Journal of Heredity - Advance Access

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Genome 10K Community of Scientists — Fri, 06 Nov 2009 00:36:48 PST

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Microsatellite Genetic Characterization of the Humpback Whale (Megaptera novaeangliae) Breeding Ground off Brazil (Breeding Stock A)

Wed, 04 Nov 2009 04:30:08 PST

The Southwestern Atlantic Ocean humpback whales wintering ground (breeding stock A) are distributed along the Brazilian coast (5–23°S), and their main mating and calving ground is in the Abrolhos Bank. We investigated genetic diversity, population structure, and relatedness of individuals sampled from the entire Southwest Atlantic humpback whale population. A total of 275 individuals sampled from 2 subregions (Abrolhos Bank, n = 229 and Praia do Forte, n = 46) were screened for 9 microsatellite loci. This population showed a high level of allelic diversity (A = 12.1) and a high mean observed heterozygosity (H_O = 0.733). No signal of significant genetic bottleneck was detected in accordance with the mitochondrial DNA data. We find no evidence of temporal (between years) genetic structure as well as no genetic differentiation between whales from the 2 subregions of the Brazilian breeding ground. We observed that the proportion of males and females in this population was approximately 1:1, which differs from the male-biased sex ratio observed in other breeding grounds. The data obtained through this study provided no evidence of kinship associations within social groups. Finally, a female sampled off South Georgia Islands showed a putative parent–offspring relationship with a female off Abrolhos Bank, supporting the migratory link between these 2 areas.

Maternal Effects on the Hygienic Behavior of Russian x Ontario Hybrid Honeybees (Apis mellifera L.)

Unger, P., Guzman-novoa, E. — Wed, 04 Nov 2009 04:30:08 PST

Strains and hybrids of Russian and Ontario honeybees (Apis mellifera L.) were evaluated for hygienic behavior at both colony and individual levels. The objectives were to determine phenotypic and genotypic variability and to study the inheritance of this behavior. At the colony level, Russian bees uncapped and removed significantly more freeze-killed brood than Ontario bees. The most hygienic Russian colonies and the least hygienic Ontario colonies were selected to perform reciprocal crosses between the strains. Bees from the hybrid colonies as well as from the parental colonies were tagged and introduced into observation hives, where hygienic behavior was directly observed on a piece of frozen brood comb. Russian and hybrid bees of Russian mother had the highest percentages of workers uncapping cells and removing brood. Conversely, Ontario and hybrid bees of Ontario mother had the lowest percentages of individuals for these variables. Differences were also observed among the 4 genotypes for their degree of specialization on hygienic tasks. Russian and hybrid bees of Russian mother showed a significantly higher uncapping frequency per individual than Ontario and hybrid bees of Ontario mother. These results demonstrate phenotypic and genotypic variability for hygienic behavior and are suggestive of maternal effects in the inheritance of hygienic traits.

Simultaneous Evaluation of Paternal and Maternal Immigrant Gene Flow and the Implications for the Overall Genetic Composition of Pinus densiflora Dispersed Seeds

Iwaizumi, M. G., Takahashi, M., Watanabe, A., Ubukata, M. — Wed, 04 Nov 2009 04:30:07 PST

When considering the genetic implications of immigrant gene flow, it is important to evaluate both the proportions of immigrant gametes and their genetic composition. We simultaneously investigated paternal and maternal gene flow in dispersed seeds in a natural population of Pinus densiflora located along a ridge. The paternity and maternity of a total of 454 dispersed seeds (in 2004 and 2005) were accurately and separately assigned to 454 candidate adult trees, by analyzing the nuclear DNA of both diploid biparentally derived embryos and haploid maternally derived megagametophytes of the seeds. The relative genetic diversities and differences between within-population and immigrant groups of both paternally and maternally derived gametes (4 groups) that formed the genotypes of the seeds were evaluated. Using 8 microsatellite markers, we found that 64.0–72.6% of paternally derived gametes, and 17.8–20.2% of maternally derived gametes, were from other populations. Principal coordinate analysis showed that the 4 gamete groups tended to be plotted at different locations on the scattergram, indicating that they each have different genetic compositions. Substantial paternal and maternal immigrant gene flow occurred in this population, and therefore, the overall genetic variation of dispersed seeds is enhanced by both paternally and maternally derived immigrant gametes.

Next Generation Sequencing in Nonmodel Organisms: Has the Future Arrived?

Johansson, M. L. — Mon, 02 Nov 2009 14:58:47 PST

Phylogenetic Analysis of Subgenus Vigna Species Using Nuclear Ribosomal RNA ITS: Evidence of Hybridization among Vigna unguiculata Subspecies

Vijaykumar, A., Saini, A., Jawali, N. — Tue, 27 Oct 2009 12:06:02 PDT

Molecular phylogeny among species belonging to subgenus Vigna (genus Vigna) was inferred based on internal transcribed spacer (ITS) sequences of 18S–5.8S–26S ribosomal RNA gene unit. Analysis showed a total of 356 polymorphic sites of which ~80% were parsimony informative. Phylogenetic reconstruction by neighbor joining and maximum parsimony methods placed the 57 Vigna accessions (belonging to 15 species) into 5 major clades. Five species viz. Vigna heterophylla, Vigna pubigera, Vigna parkeri, Vigna laurentii, and Vigna gracilis whose position in the subgenus was previously not known were placed in the section Vigna. A single accession (Vigna unguiculata ssp. tenuis, NI 1637) harbored 2 intragenomic ITS variants, indicative of 2 different types of ribosomal DNA (rDNA) repeat units. ITS variant type-I was close to ITS from V. unguiculata ssp. pubescens, whereas type-II was close to V. unguiculata ssp. tenuis. Transcript analysis clearly demonstrates that in accession NI 1637, rDNA repeat units with only type-II ITS variants are transcriptionally active. Evidence from sequence analysis (of 5.8S, ITS1, and ITS2) and secondary structure analysis (of ITS1 and ITS2) indicates that the type-I ITS variant probably does not belong to the pseudogenic rDNA repeat units. The results from phylogenetic and transcript analysis suggest that the rDNA units with the type-I ITS may have introgressed as a result of hybridization (between ssp. tenuis and ssp. pubescens); however, it has been epigenetically silenced. The results also demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. unguiculata.

In Pursuit of the Gene: From Darwin to DNA

Smocovitis, V. B. — Tue, 27 Oct 2009 12:06:00 PDT

Isolation and Phylogenetic Footprinting Analysis of the 5'-Regulatory Region of the Floral Homeotic Gene OrcPI from Orchis italica (Orchidaceae)

Aceto, S., Cantone, C., Chiaiese, P., Ruotolo, G., Sica, M., Gaudio, L. — Tue, 27 Oct 2009 12:05:59 PDT

The nucleotide sequences of regulatory elements from homologous genes can be strongly divergent. Phylogenetic footprinting, a comparative analysis of noncoding regions, can detect putative transcription factor binding sites (TFBSs) shared among the regulatory regions of 2 or more homologous genes. These conserved motifs have the potential to serve the same regulatory function in distantly related taxa. We isolated the 5'-noncoding region of the OrcPI gene, a MADS-box transcription factor involved in flower development in Orchis italica, using the thermal asymmetric interlaced polymerase chain reaction technique. This region (comprising 1352 bp) induced transient β-glucuronidase expression in the petal tissue of white Rosa hybrida flowers and represents the 5'-regulatory sequence of the OrcPI gene. Phylogenetic footprinting analysis detected conserved regions within the 5'-regulatory sequence of OrcPI and the homologous regions of Oryza sativa, Lilium regale, and Arabidopsis thaliana. Some of these sequences are known TFBSs described in databases of plant regulatory elements. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the following accession numbers: AF198055 promoter region of the PISTILLATA (PI) gene of A. thaliana; AB094985 cDNA of OrcPI (PI/GLOBOSA [PI/GLO] homologue) of O. italica; AB378089 5'-regulatory region of the OrcPI gene of O. italica; AP008211 putative promoter region of OSMADS2 (PI/GLO homologue) of O. sativa; AP008207 putative promoter region of OSMADS4 (PI/GLO homologue) of O. sativa; and AB158292 putative promoter region of the PI/GLO homologue of L. regale.

Dominant and Recessive Inheritance Patterns of Diapause in the Two-Spotted Spider Mite Tetranychus urticae

Kawakami, Y., Numata, H., Ito, K., Goto, S. G. — Wed, 21 Oct 2009 03:28:07 PDT

In this study, we investigated the diapause incidence in 3 geographic strains of the two-spotted spider mite Tetranychus urticae (Acari: Tetranychidae). Under diapause-inducing conditions of 12:12 light:dark at 15 °C, the diapause incidence was nearly 100% in a strain from northern Japan (Sapporo), whereas it was nearly 0% in 2 strains from southern Japan (Itoman and Takanabe). Reciprocal crosses clearly showed that the nondiapause phenotype is inherited in a completely dominant manner, and no maternal effect was detected. Backcrosses to the Itoman and Takanabe strains suggested that dominant nondiapause alleles control the nondiapause phenotype. To clarify the genetic basis of nondiapause in the northern population, we also established a nondiapausing variant ("selected nondiapause" abbreviated as snd) from the Sapporo strain. Crossing experiments revealed that a single recessive allele is responsible for the nondiapause phenotype. Thus, both dominant and recessive inheritance patterns of diapause were detected in the T. urticae populations studied here.

Seasonal Changes in the Long-Distance Linkage Disequilibrium in Drosophila melanogaster

Wed, 30 Sep 2009 04:40:30 PDT

Seasonal environmental changes have the potential to influence the genetic structure of species with a short generation time, such as Drosophila. We previously found the seasonal change in linkage disequilibrium (LD) between the chemoreceptor (Cr) genes in a local Japanese population (Kyoto [KY]). This could be caused by fluctuation in the population size or selection in temporally heterogeneous environments or both. Here, we analyzed the scale of LD between 51 X-linked polymorphisms (10 Cr and 41 non-Cr gene markers) in the 2 seasonal samples from the KY population and an autumn sample from 106 localities in and around Japan (Ja03au). Many of the non-Cr genes have receptor function but fewer functional connections to each other. The magnitude of LD in Ja03au did not significantly differ from that in the KY autumn sample. The lack of local differentiation was confirmed in an autumn sample from another local Japanese population. On the other hand, the magnitude of LD was significantly larger in spring than in autumn in the 2 independent KY samples. This suggests that reduction in the population size during winter increased the magnitude of LD in spring in the mainland population in Japan. Long-distance LD could be a useful measure for assessing seasonal fluctuation in effective population size.

Microsatellite Marker Development and Mendelian Analysis in the Matschie's Tree Kangaroo (Dendrolagus matschiei)

McGreevy, T. J., Dabek, L., Husband, T. P. — Sat, 26 Sep 2009 00:26:53 PDT

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered arboreal macropodid endemic to the Huon Peninsula, Papua New Guinea (PNG). We developed 5 microsatellite markers for D. matschiei, which are the first markers developed for Dendrolagus. We screened 17 additional markers that were developed for other marsupial taxa and identified 3 that were polymorphic in D. matschiei. We estimated allelic and genetic diversity with the set of 8 markers by analyzing 22 D. matschiei from Wasaunon on the Huon Peninsula, PNG. The number of alleles ranged from 2 to 9 and expected heterozygosity ranged from 0.440 to 0.794. We tested for null alleles and Mendelian inheritance by analyzing 19 pairs of D. matschiei parents and offspring from Association of Zoos and Aquariums institutions. Null alleles were not detected and Mendelian inheritance was followed for all 8 markers. We also evaluated the reliability of using the markers to amplify DNA extracted from D. matschiei fecal samples and the ability of the markers to amplify DNA samples from Goodfellow's tree kangaroo (Dendrolagus goodfellowi ssp.), Doria's tree kangaroo (Dendrolagus dorianus ssp.), and Grizzled tree kangaroo (Dendrolagus inustus ssp.). Microsatellite markers can be used to inform management decisions to conserve D. matschiei in captivity and the wild.

Sequence Divergence of Heat Shock Genes within and among 3 Oncorhynchids

Narum, S. R., Campbell, N. R. — Tue, 22 Sep 2009 08:22:00 PDT

Heat shock proteins (Hsps) are induced in response to high temperatures and other stressors, and sequence variation plays a role in regulation of expression of these genes. In this study, we investigated the sequence variation in the 3 major classes of Hsps (Hsp90, Hsp70, and low-molecular weight Hsp) within and among 3 cold-water fish species of Oncorhynchus (Oncorhynchus clarki, Oncorhynchus mykiss, and Oncorhynchus tshawytscha) with variable life history and thermal tolerance characteristics. Sequences collectively totaled 4556 bp across 9 gene fragments and 198 single nucleotide polymorphisms and 43 indel sites were observed among species. Within species, sequence variation was much lower for O. clarki than the other 2 species. Sequence variation within and among species was high in cis-regulatory regions that are potentially involved in transcription of Hsps under variable stressors. Our results indicate that Hsp genes may be locally adapted in O. clarki, whereas higher Hsp polymorphism is necessary for O. mykiss and O. tshawytscha and variation at the sequence level may have important evolutionary consequences for these species. Further studies are needed to determine the association of observed sequence variation with the regulation of Hsps and performance of fish under stress.

Temporal Variation in Population Genetic Structure of a Riverine African Cichlid Fish

Crispo, E., Chapman, L. J. — Fri, 04 Sep 2009 07:08:53 PDT

Population genetic structure in a riverine cichlid fish was recharacterized 2 years after patterns had been first described. We found that genetic structure changed, as evidenced by changes in F_ST between years among sites, significant F_ST between years "within" sites, and a significant proportion of the genetic variation partitioned between years. Most striking, signatures of isolation by distance were eradicated between years. Our study highlights that point-in-time estimates of population genetic structure might not be valid over longer time periods, particularly in systems exposed to strong seasonal or interannual variation in abiotic conditions.

Genetic Differentiation among Wild Populations of Tribolium castaneum Estimated Using Microsatellite Markers

Drury, D. W., Siniard, A. L., Wade, M. J. — Fri, 04 Sep 2009 07:08:52 PDT

We report our characterization of the genetic variation within and differentiation among wild-collected populations of the red flour beetle, Tribolium castaneum, using microsatellite loci identified from its genome sequence. We find that global differentiation, estimated as the average F_ST across all loci and between all population pairs, is 0.180 (95% confidence intervals of 0.142 and 0.218). A majority of our pairwise population comparisons (>70%) were significant even though this species is considered an excellent colonizer by virtue of its pest status. Regional genetic variation between Tribolium populations is 2–3 times that observed in the fruit fly, Drosophila melanogaster. There was a weak positive correlation between genetic distance [F_ST/(1 – F_ST)] and geographic distance [ln(km)]; pairs of populations with the highest degree of genetic differentiation (F_ST > 0.29) have been shown to exhibit significant postzygotic reproductive isolation when crossed in previous studies. We discuss the possibility that local extinction and kin-structured colonization have increased the level of genetic differentiation between Tribolium populations.

Ploidy-Mediated Reduced Segregation Facilitates Fixation of Heterozygosity in the Aromatic Grass, Cymbopogon martinii (Roxb.)

Lavania, U. C., Srivastava, S., Lavania, S. — Tue, 25 Aug 2009 06:47:46 PDT

In most medicinal and aromatic plants, the vegetative tissue (e.g., roots, stems, leaves) is the source of the economic product. These plants are inherently heterozygous (natural allelic hybrids) and maintain their genetic makeup in nature by obligate vegetative propagation. Under seed cultivation, these plants incur population heterogeneity that reduces biomass and hampers product quality. Therefore, fixation of heterozygosity is vital for maintaining uniformity in quality of the economic product and quantity of biomass under seed cultivation. Although seed-grown clonal progenies identical to the mother plant can be obtained in certain plants that show an unusual breeding system called apomixis, such a breeding system is rare in medicinal and aromatic plants of economic value. Here we show an effective experimental strategy based on a polyploid model that facilitates fixation of heterozygosity in obligate asexual species owing to tetrasomic inheritance and low segregation in C₁ progenies from high-fertility C₀ autopolyploids. Using an obligate asexual species of aromatic grass—Cymbopogon martinii, we demonstrated that progenitor diploids with distal chiasma localization and low chiasmate association in meiosis, when changed into tetraploids, entail high gametic/seed fertility reflected in high bivalent pairing and balanced anaphase segregation. Their seed progenies evince crop homogeneity owing to reduced segregation, indicating fixation of heterozygosity present in the source diploids. Because C. martinii could be maintained through obligate vegetative propagation, here is a unique opportunity to utilize the polyploid advantage through C₁ seed progenies for commercial cultivation, as well as maintenance of original C₀ stock for raising seeds without losing polyploid heterosis normally threatened in subsequent segregating progenies on account of aneuploidy and gametic instability.

New Primers for the Avian SWS1 Pigment Opsin Gene Reveal New Amino Acid Configurations in Spectral Sensitivity Tuning Sites

Odeen, A., Hastad, O. — Mon, 17 Aug 2009 07:25:26 PDT

Recently, polymerase chain reaction–based estimates of visual pigment spectral tuning from genomic DNA have offered an alternative to the authoritative but rather slow and complicated retinal microspectrophotometry method. The genomic DNA method involves sequencing a fragment of the short-wavelength sensitive pigment, type 1 (SWS1) opsin gene covering amino acid positions 86, 90, and 93 and has been utilized in a wide range of avian species. Other key tuning sites have been proposed but not sequenced in the genomic DNA–based spectral sensitivity studies. We have designed 5 new primers for sequencing gene fragments of the ultraviolet-/violet-tuned SWS1 opsin gene containing the first, second and third, and sixth and seventh -helical transmembrane regions and the spectral tuning sites 49, 86, 90, 93, 116, 118 and 298. Testing these primers on various bird species reveals some novel combinations of amino acid residues at the tuning sites. The potential significance of these on spectral tuning is discussed.

The Aunt and Uncle Effect Revisited--The Effect of Biased Parentage Assignment on Fitness Estimation in a Supplemented Salmon Population

Ford, M. J., Williamson, K. S. — Mon, 10 Aug 2009 06:39:12 PDT

We investigated differences in the statistical power to assign parentage between an artificially propagated and wild salmon population. The propagated fish were derived from the wild population and are used to supplement its abundance. Levels of genetic variation were similar between the propagated and wild groups at 11 microsatellite loci, and exclusion probabilities were >0.999999 for both groups. The ability to unambiguously identify a pair of parents for each sampled progeny was much lower than expected, however. Simulations demonstrated that the proportion of cases in which the most likely pair of parents were the true parents was lower for propagated parents than for wild parents. There was a clear relationship between parentage assignment ability and the estimated effective number of grandparents of the progeny to be assigned. If a stringent threshold for parentage assignment was used, estimates of relative fitness were biased downward for the propagated fish. The bias appeared to be largely eliminated by either fractionally assigning progeny among parents in proportion to their likelihood of parentage or by assigning progeny to the most likely set of parents without using a statistical threshold.

QTL Underlying Voluntary Exercise in Mice: Interactions with the "Mini Muscle" Locus and Sex

Nehrenberg, D. L., Wang, S., Hannon, R. M., Garland, T., Pomp, D. — Mon, 10 Aug 2009 06:39:10 PDT

Exercise improves many aspects of human health, yet many people remain inactive even when exercise is prescribed. We previously created a backcross (BC) between mice selectively bred for high levels of voluntary wheel running (VWR) and fixed for "mini muscle" (MM), a recessive mutation causing ~50% reduction in triceps surae mass. We previously showed that BC mice having the MM trait ran faster and further than mice without MM and that MM maps to chromosome 11. Here, we genotyped the BC with genome-wide single nucleotide polymorphisms to identify quantitative trait loci (QTL) controlling voluntary exercise and tissue and body mass traits and to determine whether these QTL interact with the MM locus or with sex. We detected 3 VWR QTL, representing the first voluntary exercise QTL mapped using this high running selection line, and 5 tissue mass QTL. Several interactions between trait QTL and the MM locus as well as sex were also identified. These results begin to explain the genetic architecture of VWR and further support MM as a locus having major effects, including its main effects on the muscle phenotype, its pleiotropic effects on wheel running and tissue mass traits, and through its interactions with other QTL and with sex.

Development of Novel EST-SSRs from Sacred Lotus (Nelumbo nucifera Gaertn) and Their Utilization for the Genetic Diversity Analysis of N. nucifera

Pan, L., Xia, Q., Quan, Z., Liu, H., Ke, W., Ding, Y. — Fri, 07 Aug 2009 10:20:13 PDT

Expressed sequence tags (ESTs) provide a valuable resource for the development of simple sequence repeat (SSR) or microsatellite markers. This study identified SSRs within ESTs from Nelumbo nucifera (lotus or sacred lotus), developed markers from them, and assessed the potential of those markers for diversity analysis. Within 2207 ESTs from N. nucifera downloaded from GenBank, 1483 unigenes (303 contigs and 1180 singletons) were identified. After eliminating for redundancy, 125 SSR-containing ESTs were derived, and 71 unique SSRs were detected with an average density of one SSR per 13.04 kb. Dinucleotide repeats were the dominant motif in N. nucifera, whereas the sequences AG/TC/GA/CT, AAG/TTC/GAT/AGA, and AAAGCC were the most frequent of di-, tri-, and hexanucleotide motifs, respectively. The AG/TC (40.85%) and AAG (5.63%) motifs were predominant for the di- and trinucleotide repeats, respectively. Sixty-two SSR-containing ESTs were suitable for primer design. From these sequences, 23 EST–SSR markers were developed and were applied to 39 cultivated varieties of N. nucifera, 10 accessions of wild N. nucifera, and 1 accession of Nelumbo lutea (American lotus). Genetic diversity and genetic relationships were examined by constructing unweighted pair-group method with arithmetic average dendrograms and principal coordinates analysis plots based on SSR polymorphisms. Results indicated genetic differentiation between cultivated and wild lotus and between seed lotus cultivars and rhizome lotus cultivars. These EST–SSR markers will be useful for further studies of the evolution and diversity of Nelumbo.

Detection of Cytonuclear Genomic Dissociation in the North American Captive African Elephant Collection

Lei, R., Brenneman, R. A., Schmitt, D. L., Louis, E. E. — Wed, 05 Aug 2009 02:47:59 PDT

A total of 114 captive elephants (6 Asian; 108 African) from 43 private institutions or North American zoos accredited by the Association of Zoos and Aquariums were sampled and evaluated to investigate genetic status. Because previous analyses of the captive collection indicated potential cytonuclear dissociation between mitochondrial DNA (mtDNA) sequence and microsatellite nuclear DNA genotype data, we investigated this phenomenon within the captive collection with 2 X-linked genes (BGN and PHKA2) and 1 Y-linked gene (AMELY). These data reveal that individuals with forest-derived elephant mtDNA lineages carried only savannah elephant nuclear gene haplotypes. These results are concordant with a previous study of wild populations sampled across Africa, indicating that cytonuclear genomic dissociation was captured in the founders of the North American African elephant collection. These results are important for resolving questions that can potentially impact future management and breeding programs related to the collection.

AFLP Linkage Map of Hybridizing Swallowtail Butterflies, Papilio glaucus and Papilio canadensis

Winter, C. B., Porter, A. H. — Wed, 05 Aug 2009 02:47:58 PDT

High-density linkage maps provide powerful tools for studying the genetic basis of ecologically relevant adaptations and the genomic scope of introgression. We backcrossed an F₁ hybrid male Papilio glaucus/Papilio canadensis tiger swallowtail butterfly to a pure P. glaucus female and constructed amplified fragment length polymorphism linkage maps from the progeny. The paternal map contains 309 markers distributed among 29 linkage groups, with a corrected map distance of 1167 cM (logarithm of the odds [LOD] = 4.0). The average linkage group contained 10.65 ± 4.85 markers separated by 32.7 ± 3.8 cM, with statistically significant clustering. The paternal hybrid map had 18.65% more markers than the maternal P. glaucus map, which provides a rough estimate of the extent of genetic differentiation between the species. The maternal map contains 253 markers among 28 linkage groups, without the X and Y chromosomes. Segregation distortion from expected Mendelian ratios was observed for 94/1096 scored loci (8.6%, P < 0.05). The X chromosome map includes 7 markers spanning 29.3 cM (LOD = 3.0). These naturally hybridizing, female heterogametic species are used to study important questions in the maintenance of species boundaries, sex chromosome introgression, sex-limited mimicry, and host plant use. The map will facilitate research into the physiological, ecological, and evolutionary genetics of these phenomena.

The Genetic Basis of Melanism in the Gray Squirrel (Sciurus carolinensis)

McRobie, H., Thomas, A., Kelly, J. — Thu, 30 Jul 2009 02:51:41 PDT

The black squirrel is a melanic variant of the gray squirrel (Sciurus carolinensis). We found 3 coat color variants in the gray squirrel: the wild-type gray, a jet-black, and a brown–black phenotype. These 3 morphs are due to varying distributions of eumelanin and phaeomelanin pigment in hairs. The melanocortin 1 receptor (MC1R) plays a central role in regulating eumelanin and phaeomelanin production. We sequenced the MC1R gene for all 3 coat color phenotypes and found a 24 base-pair deletion. The gray phenotype was homozygous for the wild-type allele E⁺, the jet-black phenotype was homozygous for the MC1R-24 allele E^B, and the brown–black phenotype was heterozygous for the E⁺ and E^B alleles. We conclude that melanism in gray squirrels is associated with the MC1R-24 E^B allele at amino acid positions 87–94 and that this allele is incompletely dominant to the wild-type allele. We predict that the MC1R-24 E^B allele encodes a constitutively active or hyperactive receptor.

Genetic Variation, Relatedness, and Effective Population Size of Polar Bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

Cronin, M. A., Amstrup, S. C., Talbot, S. L., Sage, G. K., Amstrup, K. S. — Fri, 24 Jul 2009 12:25:43 PDT

Polar bears (Ursus maritimus) are unique among bears in that they are adapted to the Arctic sea ice environment. Genetic data are useful for understanding their evolution and can contribute to management. We assessed parentage and relatedness of polar bears in the southern Beaufort Sea, Alaska, with genetic data and field observations of age, sex, and mother–offspring and sibling relationships. Genotypes at 14 microsatellite DNA loci for 226 bears indicate that genetic variation is comparable to other populations of polar bears with mean number of alleles per locus of 7.9 and observed and expected heterozygosity of 0.71. The genetic data verified 60 field-identified mother–offspring pairs and identified 10 additional mother–cub pairs and 48 father–offspring pairs. The entire sample of related and unrelated bears had a mean pairwise relatedness index (r_xy) of approximately zero, parent–offspring and siblings had r_xy of approximately 0.5, and 5.2% of the samples had r_xy values within the range expected for parent-offspring. Effective population size (N_e = 277) and the ratio of N_e to total population size (N_e/N = 0.182) were estimated from the numbers of reproducing males and females. N_e estimates with genetic methods gave variable results. Our results verify and expand field data on reproduction by females and provide new data on reproduction by males and estimates of relatedness and N_e in a polar bear population.

Maternal Inheritance of Racemism in the Terrestrial Snail Bradybaena similaris

Utsuno, H., Asami, T. — Fri, 17 Jul 2009 11:32:35 PDT

In metazoan animals, almost every known mutation of visceral asymmetry, which presents the polarity of primary asymmetry established in early development, reverses development in only about half or fewer of homozygotes. However, in pulmonate snails, the dextral and sinistral alleles are traditionally known to determine the polarity of offspring with complete dominance, and thus, each parent should produce either dextral or sinistral progeny. Contrary to this expectation, we found a mutant that produces both chiral morphs (enantiomorphs) within the same clutches in Bradybaena similaris. This study demonstrates that the consistent production of both enantiomorphs is determined by a maternal effect of a recessive allele, which probably randomizes the polarity. In snails that copulate simultaneously and reciprocally, a left–right reversed strain cannot usually be established or rescued from inbreeding depression by ad hoc outbreeding because a rarely found single mutant cannot reproduce due to great difficulties of mating with the wild type and selfing. Moreover, the rare recessive homozygote cannot easily be detected because it often exhibits the wild-type phenotype in maternal inheritance and breeding difficulty hampers genotyping it by phenotyping its progeny. The present strain established by virtue of rare advantages will, therefore, provide unique opportunities to investigate whole-body enantiomorphs.

The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp.

Fri, 17 Jul 2009 11:32:33 PDT

The chamois is a useful species with which to investigate the combined genetic impact of habitat fragmentation, over hunting, and translocations. Genetic variation within and between chamois (genus Rupicapra) populations was analyzed in 259 individuals from 16 sampling sites located in Italy, Spain, Slovakia, and the Czech Republic. Two mitochondrial DNA markers (control region and cytochrome b) and 11 nuclear microsatellites were typed. The principal results of this study can be summarized as follows: 1) high and significant differentiation between almost all chamois populations is observed even on a microgeographical scale, probably caused by the patchy distribution of this species, sharp geographical barriers to gene flow, and drift effects related to recent bottlenecks; 2) historical translocation events have left a clear genetic signature, including interspecific hybridization in some Alpine localities; 3) the Apennine subspecies of chamois, Rupicapra pyrenaica ornata, shows a high and similar level of divergence (about 1.5 My) from the Pyrenean (Rupicapra pyrenaica pyrenaica) and the Alpine (Rupicapra rupicapra) chamois; therefore, the specific status of these taxa should be revised. These results confirm the potential of population genetic analyses to dissect and interpret complex patterns of diversity in order to define factors important to conservation and management.

Evolution of the GST Omega Gene Family in 12 Drosophila Species

Walters, K. B., Grant, P., Johnson, D. L. E. — Thu, 16 Jul 2009 10:45:46 PDT

Gene families provide a unique system to study the evolutionary relationships between related genes both within and between organisms. We can ascertain whether members of a gene family in different species are orthologs or paralogs. We may also search for evidence that may explain why duplicate genes are present. The availability of genome sequences for 12 Drosophila species allows us to address these questions with respect to the evolution of one gene family, the glutathione S transferase (GST) omega class. This gene family is of particular interest because of its relationship with human disease and its presence in a wide range of species.

Genetic Mapping of Cgdef Gene Controlling Accumulation of 7S Globulin ({beta}-Conglycinin) Subunits in Soybean Seeds

Hayashi, M., Kitamura, K., Harada, K. — Wed, 15 Jul 2009 04:45:39 PDT

Soy protein consists of mainly 7S globulin (β-conglycinin) and 11S globulin (glycinin). The 7S globulin exerts favorable and unfavorable effects on human nutrition, food processing, and human health. Therefore, it is important for the improvement of the soy protein to control the content of 7S globulin. A mutant line lacking the 7S globulin was induced by -ray irradiation, and the deficiency is controlled by a single recessive gene, cgdef. The Cgdef gene, despite its potential for improvement of the soy protein, has not been assigned to a linkage group of a soybean genetic map. We crossed "Mo-shi-dou Gong 503" with plants homozygous or heterozygous for the Cgdef allele and screened an F2 mapping population that segregated with the cgdef allele to locate the Cgdef gene on a soybean genetic map. By linkage analysis, we assigned the Cgdef gene to chromosome 19 at the position between the Satt523 and Sat_388 simple sequence repeat (SSR) markers. Six SSR markers (Sat_134, Sat_405, Satt143, Satt398, Sat_195, and Satt694) and 2 amplified fragment length polymorphism markers identified previously were mapped at the same position of the Cgdef gene. These markers should enable to conduct map-based cloning of the Cgdef gene.

Localization and Characterization of 170 BAC-Derived Clones and Mapping of 94 Microsatellites in the Hessian Fly

Schemerhorn, B. J., Crane, Y. M., Morton, P. K., Aggarwal, R., Benatti, T. — Fri, 10 Jul 2009 11:02:54 PDT

Ninety-four microsatellites from enriched genomic libraries of Hessian fly (Hf, Mayetiola destructor [Say]) were localized to 170 cognate clones in an Hf bacterial artificial chromosome (BAC) library. These microsatellite-positive BAC clones were physically mapped to polytene chromosomes by fluorescent in situ hybridization. The mapped microsatellite loci can be used to study the genetic diversity and population structure of Hf.

Genetic Mapping of Resistance to Phomopsis Seed Decay in the Soybean Breeding Line MO/PSD-0259 (PI562694) and Plant Introduction 80837

Jackson, E. W., Feng, C., Fenn, P., Chen, P. — Thu, 09 Jul 2009 05:18:58 PDT

Resistance to Phomopsis seed decay (PSD) in soybean (Glycine max [L.] Merr.) could provide dependable control of this important disease that affects seed quality. Studies have shown that single dominant genes that are allelomorphically different confer low levels of PSD in MO/PSD-0259 and PI 80837. The objectives of this research were to identify simple sequence repeat (SSR) markers linked to genes for PSD resistance in PI 80837 and MO/PSD-0259 and to associate the resistance genes to known linkage groups. Crosses were made between the PSD-susceptible cultivar Agripro 350 and each of the resistant lines MO/PSD-0259 and PI 80837. F₂ populations from each cross were grown and inoculated in the field. Individual plant reactions were characterized by determining the levels of seed infection, and DNA of F₂ plants was extracted for SSR analysis and mapping. F₂ segregation data showed that different single dominant genes condition PSD resistance in MO/PSD-0259 and PI 80837. Resistance in PI 80837 was linked to Sat_177 (4.3 cM) and Sat_342 (15.8 cM) on molecular linkage group (MLG) B2. In MO/PSD-0259, resistance was linked to Sat_317 (5.9 cM) and Sat_120 (12.7 cM) on MLG F. These data support work by Berger and Minor (Berger RD, Minor HC. 1999. An restriction fragment length polymorphism (RFLP) marker associated with resistance to Phomopsis seed decay in soybean PI 417479. Crop Sci 39:800–805.) in which PSD resistance in PI 417479, the resistant parent used to develop MO/PSD-0259, was associated with RFLP marker A708 on MLG F. These SSR markers should be useful in selection for resistant genotypes in breeding programs.

Genetic Diversification, Vicariance, and Selection in a Polytypic Frog

Robertson, J. M., Zamudio, K. R. — Thu, 09 Jul 2009 05:18:57 PDT

Spatial patterns of heritable phenotypic diversity reflect the relative roles of gene flow and selection in determining geographic variation within a species. We quantified color differentiation and genetic divergence among 20 populations of the red-eyed tree frog (Agalychnis callidryas) in lower Central America. Phylogenetic analyses revealed 5 well-supported mitochondrial DNA clades, and we infer from our phylogeny that geographic barriers have played a large role in structuring populations. Two phenotypic characters varied independently among isolated population groups: Flank coloration distinguished Caribbean from Pacific individuals, whereas leg coloration exhibited a more complex geographic pattern. We detected 3 generalized spatial patterns of genetic and phenotypic diversity: 1) phenotypic differentiation in the presence of historical connectivity, 2) phenotypic uniformity across genetically differentiated regions, and 3) codistribution of genetic and phenotypic characters. These patterns indicate that phenotypic diversification is highly regionalized and can result from spatial variation in localized adaptations, geographic isolation, genetic drift, and/or evolutionary stasis. Although the mode of selection underlying color variation was not the focal objective of this study, we discuss the possible roles of natural and sexual selection in mediating population differentiation. Our study underscores the fact that selection gradients vary across relatively small spatial scales, even in species that occupy relatively homogeneous environments.

Inheritance of Salt Tolerance in Wild Soybean (Glycine soja Sieb. and Zucc.) Accession PI483463

Lee, J.-D., Shannon, J. G., Vuong, T. D., Nguyen, H. T. — Thu, 25 Jun 2009 07:53:07 PDT

Tolerant soybean (Glycine max [L.] Merr.) cultivars aid in reducing salt damage in problem fields. New genes are important to reduce losses from salt injury. Objectives of this study were to determine inheritance of salt tolerance in wild soybean (Glycine soja Sieb. and Zucc.) PI483463 and to test allelism of tolerance genes from genotypes PI483463 and S-100, a common ancestor of southern in US cultivars. Tolerant (T) PI483463 was crossed to sensitive (S) cultivar Hutcheson to study inheritance. PI483463 (T) was crossed with S-100 (T) to test for allelism. Parents, F₁ plants, F₂ populations, and F_2:3 lines were assayed in a 100 mM salt solution to determine tolerance. F₂ from T x S cross segregated 3(T):1 (S) and the F_2:3 lines responded 1 (T): 2 (segregating):1 (S). F₂ plants from PI483463 (T) x S-100 (T) segregated 15 (T):1 (S) indicating different genes from the 2 sources. Results showed that G. soja line PI483463 had a single dominant gene for salt tolerance, which was different than the gene in G. max line S-100. The symbol, Ncl2, was designated for this new salt tolerance allele.

Patterns of Nucleotide Diversity at the Methionine Synthase Locus in Fragmented and Continuous Populations of a Wind-Pollinated Tree, Quercus mongolica var. crispula

Quang, N. D., Ikeda, S., Harada, K. — Tue, 16 Jun 2009 11:02:33 PDT

Genetic variation is usually high within populations, and differentiation is usually low among populations of wind-pollinated outcrossing trees. As a result, population contraction causes little change in the degree of genetic diversity and differentiation among populations. The aim of this work was to determine whether or not a recent population decline has influenced the allele frequency spectrum and association among variants of different sites on the nuclear housekeeping locus methionine synthase (1376–1418 bp in length) in the oak species Quercus mongolica var. crispula. A total of 122 sequences from 18 populations were randomly sampled and analyzed in this study. Results showed that nucleotide variation was generally high within populations, and differentiation was very low among populations. Genetic diversity was slightly reduced in samples taken from the area with a recent strong reduction in population size. Nevertheless, the allele frequency spectrum was skewed toward rare variants, and the association among variants of different sites was significantly more nonrandom within these samples compared with those from the area without such a population size reduction. This pattern was robustly supported by coalescent simulations.

Mapping of Quantitative Trait Loci for Grain Iron and Zinc Concentration in Diploid A Genome Wheat

Thu, 11 Jun 2009 07:25:17 PDT

Micronutrients, especially iron (Fe) and zinc (Zn), are deficient in the diets of people in underdeveloped countries. Biofortification of food crops is the best approach for alleviating the micronutrient deficiencies. Identification of germplasm with high grain Fe and Zn and understanding the genetic basis of their accumulation are the prerequisites for manipulation of these micronutrients. Some wild relatives of wheat were found to have higher grain Fe and Zn concentrations compared with the cultivated bread wheat germplasm. One accession of Triticum boeoticum (pau5088) that had relatively higher grain Fe and Zn was crossed with Triticum monococcum (pau14087), and a recombinant inbred line (RIL) population generated from this cross was grown at 2 locations over 2 years. The grains of the RIL population were evaluated for Fe and Zn concentration using atomic absorption spectrophotometer. The grain Fe and Zn concentrations in the RIL population ranged from 17.8 to 69.7 and 19.9 to 64.2 mg/kg, respectively. A linkage map available for the population was used for mapping quantitative trait loci (QTL) for grain Fe and Zn accumulation. The QTL analysis led to identification of 2 QTL for grain Fe on chromosomes 2A and 7A and 1 QTL for grain Zn on chromosome 7A. The grain Fe QTL were mapped in marker interval Xwmc382-Xbarc124 and Xgwm473-Xbarc29, respectively, each explaining 12.6% and 11.7% of the total phenotypic variation and were designated as QFe.pau-2A and QFe.pau-7A. The QTL for grain Zn, which mapped in marker interval Xcfd31-Xcfa2049, was designated as QZn.pau-7A and explained 18.8% of the total phenotypic variation.

Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants

Livingstone, K., Anderson, S. — Thu, 11 Jun 2009 07:25:16 PDT

Cellular metabolic networks depend on the products of many loci for proper functioning. These interrelationships between loci at the phenotypic level raise the question of whether they evolve independently. Previous research has demonstrated that in the anthocyanin pathway, which produces important secondary metabolites in plants, the genes encoding downstream enzymes show an increased rate of change at nonsynonymous sites when compared with upstream loci due to relaxed constraint. To test whether this pattern exists more broadly, we compared a set of 4 genes encoding enzymes of the carotenoid biosynthetic pathway, which produces a set of distinct colored secondary metabolites in plants. Comparisons between copies of phytoene desaturase, -carotene desaturase, lycopene β-cyclase, and zeaxanthin epoxidase from 6 taxa indicate that the 3 upstream enzymes (phytoene desaturase, -carotene desaturase, and lycopene β-cyclase) have similar proportions of codons under selective constraint, whereas the most downstream enzyme (zeaxanthin epoxidase) has more codons evolving under relaxed constraint. Overall, nonsynonymous substitution rates appear to be highest for zeaxanthin epoxidase, whereas synonymous substitution rates were highest for the intermediate enzyme lycopene β-cyclase. Analysis of codon bias shows that only lycopene β-cyclase may be under slight selection pressure for codon usage. Taken together, these results show that the enzymes of the carotenoid biosynthetic pathway are under strong selective constraint but that the most downstream enzyme is under the least constraint.