Latest Articles Include:
- Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae
Janes DE Ezaz T Marshall Graves JA Edwards SV - J Hered 100(2):125-136 (2009)
Pseudoautosomal regions (PARs) shared by avian Z and W sex chromosomes are typically small homologous regions within which recombination still occurs and are hypothesized to share the properties of autosomes. We capitalized on the unusual structure of the sex chromosomes of emus, Dromaius novaehollandiae, which consist almost entirely of PAR shared by both sex chromosomes, to test this hypothesis. We compared recombination, linkage disequilibrium (LD), GC content, and nucleotide diversity between pseudoautosomal and autosomal loci derived from 11 emu bacterial artificial chromosome (BAC) clones that were mapped to chromosomes by fluorescent in situ hybridization. Nucleotide diversity ({pi} = 4Ne{micro}) was not significantly lower in pseudoautosomal loci (14 loci, 1.9 {+/-} 2.4 x 10-3) than autosomal loci (8 loci, 4.2 {+/-} 6.1 x 10-3). By contrast, recombination per site within BAC-end sequences ({rho} = 4Nc) (pseudoautosomal, 3.9 {+/-} 6.9 x 10-2; autosomal, 2.3 {+/-! } 3.7 x 10-2) was higher and average LD (D') (pseudoautosomal, 4.2 {+/-} 0.2 x 10-1; autosomal, 4.7 {+/-} 0.5 x 10-1) slightly lower in pseudoautosomal sequences. We also report evidence of deviation from a simple neutral model in the PAR and in autosomal loci, possibly caused by departures from demographic equilibrium, such as population growth. This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation. - Evolution of Microsatellite Loci in the Adaptive Radiation of Hawaiian Honeycreepers
Eggert LS Beadell JS McClung A McIntosh CE Fleischer RC - J Hered 100(2):137-147 (2009)
Previous studies have examined germ-line mutations to infer the processes that generate and maintain variability in microsatellite loci. Few studies, however, have examined patterns to infer processes that act on microsatellite loci over evolutionary time. Here, we examine changes in 8 dinucleotide loci across the adaptive radiation of Hawaiian honeycreepers. The loci were found to be highly variable across the radiation, and we did not detect ascertainment bias with respect to allelic diversity or allele size ranges. In examining patterns at the sequence level, we found that changes in flanking regions, repeat motifs, or repeat interruptions were often shared between closely related species and may be phylogenetically informative. Genetic distance measures based on microsatellites were strongly correlated with those based on mitochondrial DNA (mtDNA) sequences as well as with divergence time up to 3 My. Phylogenetic inferences based on microsatellite genetic distances! consistently recovered 2 of the 4 honeycreeper clades observed in a tree based on mtDNA sequences but differed from the mtDNA tree in the relationships among clades. Our results confirm that microsatellite loci may be conserved over evolutionary time, making them useful in population-level studies of species that diverged from the species in which they were characterized as long as 5 Ma. Despite this, we found that their use in phylogenetic inference was limited to closely related honeycreeper species. - Y Chromosome Haplotype Analysis in Portuguese Cattle Breeds Using SNPs and STRs
Ginja C Telo da Gama L Penedo MC - J Hered 100(2):148-157 (2009)
DNA samples from 307 males of 13 Portuguese native cattle breeds, 57 males of the 3 major exotic breeds in Portugal (Charolais, Friesian, and Limousin), and 5 Brahman (Bos indicus) were tested for 5 single nucleotide polymorphisms, 1 "indel," and 7 microsatellites specific to the Y chromosome. The 13 Y-haplotypes defined included 3 previously described patrilines (Y1, Y2, and Y3) and 10 new haplotypes within Bos taurus. Native cattle contained most of the diversity with 7 haplotypes (H2Y1, H3Y1, H5Y1, H7Y2, H8Y2, H10Y2, and H12Y2) found only in these breeds. H6Y2 and H11Y2 occurred in high frequency across breeds including the exotics. Introgression of Friesian cattle into Ramo Grande was inferred through their sharing of haplotype H4Y1. Among the native breeds, Mertolenga had the highest haplotype diversity (0.68 {+/-} 0.07), Brava de Lide was the least differentiated. The analyses of molecular variance showed significant (P < 0.0001) differences between breeds with m! ore than 64% of the total genetic variation found among breeds within groups and 33-35% within breeds. The detection of INRA189-104 allele in 8 native breeds suggested influence of African cattle in breeds of the Iberian Peninsula. The presence in Portuguese breeds of Y1 patrilines, also found in aurochs, could represent more ancient local haplotypes. - Assessing Natural Introgression in 2 Biomedical Model Species, the Rhesus Macaque (Macaca mulatta) and the Long-Tailed Macaque (Macaca fascicularis)
Bonhomme M Cuartero S Blancher A Crouau-Roy B - J Hered 100(2):158-169 (2009)
Rhesus macaque (Macaca mulatta) and long-tailed macaque (Macaca fascicularis) are the 2 most commonly used primate model species in biomedical sciences. Although morphological studies have revealed a weak hybridization at the interspecific contact zone, in the north of Indochina, a molecular study has suggested an ancient introgression from rhesus to long-tailed macaque into the Indo-Chinese peninsula. However, the gene flow between these 2 taxa has never been quantified using genetic data and theoretical models. In this study, we have examined genetic variation within and between the parapatric Chinese rhesus macaque and Indo-Chinese long-tailed macaque populations, using 13 autosomal, 5 sex-linked microsatellite loci and mitochondrial DNA sequence data. From these data, we assessed genetic structure and estimated gene flow using a Bayesian clustering approach and the "Isolation with Migration" model. Our results reveal a weak interspecific genetic differentiation at ! both autosomal and sex-linked loci, suggesting large population sizes and/or gene flow between populations. According to the Bayesian clustering, Chinese rhesus macaque is a highly homogeneous gene pool that contributes strongly to the current Indo-Chinese long-tailed macaque genetic makeup, whether or not current admixture is assumed. Coalescent simulations, which integrated the characteristics of the loci, pointed out 1) a higher effective population size in rhesus macaque, 2) no mitochondrial gene flow, and 3) unilateral and male-mediated nuclear gene flow of [~]10 migrants per generation from rhesus to long-tailed macaque. These patterns of genetic structure and gene flow suggest extensive ancient introgression from Chinese rhesus macaque into the Indo-Chinese long-tailed macaque population. - Population Structure and Genetic Diversity of Moose in Alaska
Schmidt JI Hundertmark KJ Bowyer RT McCracken KG - J Hered 100(2):170-180 (2009)
Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (HE = 0.483-0.612), and private alleles ranged from 0 to 6. Both FST and RST indicated significant population structure (P < 0.001) with FST < 0.109 and RST < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other m! oose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R2 = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast. - Fluctuating Asymmetry in Hybrids of Sibling Species, Drosophila ananassae and Drosophila pallidosa, Is Trait and Sex Specific
Vishalakshi C Singh BN - J Hered 100(2):181-191 (2009)
Due to inconsistent results of the empirical studies, the relationship between fluctuating asymmetry (FA, a measure of developmental stability) and interspecific hybridization has been the subject of intense debates. In the present study, we have assessed the impact of interspecific hybridization between 2 sibling species of Drosophila: Drosophila ananassae and Drosophila pallidosa on the levels of FA over 3 generations. Trait size of different morphological traits, namely, sternopleural bristle number, wing length (WL), wing to thorax (W/T) ratio, sex comb tooth number (SCTN), and ovariole number differed significantly among parental species and their hybrids of different generations in both the sexes. However, the levels of FA of different morphological traits were similar in parental species and their hybrids of different generations in males (except SCTN) and in females (except for WL and W/T ratio). These results are interpreted in terms of developmental stability! as a function of a balance between the level of heterozygosity and the disruption of coadapted gene complexes. - Wolbachia in the Culex pipiens Group Mosquitoes: Introgression and Superinfection
Walker T Song S Sinkins SP - J Hered 100(2):192-196 (2009)
Wolbachia bacteria in mosquitoes induce cytoplasmic incompatibility (CI), where sperm from Wolbachia-infected males can produce inviable progeny. The wPip strain in the Culex pipiens group of mosquitoes produces a complexity of CI crossing types. Several factors are thought to be capable of influencing the expression of CI including Wolbachia strain type and host genotype. In this study, the unidirectional CI that occurs between 2 C. pipiens complex laboratory strains, Col and Mol, was further investigated by nuclear genotype introgression. The unidirectional CI between Col and Mol was not found to be influenced by host genetic background, in contrast to a previous introgression study carried out using bidirectionally incompatible C. pipiens group strains. A line containing both wPip strain variants superinfection was also generated by embryonic cytoplasmic transfer. The same crossing type as the parental Col strain was observed in the superinfected line. Quantitative ! polymerase chain reaction demonstrated a low density of the injected wPipMol variant in the superinfected line after 18 generations, which was considered likely to be responsible for the crossing patterns observed. The Wolbachia density was also shown to be lower in the parental Mol strain males compared with Col strain males, and no inverse relationship between WO phage and Wolbachia density could be detected. - Assessing Parent Numbers from Offspring Genotypes: The Importance of Marker Polymorphism
Sefc KM Koblmüller S - J Hered 100(2):197-205 (2009)
Methods to infer parent numbers from offspring genotypes either determine the minimum number of parents required to explain alleles and multilocus genotypes detected in the offspring or use models to incorporate information on population allele frequencies and allele segregation. Disparate results by different approaches suggest that one or perhaps all methods are subject to bias. Here, we investigate the performance of minimum parent number estimates, maximum likelihood, and Bayesian analyses (programs COLONY and PARENTAGE) with respect to marker information content in simulated data sets without knowledge of parental genotypes. Offspring families of different sizes were assumed to share one parent and to be sired by 1 or 5 additional parents. All methods committed large errors in terms of underestimation (minimum value) and overestimation (COLONY), or both (PARENTAGE) of parent numbers, unless the data were highly informative, and their relative performances depended! on full-sib group sizes and sire numbers. Increasing the number of markers with low gene diversity (He [≤] 0.68) yielded only slow improvement of the results, but all 3 methods performed well with 5-7 markers of He = 0.84. We emphasize the importance of high marker polymorphism for inferring parent numbers and individual parent contributions, as well as for the detection of monogamous reproduction. - Phylogeographical Structure of the Neotropical Forest Tree Hymenaea courbaril (Leguminosae: Caesalpinioideae) and Its Relationship with the Vicariant Hymenaea stigonocarpa from Cerrado
Ramos AC De Lemos-Filho JP Lovato MB - J Hered 100(2):206-216 (2009)
The phylogeography of Hymenaea courbaril var. stilbocarpa from Atlantic Forest and riverine forests of the Cerrado biome in central and southeastern Brazil was investigated. The data were compared with those of its congeneric Hymenaea stigonocarpa, a typical tree from savanna. In the Cerrado, H. courbaril var. stilbocarpa is found in sites contiguous with those of H. stigonocarpa, and they share common life-history attributes. The psbC/trnS3 region of the chloroplast DNA was sequenced in 149 individuals of H. courbaril var. stilbocarpa. High genetic variation was found in this species, with the identification of 18 haplotypes, similarly to what was found in H. stigonocarpa with 23 haplotypes in the same geographic region. Populations of H. courbaril var. stilbocarpa could be structured in 3 phylogeographic groups. Spatial analysis of molecular variation indicated that 46.4% of the genetic variation was due to differences among these groups. Three haplotypes were shared! by H. courbaril var. stilbocarpa and H. stigonocarpa, and only 10.5% of the total genetic variation could be attributed to between-species difference. We surmise that during the glacial times, H. courbaril var. stilbocarpa populations must have gone extinct in most parts of the southern of its present-day occurrence area. After climate amelioration, these areas were probably recolonized from northern and eastern. The relatively similar phylogeographic structure of vicariant Hymenaea species suggests that they were subjected to the same impacts during the Quaternary climatic fluctuations. The sharing of haplotypes and the genetic similarity between the 2 Hymenaea species suggest the existence of ancestral polymorphism and/or hybridization. - The Maize enr System of r1 Haplotype-Specific Aleurone Color Enhancement Factors
Stinard PS Kermicle JL Sachs MM - J Hered 100(2):217-228 (2009)
We describe a family of 3 dominant r1 haplotype-specific enhancers of aleurone color in Zea mays. Stable alleles of the 3 enhancement of r1 loci (enr1, enr2, and enr3) intensify aleurone color conferred by certain pale and near-colorless r1 haplotypes. In addition, unstable alleles of enr1 act on the same set of r1 haplotypes, producing spotted kernels. Components of this instability cross react with the Fcu system of instability. Two of the enr loci are linked with one another but none of the 3 are linked with r1. The r1 haplotypes affected by enr alleles overlap those affected by the inr family of r1 haplotype-specific inhibitors of aleurone color, suggesting a possible interaction. - On the Genetic Control of Heterosis for Fruit Shape in Melon (Cucumis Melo L.)
Fernández-Silva I Moreno E Eduardo I Arús P Alvarez JM Monforte AJ - J Hered 100(2):229-235 (2009)
The objective of the present work is to study the genetic basis of heterosis for fruit shape (FS) in melon observed in a cross between the Spanish cultivar "Piel de Sapo" (PS) and the Korean accession PI 161375 (Songwang Charmi [SC]) using a set of near-isogenic lines (NILs) with contrasting phenotypes for FS, each carrying a single chromosomal introgression from SC within the genetic background of PS. We investigated the FS of homozygous NILs, hybrids NIL x PS, and all 2-way crosses between NILs to test the main heterosis hypotheses (dominance, overdominance, and epistatic interactions). Gene action of alleles of quantitative trait loci inducing fruit enlargement was dominance, whereas those inducing rounder fruit were additive or recessive. Only minor epistatic interactions were found. Therefore, the most plausible explanation for FS heterosis in this cross is in agreement with the dominance complementation hypothesis. Over 70% of the hybrid heterosis could be achiev! ed by combining just 2 loci, indicating that the genetic control of FS heterosis in this cross is relatively simple. FS is proposed as a reproductive trait in melon because of the high correlation to the number of seeds produced along the fruit longitudinal axis. - Ancestral T-Box Mutation Is Present in Many, but Not All, Short-Tailed Dog Breeds
Hytönen MK Grall A Hédan B Dréano S Seguin SJ Delattre D Thomas A Galibert F Paulin L Lohi H Sainio K André C - J Hered 100(2):236-240 (2009)
Dogs differ greatly in their morphological characteristics including various tail phenotypes. Congenitally short-tailed dogs are present in many breeds; however, the causative mutation located in the T-box transcription factor T gene (C189G) had only been described in the bobtailed Pembroke Welsh Corgis. We investigated here the presence of the T gene mutation in 23 other breeds (360 dogs, including 156 natural short tailed) in which natural bobtailed dogs exist. In the 17 breeds in which the C189G mutation was observed, there was a perfect correlation between this mutation and the short-tail phenotype. However, 6 breeds did not carry the known substitution or any other mutations in the T gene coding regions. No dogs were found to be homozygous for the C189G mutation, suggesting that the homozygous condition is lethal. In order to study the effect of the T gene mutation on litter size, we compared the number of puppies born from short-tailed parents to that born from l! ong-tailed parents. In the Swedish Vallhund breed, we observed a 29% decrease in the litter size when both parents were short tailed. Given that the T gene mutation is not present in all breeds of short-tailed dog, there must be yet other genetic factors affecting tail phenotypes to be discovered. - Sequence Analysis and Polymorphism Discovery in 4 Members of the Bovine Cathelicidin Gene Family
Gillenwaters EN Seabury CM Elliott JS Womack JE - J Hered 100(2):241-245 (2009)
Cathelicidins (CATHLs) are small, cationic antimicrobial peptides that establish an early innate immune defense against infections in mammals. Beyond their wide spectrum of antimicrobial activity, these peptides play important roles in wound repair, chemotactic activity, and apoptosis. Thus, polymorphisms present in bovine CATHLs 2, 5, 6, and 7 could potentially underlie inherited differences in innate immunity and disease resistance. The purpose of the present study was to characterize single nucleotide polymorphisms (SNPs) and insertion-deletion (indel) polymorphisms within the bovine CATHL gene family. Comparative sequence analysis for 10 domestic cattle breeds representing both Bos taurus and Bos indicus revealed 60 SNPs, 7 of which were nonsynonymous and 5 indel mutations. Characterization of these novel polymorphisms is central to developing a firm understanding regarding what effects, if any, nonsynonymous CATHL variation has with respect to bovine innate immuni! ty. - Simultaneous Extraction of High-Quality RNA and DNA from Small Tissue Samples
Triant DA Whitehead A - J Hered 100(2):246-250 (2009)
Purification of high-quality DNA and RNA from a single sample is becoming increasingly important for studies seeking both genomic and transcriptomic data. We compare different methods for isolating DNA and RNA from fish embryos (Gulf killifish; Fundulus grandis) and describe an optimal technique to extract high-quality DNA and RNA from a single embryo. The optimal method utilizes a chaotropic buffer and spin column technology. From embryos weighing [~]4 mg, we were able to isolate an average of 6.1 {micro}g of DNA and 1.1 {micro}g of RNA per sample. Relative amounts of DNA and RNA can be adjusted as needed per study. Although these extraction trials were conducted on fish embryos, they can be potentially applied to small samples that typically do not yield high concentrations of nucleic acids. - Mendelian Inheritance of Pupal Diapause in the Flesh Fly, Sarcophaga bullata
Han B Denlinger DL - J Hered 100(2):251-255 (2009)
Pupal diapause (dormancy) in the flesh fly, Sarcophaga bullata, is induced by short-day photoperiods and low temperature. In this study, the inheritance mode of diapause was investigated by crossing a nondiapausing (nd) strain of S. bullata with 2 diapausing strains having different diapause capacities. The results consistently indicated that diapause incidence is inherited in a simple Mendelian pattern, thus a single gene or a small gene cluster linked to the photoperiodic clock controls the seasonal response of diapause. The fact that the nd strain lacked daily rhythmicity in adult eclosion and showed altered expression of 2 circadian clock genes suggests that the photoperiodic and circadian clocks are related through a shared molecular component in S. bullata. - Development of EST-SSR Markers for the Study of Population Structure in Lettuce (Lactuca sativa L.)
Simko I - J Hered 100(2):256-262 (2009)
A set of 61 simple sequence repeat (SSR) markers was developed from the 19 523 Lactuca sativa and Lactuca serriola unigenes. Approximately 4.5% of the unigenes contained a perfect SSR at least 20 bp long, corresponding to roughly 1 perfect SSR per 14.7 kb. Marker polymorphism was tested on a set comprising 96 accessions representing all major horticultural types and 3 wild species (L. serriola, Lactuca saligna, and Lactuca virosa). Both the average marker heterozygosity (UHe = 0.32) and the number of different alleles per locus (Na = 3.56) were significantly reduced in expressed sequence tag (EST)-SSRs as compared with anonymous SSRs (UHe = 0.59, Na = 5.53). Marker transfer rate to the wild species corresponded to the decreasing sexual compatibility with L. sativa and was higher for EST-SSRs (100% L. serriola, 87% L. saligna, and 75% L. virosa) than for anonymous SSRs (93%, 66%, and 42%, respectively). Assessment of population structure among 90 L. sativa cultivars wit! h SSRs was in good agreement with classification into the horticultural types. The average marker heterozygosity was smallest in iceberg (0.097), Latin (0.140), and romaine-type (0.151) cultivars while highest in leaf (green leaf 0.208 and red leaf 0.240) lettuces. The level of marker heterozygosity is in accord with morphological variability observed in different horticultural types. - Putative Quantitative Trait Loci Associated with Calcium Content in Soybean Seed
Zhang B Chen P Shi A Hou A Ishibashi T Wang D - J Hered 100(2):263-269 (2009)
Seed calcium content is an important quality attribute of specialty soybean [Glycine max (L.) Merr.] for soyfoods. However, analyzing seed for calcium content is time consuming and labor intensive. Knowing quantitative trait loci (QTL) for seed calcium will facilitate the development of elite cultivars with proper calcium content through marker-assisted selection (MAS). The objective of this study was to identify major QTL associated with calcium content in soybean seed. Calcium content was tested in 178 F2:3 and 157 F2:4 lines derived from the cross of SS-516 (low calcium) x Camp (high calcium). The F2:3 lines were genotyped with 148 simple sequence repeat markers in a previous study on seed hardness, and the genotypic data were used in the QTL analysis of the current study. Four QTL designated as Ca1, Ca2, Ca3, and Ca4 on linkage groups (LGs) A2, I, and M were identified by both single-marker analysis and composite-interval mapping, and the QTL accounted for 10.7%, 1! 6.3%, 14.9%, and 9.7% of calcium content variation, respectively. In addition, multiple-interval mapping analysis revealed a significant dominant-by-dominant interaction effect between Ca1 and Ca3, which accounted for 4.3% calcium content variation. These QTL will facilitate the implementation of MAS for calcium content in soybean-breeding programs. - Announcements
- J Hered 100(2):270-271 (2009)
No comments:
Post a Comment