Journal of Heredity - current issue

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Wed, 11 Nov 2009 04:10:27 PST

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Wed, 11 Nov 2009 04:10:27 PST

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Wed, 11 Nov 2009 04:10:27 PST

Wed, 11 Nov 2009 04:10:28 PST

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

Genome 10K Community of Scientists — Wed, 11 Nov 2009 04:10:28 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.

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, 11 Nov 2009 04:10:28 PST

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.

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. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Wed, 11 Nov 2009 04:10:28 PST

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.

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

McRobie, H., Thomas, A., Kelly, J. — Wed, 11 Nov 2009 04:10:28 PST

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 Diversification, Vicariance, and Selection in a Polytypic Frog

Robertson, J. M., Zamudio, K. R. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Drury, D. W., Siniard, A. L., Wade, M. J. — Wed, 11 Nov 2009 04:10:28 PST

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.

Evolution of the GST Omega Gene Family in 12 Drosophila Species

Walters, K. B., Grant, P., Johnson, D. L. E. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Livingstone, K., Anderson, S. — Wed, 11 Nov 2009 04:10:28 PST

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.

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. — Wed, 11 Nov 2009 04:10:28 PST

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

Wed, 11 Nov 2009 04:10:28 PST

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.

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. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Odeen, A., Hastad, O. — Wed, 11 Nov 2009 04:10:28 PST

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.

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. — Wed, 11 Nov 2009 04:10:28 PST

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.

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. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Hayashi, M., Kitamura, K., Harada, K. — Wed, 11 Nov 2009 04:10:28 PST

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.

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

Johansson, M. L. — Wed, 11 Nov 2009 04:10:28 PST

In Pursuit of the Gene: From Darwin to DNA

Smocovitis, V. B. — Wed, 11 Nov 2009 04:10:28 PST

Announcements

Wed, 11 Nov 2009 04:10:28 PST

Journal of Heredity - current issue

Cover

Edboard

Subcription

Table of Contents

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

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

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

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

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

Genetic Diversification, Vicariance, and Selection in a Polytypic Frog

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

Evolution of the GST Omega Gene Family in 12 Drosophila Species

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

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

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

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

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

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

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

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

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

In Pursuit of the Gene: From Darwin to DNA

Announcements