show that double homozygotes Aft/Aft hp-1/hp-1 plants displayed a more-than-additive effect on the production of fruit anthocyanidins and flavonols.
Abstract: The tomato Anthocyanin fruit (Aft) genotype is characterized by purple color in skin and outer pericarp of its fruits due to higher levels of anthocyanins—flavonoid metabolites. Our objectives were to carry out metabolic and molecular characterization of this genotype, emphasizing its interaction with the high pigment-1 (hp-1) mutation, known to increase flavonoids in tomato fruits. These objectives fit the growing interest in developing tomato fruits with higher levels of functional metabolites. Our results show that 1) Aft fruits are also characterized by significantly higher levels of the flavonols quercetin and kaempferol, thus enhancing their functional value; 2) the tomato Anthocyanin1 (Ant1) gene, encoding a Myb transcription factor, displayed nucleotide and amino acid polymorphisms between the Aft genotype and cultivated genotypes; 3) a DNA marker based on Ant1 showed that the Aft trait is encoded by a single locus on chromosome 10 fully associated with Ant1; and 4) double homozygotes Aft/Aft hp-1/hp-1 plants displayed a more-than-additive effect on the production of fruit anthocyanidins and flavonols. This effect was manifested by approximately 5-, 19-, and 33-fold increase of petunidin, malvidin, and delphinidin, respectively, in the double mutants compared with the cumulative levels of their parental lines.
82 citations
TL;DR: Comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.
Abstract: Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, ESTSSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, FIS, FST, population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.
81 citations
TL;DR: The program "Nb_HetEx" estimates the effective number of breeders (N(b) that produced the sampled progeny based on genotype counts contained in that sample using the temporal method.
Abstract: The program "Nb_HetEx" estimates the effective number of breeders (N b ) that produced the sampled progeny based on genotype counts contained in that sample. When the number of breeders is very small, there is an excess of heterozygotes in their progeny: the smaller the number of breeders, the larger the heterozygote excess. The Nb_ HetEx program also estimates N e through the temporal method.
77 citations
TL;DR: Genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species, with unprecedentedly low levels of allelic diversity and heterozygosity.
Abstract: Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A 5 1.1, He 5 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P 5 0.002), but simulations indicate low genetic diversity (He , 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (FIS 5 0.018) or population structure (K 5 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to ;1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.
75 citations
TL;DR: In this paper, the mtDNA polymorphism of 304 Macaca fascicularis (M. f. f) individuals was studied, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius).
Abstract: We studied the mitochondrial DNA (mtDNA) polymorphism of 304 Macaca fascicularis fascicularis (M. f. fascicularis) individuals, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius). By sequencing a 590-bp fragment in the hypervariable II region of the D-loop region, we defined 70 haplotypes. The homologous region was also characterized in 22 Chinese Macaca mulatta and 2 Macaca sylvanus. The phylogenetic analysis confirms the monophyly of M. f. fascicularis and defines 2 haplotype groups inside the M. f. fascicularis clade: one ‘‘insular,’’ encompassing 6 Philippines, 2 Mauritius, and 31 Indonesian haplotypes, the other ‘‘continental’’ that contains all Indochinese and 6 Indonesian haplotypes. Continental and insular group divergence time was estimated to be approximately 10 6 years before present (BP). Among Indonesian haplotypes, some have a continental origin. This suggests either direct migration from mainland to Indonesia or that remnant lineages from an ancient population genetically close to the mainland (i.e., in the Sunda Shelf, ,550 000 years BP) were subsequently brought southward to Indonesia. The low nucleotide diversity in the Philippines population suggests a bottleneck following colonization by Indonesian individuals, around 110 000 years BP. mtDNA and further observations of nuclear genetic data corroborate the mixed origin (Indonesian/continental) hypothesis of Mauritius individuals and a population bottleneck.
TL;DR: 5 OR genes investigated for polymorphic sites proved to have allelic variants, the majority of which lead to protein sequence alteration, which suggests a role of specific alleles in odor detection and a linkage between single-nucleotide polymorphism and odor recognition efficiency.
Abstract: The outstanding sensitivity of the canine olfactory system has been acknowledged by using sniffer dogs in military and civilian service for detection of a variety of odors. It is hypothesized that the canine olfactory ability is determined by polymorphisms in olfactory receptor (OR) genes. We investigated 5 OR genes for polymorphic sites which might affect the olfactory ability of service dogs in different fields of specific substance detection. All investigated OR DNA sequences proved to have allelic variants, the majority of which lead to protein sequence alteration. Homozygous individuals at 2 gene loci significantly differed in their detection skills from other genotypes. This suggests a role of specific alleles in odor detection and a linkage between single-nucleotide polymorphism and odor recognition efficiency.
TL;DR: Using georeferenced multilocus microsatellite genotypes in spatially implicit and spatially explicit models to characterize patterns of landscape genetic structure in river otters in Louisiana, it is likely that any genetic differentiation among subpopulations is exacerbated by relatively poor dispersal.
Abstract: For North American river otters (Lontra canadensis) in Louisiana, statewide distribution, availability of aquatic habitats, and the absence of physical barriers to dispersal might suggest that they exist as a large, panmictic population. However, the wide variety of habitat types in this region, and the dynamic nature of these habitats over time, could potentially structure river otter populations in accordance with cryptic landscape features. Recently developed landscape genetic models offer a spatially explicit approach that could be useful in identifying potential barriers to the movement of river otters through the dynamic aquatic landscape of Louisiana. We used georeferenced multilocus microsatellite genotypes in spatially implicit (STRUCTURE) and spatially explicit (GENELAND) models to characterize patterns of landscape genetic structure. All models identified 3 subpopulations of river otters in Louisiana, corresponding to Inland, Atchafalaya River, and Mississippi River regions. Variation in breeding seasonality, brought about by variation in prey abundance between inland and coastal populations, may have contributed to genetic differentiation among populations. It is also possible that the genetic discontinuities we observed indicate a correlation between otter distribution and access to freshwater. Regardless of the mechanism, it is likely that any genetic differentiation among subpopulations is exacerbated by relatively poor dispersal.
TL;DR: A genome scan in a Holstein x Charolais cross cattle population was carried out to identify quantitative trait loci influencing temperament-related traits, and no overlapping QTL were identified for the traits measured by the 2 different tests, supporting the hypothesis that different genetic factors influence behavioral responses to different situations.
Abstract: In addition to its potential contribution to improving animal welfare, the study of the genetics of cattle behavior may provide more general insights into the genetic control of such complex traits. We carried out a genome scan in a Holstein x Charolais cross cattle population to identify quantitative trait loci (QTL) influencing temperament-related traits. Individuals belonging to the second-generation of this population (F(2) and backcross individuals) were subjected to 2 behavioral tests. The flight from feeder (FF) test measured the distance at which the animal moved away from an approaching human observer, whereas the social separation (SS) test categorized different activities which the animal engaged in when removed from its penmates. The entire population was genotyped with 165 microsatellite markers. A regression interval mapping analysis identified 29 regions exceeding the 5% chromosome-wide significance level, which individually explained a relatively small fraction of the phenotypic variance of the traits (from 3.8% to 8.4%). One of the significant associations influencing an FF test trait on chromosome 29 reached the 5% genome-wide significance level. Eight other QTL, all associated with an SS test trait, reached the 1% chromosome-wide significance level. The location of some QTL coincided with other previously reported temperament QTL in cattle, whereas those that are reported for the first time here may represent general loci controlling temperament differences between cattle breeds. No overlapping QTL were identified for the traits measured by the 2 different tests, supporting the hypothesis that different genetic factors influence behavioral responses to different situations.
TL;DR: The results obtained in this study suggest that C. gigas EST-SSRs will complement the currently available genomic SSR markers and may be useful for comparative mapping, marker-assisted selection, and evolutionary studies.
Abstract: A total of 147 microsatellite-containing expressed sequence tags (ESTs) (3.63%) were detected from 4053 ESTs of the Pacific oyster (Crassostrea gigas) in GenBank. The average density of simple sequence repeats (SSRs) was 1 per 8.25 kb of EST after redundancy elimination. Dinucleotide repeat motifs appeared to be the most abundant type. Sixteen new polymorphic EST-SSRs were developed. The number of alleles per locus varied from 3 to 12, with an average of 5.9 alleles per locus. Marker transferability was tested on 2 other Crassostrea species, and 14 loci gave successful amplifications in both species. Twenty EST-SSRs were tested on 3 families of C. gigas for examination of inheritance mode of EST-SSRs. Thirty-five tests of segregation ratios revealed 5 significant departures from expected Mendelian ratios, 4 of which confirmed Mendelian expectations when accounting for the presence of null alleles. Null alleles were detected at 3 loci (15.0%) of the 20 loci, and the frequency of null alleles at EST-SSRs was lower than that in genomic SSRs in C. gigas. The results obtained in this study suggest that C. gigas EST-SSRs will complement the currently available genomic SSR markers and may be useful for comparative mapping, marker-assisted selection, and evolutionary studies.
TL;DR: This study successfully provides, for the first time in a moss, a sex-specific DNA marker that allows reliable determination of gender and sex ratio determination at any stage in the life cycle.
Abstract: Most dioecious plants do not exhibit discernible sexual dimorphism before sexual maturity. Therefore, it is impossible to address any sex-related questions during the prereproductive phase unless a genetic sex marker is available for gender determination. The aim of the present study was to develop a genetic sex marker for the moss Pseudocalliergon trifarium to allow gender and sex ratio determination at any stage in the life cycle. A high proportion of P. trifarium populations do not express sex. The screening of genomic DNA with inter simple sequence repeat (ISSR) primers was used to discover sex-specific polymerase chain reaction (PCR) amplification products. A presumably female-specific band was found, excised from the gel, cloned, and sequenced. A sequence-walking method was used to characterize the same region in males. A primer pair was designed to allow the amplification of a 159-bp portion of the female-specific DNA region. All tested material, up to 16-yearold herbarium specimens, provided unambiguous amplification products. This study successfully provides, for the first time in a moss, a sex-specific DNA marker. It allows reliable determination of gender and sex ratios. The short length of the amplification product is an advantage as satisfactory PCR products are more likely when the targeted sequence is short. The amount of variation in the DNA region shared by both sexes was relatively high. If the male sequence can be better characterized, the sex-specific regions could possibly be used to evaluate sex-specific phylogeographic patterns.
TL;DR: The results suggest that epistatic interactions of genes may play as important a role in the genetic architecture of physical activity traits as single-locus effects and need to be considered in future candidate gene identification studies.
Abstract: We recently identified several (4-8) quantitative trait loci (QTL) for 3 physical activity traits (daily distance, duration, and speed voluntarily run) in an F(2) population of mice derived from an original intercross of 2 strains that exhibited large differences in activity. These QTL cumulatively explained from 11% to 34% of the variation in these traits, but this was considerably less than their total genetic variability estimated from differences among inbred strains. We therefore decided to test whether epistatic interactions might account for additional genetic variation in these traits in this same population of mice. We conducted a full genome epistasis scan for all possible interactions of QTL between each pair of 20 chromosomes. The results of this scan revealed an abundance of epistasis, with QTL throughout the genome being involved in significant interactions. Overall, epistatic effects contributed an average of 26% of the total variation among the 3 activity traits. These results suggest that epistatic interactions of genes may play as important a role in the genetic architecture of physical activity traits as single-locus effects and need to be considered in future candidate gene identification studies.
TL;DR: Support is provided for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters and effects of sample size on estimates from hypervariable loci are discussed.
Abstract: A comparative study between microsatellite and allozyme markers was conducted on the genetic structure and mating system in natural populations of Euterpe edulis Mart. Three cohorts, including seedlings, saplings, and adults, were examined in 4 populations using 10 allozyme loci and 10 microsatellite loci. As expected, microsatellite markers had a much higher degree of polymorphism than allozymes, but estimates of multilocus outcrossing rate ð ˆ tm51:00Þ; as well as estimates of genetic structure (FIS, GST), were similar for the 2 sets of markers. Estimates of RST, for microsatellites, were higher than those of GST, but results of both statistics revealed a close agreement for the genetic structure of the species. This study provides support for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters. Effects of sample size on estimates from hypervariable loci are also discussed in this paper.
TL;DR: A resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado, shows that the overall level of genetic variation is not exceptionally high compared with available estimates from temperate plant species.
Abstract: Resequencing studies provide the ultimate resolution of genetic diversity because they identify all mutations in a gene that are present within the sampled individuals. We report a resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado. The sample includes 21 wild accessions from Mexico, Costa Rica, Ecuador, and the Dominican Republic. Estimated levels of nucleotide polymorphism and linkage disequilibrium (LD) are obtained from fully resolved haplotype data from 4 nuclear loci that span 5960 nucleotide sites. Results show that, although avocado is a subtropical tree crop and a predominantly outcrossing plant, the overall level of genetic variation is not exceptionally high (nucleotide diversity at silent sites, pi(sil) = 0.0102) compared with available estimates from temperate plant species. Intralocus LD decays rapidly to half the initial value within about 1 kb. Estimates of recombination rate (based on the sequence data) show that the rate is not exceptionally high when compared with annual plants such as wild barley or maize. Interlocus LD is significant owing to substantial population structure induced by mixing of the 3 botanical races of avocado.
TL;DR: The results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.
Abstract: We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (FCT 5 0.264; P , 0.05) and a relatively lower differentiation among populations within regions (FSC 5 0.218; P , 0.0001). Microsatellite variation significantly differentiated among populations within regions (FSC 5 0.019; P , 0.0001) but not at the regional levels (FCT 5 0.000; P . 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.
TL;DR: The results suggest that PDV genes evolve through natural selection and are genetically linked to factors of suppression of local host resistance, which is linked to parasitoid adaptation to host resistance in biological control.
Abstract: CrV1, a polydisperse DNA virus (polydnavirus or PDV) gene contributes to the suppression of host immunity in Cotesia genus parasitoids. Its molecular evolution was analyzed in relation to levels of resistance in the sympatric host species. Natural selection for nonsynonymous substitutions (positive Darwinian selection) was observed at specific amino acid sites among CrV1 variants; particularly, between parasitoid strains immune suppressive and nonimmune suppressive to the main resistant stem borer host, Busseola fusca. In Cotesia sesamiae, geographic distribution of CrV1 alleles in Kenya was correlated to the relative abundance of B. fusca. These results suggest that PDV genes evolve through natural selection and are genetically linked to factors of suppression of local host resistance. We discuss the forces driving the evolution of CrV1 and its use as a marker to understand parasitoid adaptation to host resistance in biological control.
TL;DR: Three transgenic Anopheles stephensi lines were established that strongly inhibit transmission of the mouse malaria parasite Plasmodium berghei, but in cage experiments, where each of the 3 homozygous transgenic mosquitoes was mixed with nontransgenic mosquitoes, transgene frequency of all 3 lines decreased with time.
Abstract: Three transgenic Anopheles stephensi lines were established that strongly inhibit transmission of the mouse malaria parasite Plasmodium berghei. Fitness of the transgenic mosquitoes was assessed based on life table analysis and competition experiments between transgenic and wild-type mosquitoes. Life table analysis indicated low fitness load for the 2 single-insertion transgenic mosquito lines VD35 and VD26 and no load for the double-insertion transgenic mosquito line VD9. However, in cage experiments, where each of the 3 homozygous transgenic mosquitoes was mixed with nontransgenic mosquitoes, transgene frequency of all 3 lines decreased with time. Further experiments suggested that reduction of transgene frequency is a consequence of reduced mating success, reduced reproductive capacity, and/or insertional mutagenesis, rather than expression of the transgene itself. Thus, for transgenic mosquitoes released in the field to be effective in reducing malaria transmission, a driving mechanism will be required.
TL;DR: SubILs carrying donor segments with candidate genes for flowering time and reduced fertility were used to demonstrate the usefulness of the reciprocal ILs for quantitative trait loci detection and fine mapping.
Abstract: Two new large reciprocal sets of introgression lines (ILs) were created between the Arabidopsis accessions Col-0 and C24. In both sets (78 ILs with Col-0 background and 62 ILs with C24 background), the donor segments cover almost the entire genome with an average substitution size of 18.3 cM. In addition to the basic sets of ILs, further subILs were developed for 2 genomic regions allowing better mapping resolution. SubILs carrying donor segments with candidate genes for flowering time and reduced fertility were used to demonstrate the usefulness of the reciprocal ILs for quantitative trait loci detection and fine mapping. For subIL development at high resolution around the reduced fertility locus, we used modified CelI-based assays in one-well format for both marker development and genotyping. This serves as a very flexible and cost-effective approach.
TL;DR: Backcross (BC) mice exhibited a 50:50 ratio of normal to MM phenotypes and linkage mapping of MM in this BC population to a 2.6335-Mb interval on MMU11 was reported on.
Abstract: From the Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599 (Hartmann, Mun˜oz, and Pomp);the Department of Biology, University of California, Riverside, CA 92521 (Garland, Hannon, and Kelly); the Department ofCell and Molecular Physiology, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599(Pomp).Address correspondence to D. Pomp at the address above, or e-mail: dpomp@unc.edu.Prolonged selective breeding of Hsd:ICR mice for high levelsof voluntary wheel running has favored an unusualphenotype (mini-muscle [MM]), apparently caused bya single Mendelian recessive allele, in which hindlimb musclemass is reduced by almost 50%. We recently described thecreation and phenotypic characterization of a populationsuitable for mapping the genomic location of the MM gene.Specifically, we crossed females from a high-runner linefixed for the MM allele with male C57BL/6J. F1 males werethen backcrossed to the MM parent females. Backcross(BC) mice exhibited a 50:50 ratio of normal to MMphenotypes. Here, we report on linkage mapping of MM inthis BC population to a 2.6335-Mb interval on MMU11. Thisregion harbors ;100 expressed or predicted genes, manyof which have known roles in muscle development and/orfunction. Identification of the genetic variation that underliesMM could potentially be very important in understandingboth normal muscle function and disregulation of musclephysiology leading to disease.Prolonged selective breeding of Hsd:ICR mice for highlevels of voluntary wheel running has favored an unusualphenotype (mini-muscle [MM]), apparently caused bya single Mendelian recessive allele, in which hindlimbmuscle mass is reduced by almost 50%. This phenotype wasoriginally observed in 2 of 4 replicate selected lines (termedHR for high runner) and in 1 of 4 control (nonselected) lines(Garland et al. 2002). Analyses of data from the first 22generations of the selection experiment indicated that themutant allele was present at a frequency of approximately7% in the base population (outbred Hsd:ICR mice). Five ofthe 8 total lines apparently lost the allele by random geneticdrift. In one control line, the phenotype, representinghomozygotes, was observed at a frequency of 0–10% for thefirst 22 generations (Garland et al. 2002) and was thenapparently lost (T Garland Jr. unpublished observations).The 2 selected lines that have exhibited the phenotypeshowed an increase in frequency consistent with positiveselection (Garland et al. 2002). In one (lab designated line 6),the phenotype remains polymorphic as of generation 50. Inthe other (lab designated line 3), the mutation apparentlyhad gone to fixation by generation 36 (Syme et al. 2005).The most characteristic phenotype of MM allelehomozygotes is a 50% reduction in mass of the tricepssurae muscle complex (Garland et al. 2002) as well as inmass of mixed hindlimb muscle exclusive of the tricepssurae (Houle-Leroy et al. 2003). Beyond this, the MM allelehas many pleiotropic effects in homozygotes, includinga doubling of mass-specific aerobic capacity as comparedwith wild-type muscle (Houle-Leroy et al. 2003), alteredfiber type composition in the gastrocnemius (Guderley et al.2008), altered muscle contractile performance (Syme et al.2005), an increase in size of their ventricles, liver, and spleen(Garland et al. 2002; Swallow et al. 2005), and longer andthinner hindlimb bones (Kelly et al. 2006). Many of theseeffects seem conducive to the support of endurance running(Garland 2003; Guderley et al. 2006; Rezende et al. 2006).To date, clearly deleterious consequences of the MM allelehave not been reported.Although the physiological consequences of MM arebecoming well understood, the nature of the underlyingmutation has not been characterized. Identification of theMM gene, and how variation within that gene leads to theMM phenotype, would be important for understanding bothnormal and abnormal muscle development in mammalianspecies. We recently described the creation and phenotypiccharacterization of a population suitable for mapping thegenomic location of the MM gene (Hannon et al. 2008). Wecrossed females from the HR line that is fixed for the MM
TL;DR: Parentage analyses confirmed several observations based on field studies and verified the successful integration and reproduction of several cheetahs following natural dispersal or translocation, suggesting this is a generally panmictic population.
Abstract: The extent and geographic patterns of molecular genetic diversity of the largest remaining free-ranging cheetah population were described in a survey of 313 individuals from throughout Namibia. Levels of relatedness, including paternity/maternity (parentage), were assessed across all individuals using 19 polymorphic microsatellite loci, and unrelated cheetahs (n 5 89) from 7 regions were genotyped at 38 loci to document broad geographical patterns. There was limited differentiation among regions, evidence that this is a generally panmictic population. Measures of genetic variation were similar among all regions and were comparable with Eastern African cheetah populations. Parentage analyses confirmed several observations based on field studies, including 21 of 23 previously hypothesized family groups, 40 probable parent/offspring pairs, and 8 sibling groups. These results also verified the successful integration and reproduction of several cheetahs following natural dispersal or translocation. Animals within social groups (family groups, male coalitions, or sibling groups) were generally related. Within the main study area, radio-collared female cheetahs were more closely interrelated than similarly compared males, a pattern consistent with greater male dispersal. The long-term maintenance of current patterns of genetic variation in Namibia depends on retaining habitat characteristics that promote natural dispersal and gene flow of cheetahs.
TL;DR: This paper estimates the transmission of heterozygosity on an individual chromosome basis through pachytene analysis of chromosomes of haploids of Solanum tuberosum Andigena Group (2n = 4x = 48), a South American cultivated potato.
Abstract: Polyploid plants are formed when numerically unreduced (2n) gametes participate in fertilization. Based on cytological and genetic analyses, modes of 2n gamete formation have been determined for a number of plant species. Gametes formed by a first-division restitution (FDR) mechanism contain nonsister chromatids near the centromere, whereas those formed by second-division restitution (SDR) contain sister chromatids. These mechanisms differ in the proportion of heterozygous loci they transmit intact to offspring. This paper estimates the transmission of heterozygosity on an individual chromosome basis through pachytene analysis of chromosomes of haploids (2n = 2x = 24) of Solanum tuberosum Andigena Group (2n = 4x = 48), a South American cultivated potato. Transmission of heterozygosity by FDR and SDR 2n gametes was calculated for 6 different cytogenetic assumptions. FDR was more than twice as effective as SDR in transmission of heterozygosity under all 6 scenarios. Rates of transmission of heterozygosity were similar in each situation. Transmission of heterozygosity by FDR was also compared with transmission of heterozygosity by tetrasomic inheritance and found to be approximately 50% more effective.
TL;DR: A recent evolutionary history for this species is revealed that differs from that of most other widespread North American passerines and evidence for limited gene flow in a species with potentially large dispersal distances is provided.
Abstract: Genetic analyses for many widespread North American species have revealed significant east-west differentiation, indicating that many survived through the Pleistocene in 2 glacial refugia-1 in the eastern and 1 in the western part of the continent. It remains unclear, however, whether other areas may have served as important glacial refugia. Moreover, many such species exhibit widespread genetic similarity within eastern and western regions because of recent expansion from small refugial populations, making it difficult to evaluate current-day levels of gene flow. In this study, we used mitochondrial DNA (mtDNA) control region sequence and amplified fragment length polymorphism markers to survey genetic variation in a widespread migratory bird, the American redstart (Setophaga ruticilla). mtDNA analyses revealed a pattern that contrasts with that found for most other widespread species studied to date: most redstart populations across North America appear to have spread out from a single glacial refugium, possibly located in the southeastern United States, whereas populations in far-eastern Canada may have survived in a second glacial refugium located on the now-submerged Atlantic coastal shelf off the coast of Newfoundland. A pattern of isolation by distance in mtDNA suggested some constraints on current-day gene flow among extant redstart populations. This study thus reveals a recent evolutionary history for this species that differs from that of most other widespread North American passerines and provides evidence for limited gene flow in a species with potentially large dispersal distances.
TL;DR: It is found that the tdy1-R mutant leaves retain large amounts of starch on prolonged dark treatment, consistent with a defect in starch catabolism, and this data suggest that Tdy1 may function in sucrose export from leaves.
Abstract: In regions of their leaves, tdy1-R mutants hyperaccumulate starch. We propose 2 alternative hypotheses to account for the data, that Tdy1 functions in starch catabolism or that Tdy1 promotes sucrose export from leaves. To determine whether Tdy1 might function in starch breakdown, we exposed plants to extended darkness. We found that the tdy1-R mutant leaves retain large amounts of starch on prolonged dark treatment, consistent with a defect in starch catabolism. To further test this hypothesis, we identified a mutant allele of the leaf expressed small subunit of ADP-glucose pyrophosphorylase (agps-m1), an enzyme required for starch synthesis. We determined that the agps-m1 mutant allele is a molecular null and that plants homozygous for the mutation lack transitory leaf starch. Epistasis analysis of tdy1-R; agps-m1 double mutants demonstrates that Tdy1 function is independent of starch metabolism. These data suggest that Tdy1 may function in sucrose export from leaves.
TL;DR: Analysis of covariance revealed that MM individuals ran significantly more on days 5 and 6 of a 6-day exposure to running wheels, were smaller in body mass, and had larger ventricles and spleens, and in the BC, analysis of covance revealed this gene of major effect has gone to fixation in one selected line, remains polymorphic in another, and is now undetectable in the one C line.
Abstract: From outbred Hsd:ICR mice, we selectively bred 4 replicate lines for high running (High-Runner [HR] lines) on wheels while maintaining 4 nonselected lines as controls (C lines). An apparent Mendelian recessive, the "mini-muscle" (MM) allele, whose main phenotypic effect is to reduce hindlimb muscle mass by 50%, was discovered in 2 HR lines and 1 C line. This gene of major effect has gone to fixation in one selected line, remains polymorphic in another, and is now undetectable in the one C line. Homozygotes exhibit various pleiotropic effects, including a doubling of mass-specific muscle aerobic capacity, and larger hearts, livers, and spleens. To create a population suitable for mapping the genomic location of the MM allele and to better characterize its pleiotropic effects, we crossed females fixed for the MM allele with male C57BL/6J. F(1) males were then backcrossed to the MM parent females. Backcross (BC) mice (N = 404) were dissected, and a 50:50 ratio of normal to MM phenotype was observed with no overlap in relative muscle mass. In the BC, analysis of covariance revealed that MM individuals ran significantly more on days 5 and 6 of a 6-day exposure to running wheels (as in the routine selective-breeding protocol), were smaller in body mass, and had larger ventricles and spleens.
TL;DR: Phylogeny and geographical distribution of the 3 cytb lineages show the effects of limited latitudinal range expansions, contractions, and hybridizations among highly divergent lineages, along with a major role of the glacial ice sheets of the Alps and the Pyrenees as barriers to gene flow, on the diversification of extant taxa.
Abstract: The chamois provides an excellent model for exploring the effect of historical and evolutionary events on diversification. We investigate cytochrome b (cytb) sequences in the 10 recognized subspecies of Rupicapra classified within 2 species: Rupicapra pyrenaica, with the subspecies parva, pyrenaica, and ornata, and Rupicapra rupicapra, with cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica, and caucasica. A fragment of 349 bp of the cytb was sequenced in 189 individuals. We identified 3 cytb lineages: Clade West in Iberia and Western Alps; Clade Central in the Apennines and the Massif of Chartreuse; and Clade East present in populations to the east of the Alps. The 2 proposed species were polyphyletic; the clades West and Central are represented in both, whereas the Clade East is restricted to R. rupicapra. In contrast to the current systematic, cytb phylogenies suggest the classification of the 10 subspecies of chamois into a single species, R. rupicapra. Phylogeny and geographical distribution of the 3 lineages show the effects of limited latitudinal range expansions, contractions, and hybridizations among highly divergent lineages, along with a major role of the glacial ice sheets of the Alps and the Pyrenees as barriers to gene flow, on the diversification of extant taxa.