Journal of Heredity - current issue

Battle and Ballet: Molecular Interactions between the Sexes in Drosophila

Wolfner, M. F. — 2009-06-11

Varied and fascinating interactions occur between males and females to lead to the production of progeny. Interactions between the sexes continue even after the act of mating—but at the molecular and cellular level instead of between individual animals. Molecules transferred from males to females during mating (via the seminal fluid) exert potent effects on females’ physiology and (at least in some animals) on behavior. Taking advantage of genetic, genomic, and biochemical tools for Drosophila, we investigate molecular interactions that underlie this form of chemical communication. Recent data show that molecules and cells from both sexes participate in this "ballet," facilitating the mutually beneficial outcome of increased progeny production. Examples to be presented include the storage and utilization of sperm in the mated female, and a proteolytic pathway that begins in the male but ends in the female and involves both male and female contributions. Despite the joint benefit of increased progeny production, the "interests" of the mating male can differ from those of his mate. Over evolutionary time this disconnect can, in theory, precipitate a "battle" between the sexes, potentially leading to the rapid sequence changes that have been observed for some seminal proteins across species.

Conservation Genetics and North American Bison (Bison bison)

Hedrick, P. W. — 2009-06-11

The many millions of North American bison in the mid-19th century were reduced to near extinction by the middle 1880s. Plains bison, the subspecies found in the United States, were saved from extinction primarily by 5 private ranchers and the survival of a small herd in what is now Yellowstone National Park. This bottleneck resulted in the present-day plains bison population being descended from less than 100 founders. In addition, many conservation herds have cattle ancestry because of hybridization promoted by these ranchers in the late 1800s and early 1900s. Today, although there are around 500 000 plains bison in North America, only 4% (20 000) are in conservation herds. Only 1 conservation herd with no known ancestry from cattle has an effective population size of more than 1000. Here I review and evaluate this situation and provide recommendations for the reduction of cattle ancestry, avoidance of inbreeding depression, and maintenance of genetic variation in the conservation herds of bison.

The "Useful Questions of Heredity" before Mendel

Orel, V. — 2009-06-11

Now Emeritus Head of the Mendelianum (Mendel Museum) in Brno, Czech Republic, Vítezslav Orel began his academic career as a student at the Brno Agriculture University. His work was interrupted first by the Nazi invasion and then by the communist revolution, when the science of genetics was denounced and replaced by Lysenko pseudogenetics. V. O. was dismissed from his position at the Poultry Research Institute and assigned to work at a small duck farm outside Brno. When the "Lysenkoist madness" subsided, Professor Jaroslav Krizenecky (1896–1964), teacher of V. O., was allowed to develop the museum in recognition of Mendel's contributions. V. O. assisted him by conducting research on the history of Mendel and of genetics. On Jaroslav Krizenecky's death, V. O. became head of the Mendelianum. V. O. has become an internationally recognized figure in the study of the history of science, having published nearly 200 papers in Czech and 10 other languages. Orel's most recent books, published by Oxford University Press, make use of the rich archives of the Mendelianum that he helped create. Gregor Mendel—The First Geneticist (Orel 1996) is the definitive biography of Mendel, and in 2001, V. O. and co-author R. J. Wood published Genetic Prehistory in Selective Breeding: A Prelude to Mendel. (Biography from Margaret H. Peaslee)

Population Genetics of Astragalus bibullatus (Fabaceae) Using AFLPs

Baskauf, C. J., Burke, J. M. — 2009-06-11

Astragalus bibullatus (Fabaceae) is an endangered plant species endemic to limestone cedar glades in Tennessee. Data from 134 amplified fragment length polymorphism (AFLP) fragments indicate that populations of this species are genetically very similar, with genetic identity values ranging from 0.976 to 0.991. Approximately 10% of the species’ total genetic variation is due to differences among populations (F_ST = 0.102), and a principle coordinate analysis based on genetic distance among individuals revealed considerable overlap between populations. Averaging across populations, 38.4% of the AFLP markers were polymorphic, and the mean expected heterozygosity was 0.120. These estimates are higher than what has previously been reported for this species based on a survey of allozyme variation. Despite the overall similarity of populations of this species, a model-based clustering approach revealed the presence of 2 (possibly 3) genetically distinct subgroups. The results of this study highlight the utility of DNA-based markers for conservation genetic studies in genetically depauperate species and reveal that detectable levels of genetic substructuring may be present even in relatively undifferentiated species.

Genetic diversity and stress of Ricotia lunaria in "Evolution Canyon," Israel

Kossover, O., Frenkel, Z., Korol, A., Nevo, E. — 2009-06-11

We examined the genetic diversity and divergence of Ricotia lunaria, a family relative species of Arabidopsis thaliana, sampled from 6 stations on 2 opposing slopes, the south-facing slope ("African" or AS) and north-facing slope ("European" or ES), separated on average by 200 m, at "Evolution Canyon," Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. The density of R. lunaria populations was slope specific: a higher density and smaller plants were observed on the AS. In addition, the density was positively correlated with annual plant cover. The interslope and intraslope genetic diversities of R. lunaria populations were examined using the amplified fragment length polymorphism (AFLP) technique with 5 primer pairs. Ricotia lunaria populations inhabiting the ES and AS differed, and among the 468 scored loci, 304 (65%) were polymorphic (at P ≥ 0.05 level). Polymorphism values obtained for AS and ES populations were similar (52% vs. 56%), but different loci were polymorphic in different populations; 40% of polymorphic loci were identical on both the ES and AS, 16% were polymorphic for the ES only, and 12% were polymorphic only for the AS. The AFLP results grouped the analyzed genotypes into 2 distinct clusters: one cluster included the plants belonging to the AS and the other included ES plants. The unbiased estimate of Nei genetic distances (D) indicated significantly higher interslope (D = 0.124 ± 0.011) than intraslope (D = 0.076 ± 0.015) differences (P < 0.001 in t-test). Correspondingly, mean intraslope gene flow was significantly higher than the interslope gene flow (2.9 ± 0.6 vs. 1.9 ± 0.2). Natural selection appears to adaptively diverge the plant ecotypes on the opposite slope, both phenotypically and genotypically. This includes significant divergence in flowering time likely to initiate incipient sympatric speciation.

Methods and Prospects for Using Molecular Data in Captive Breeding Programs: An Empirical Example Using Parma Wallabies (Macropus parma)

Ivy, J. A., Miller, A., Lacy, R. C., DeWoody, J. A. — 2009-06-11

Zoo and aquarium breeding programs rely on accurate pedigrees to manage the genetics and demographics of captive populations. Breeding recommendations are often encumbered, however, by unknown parentage. If an individual has any amount of unknown ancestry, the relationships between that individual and all other individuals in a population are ambiguous, and breeding recommendations cannot be tailored to maximize genetic diversity and minimize inbreeding. In those situations, breeding program management might be improved by the incorporation of molecular data. We developed microsatellite markers for the parma wallaby (Macropus parma) and investigated how genetic data might be used to improve the management of the captive population. The parma wallaby is a small marsupial found in fragmented forests near the coast of New South Wales, Australia. Because the species is of conservation concern, the captive population in North America is managed by recurring breeding recommendations. The effectiveness of the population's management is hampered, however, because over half of the individuals have some amount of unknown ancestry. We used microsatellite data to resolve unknown parentage, described how molecular estimates of relatedness might inform future breeding recommendations, and used computer simulations to investigate how molecular estimates of relatedness among founders might contribute to the genetic management of the population. Our results indicated that microsatellite appraisals of parentage were useful with respect to clarifying pedigrees but that molecular assessments of founder relatedness provided very marginal benefits with regard to the preservation of genetic diversity and the avoidance of inbreeding.

Fast versus Slow Larval Growth in an Invasive Marine Mollusc: Does Paternity Matter?

Le Cam, S., Pechenik, J. A., Cagnon, M., Viard, F. — 2009-06-11

Reproductive strategies and parental effects play a major role in shaping early life-history traits. Although polyandry is a common reproductive strategy, its role is still poorly documented in relation to paternal effects. Here, we used as a case study the invasive sessile marine gastropod Crepidula fornicata, a mollusc with polyandry and extreme larval growth variation among sibling larvae. Based on paternity analyses, the relationships between paternal identity and the variations in a major early life-history trait in marine organisms, that is, larval growth, were investigated. Using microsatellite markers, paternities of 437 fast- and slow-growing larvae from 6 broods were reliably assigned to a set of 20 fathers. No particular fathers were found responsible for the specific growth performances of their offspring. However, the range of larval growth rates within a brood was significantly correlated to 1) an index of sire diversity and 2) the degree of larvae relatedness within broods. Multiple paternity could thus play an important role in determining the extent of pelagic larval duration and consequently the range of dispersal distances achieved during larval life. This study also highlighted the usefulness of using indices based on fathers’ relative contribution to the progeny in paternity studies.

Heterochromatin-Mediated Gene Silencing Is Not Affected by Drosophila CBP Activity

Smolik, S. M. — 2009-06-11

Cyclic AMP Response Element Binding protein (CREB)-binding protein (CBP) is an acetyltransferase important for modifying histones and chromatin-associated proteins and thus affecting transcription and other DNA metabolic processes. We found that the Drosophila CBP (dCBP) is associated with the NAD⁺-dependent deacetylase, SIR2, which was originally identified as a silencing information regulator in yeast that models silenced and repeated sequence chromatin such as centric heterochromatin, telomeres, and the repeated rDNA sequences. As in yeast, Drosophila sir2 (dsir2) affects the formation and/or function of centric heterochromatin. The fact that we found dCBP in immunecomplexes with dSIR2 in vivo and found that dCBP can interact with dSIR2 directly in vitro suggested that dCBP might affect the packaging of silencing heterochromatin as well. A careful study of the dCBP mutations provides evidence that dCBP does not affect the formation and/or function of centric heterochromatin and thus may affect other dSIR2 functions.

Hermes Transposon Distribution and Structure in Musca domestica

2009-06-11

Hermes are hAT transposons from Musca domestica that are very closely related to the hobo transposons from Drosophila melanogaster and are useful as gene vectors in a wide variety of organisms including insects, planaria, and yeast. hobo elements show distinct length variations in a rapidly evolving region of the transposase-coding region as a result of expansions and contractions of a simple repeat sequence encoding 3 amino acids threonine, proline, and glutamic acid (TPE). These variations in length may influence the function of the protein and the movement of hobo transposons in natural populations. Here, we determine the distribution of Hermes in populations of M. domestica as well as whether Hermes transposase has undergone similar sequence expansions and contractions during its evolution in this species. Hermes transposons were found in all M. domestica individuals sampled from 14 populations collected from 4 continents. All individuals with Hermes transposons had evidence for the presence of intact transposase open reading frames, and little sequence variation was observed among Hermes elements. A systematic analysis of the TPE-homologous region of the Hermes transposase-coding region revealed no evidence for length variation. The simple sequence repeat found in hobo elements is a feature of this transposon that evolved since the divergence of hobo and Hermes.

The Candidate Gene XIRP2 at a Quantitative Gene Locus on Equine Chromosome 18 Associated with Osteochondrosis in Fetlock and Hock Joints of South German Coldblood Horses

Wittwer, C., Hamann, H., Distl, O. — 2009-06-11

A whole-genome scan for radiological signs of osteochondrosis (OC) and osteochondrosis dissecans (OCD) in South German Coldblood (SGC) horses using 250 microsatellite markers identified a genome-wide significant quantitative trait locus (QTL) for fetlock OCD and a chromosome-wide QTL for hock OC on Equus caballus chromosome (ECA) 18 at a relative position of 45.9–78.2 cM. The aim of this study was to analyze associations of single-nucleotide polymorphisms (SNPs) in candidate genes for OC in this QTL region using 96 SGC horses. The OC-QTL on ECA18 could be confirmed and narrowed down to an interval of 13 Mb between GALNT13 and Xin actin-binding repeat containing 2 (XIRP2). SNPs in the XIRP2 gene were significantly associated with fetlock OC, fetlock OCD, and hock OC. The significant associations of SNPs in XIRP2 could be confirmed in linear animal models controlling for systematic environmental and residual quantitative genetic effects. The significant additive genetic effects of the intronic SNPs (AJ885515:g.159A>G, AJ885515:g.445T>C) in XIRP2 were 0.15 (P = 0.01) for fetlock OC, 0.27 (P = 0.01) for fetlock OCD, and 0.15–0.16 (P = 0.01–0.02) for hock OC. Homozygous (A/A or T/T) and heterozygous horses were at a 1.3- to 2.4-fold higher risk for fetlock and hock OC. These results suggest that dominant variants of XIRP2 may be involved in pathogenesis of equine OC.

Coordinated and Fine-Scale Control of Homoeologous Gene Expression in Allotetraploid Cotton

Flagel, L. E., Chen, L., Chaudhary, B., Wendel, J. F. — 2009-06-11

Within polyploid plant species, it has been demonstrated that homoeologous genes (genes duplicated by polyploidy) often display dynamic expression patterns. To determine if chromosomal location plays a role in establishing these expression patterns, we analyzed the relative levels of homoeolog expression among linked genes from 2 locations in the cotton genome. Genes from the region containing the alcohol dehydrogenase A gene show coordinated expression across several tissues, whereas genes from the region containing cellulose synthase A do not. These results indicate that changes in homoeolog expression may be constrained by linkage in some genomic regions, whereas in other regions, homoeolog expression is largely decoupled from physical proximity. Furthermore, these results suggest that both large- and small-scale regulatory mechanisms may control homoeolog expression patterns.

Gene Expression in a Wild Autopolyploid Sunflower Series

Church, S. A., Spaulding, E. J. — 2009-06-11

Polyploidy, or genome doubling, is a common mechanism in the evolution of plants. This genome duplication can rapidly lead to genomic changes between ploidy levels. In particular, allopolyploids that result from interspecific hybridization can show a large number of changes in gene expression immediately after the polyploidy event. These are likely due to epigenetic changes that do not alter the underlying DNA sequence. This may be due in part to the hybrid origin of these allopolyploids. In autopolyploids, a small number of studies have shown that there may also be some gene expression changes between ploidy levels, albeit to a much smaller degree. However, these studies have focused on inbred lines of single populations. This study examines silencing and/or novel gene expression in diploid, autotetraploid, and autohexaploid lineages of Helianthus decapetalus. Using cDNA-amplified fragment length polymorphism, we examined gene expression in 5 populations of these lineages. The results show no ploidy level–specific differences in gene silencing or novel gene expression. All gene expression differences are among populations and may be due to independent evolutionary origins. These results support the conclusions of previous studies that gene expression differences among allopolyploids are likely due in large part to the hybrid nature of these lineages.

Improved Genetic Mapping of Endosperm Traits Using NCIII and TTC Designs

Wang, X., Song, W., Yang, Z., Wang, Y., Tang, Z., Xu, C. — 2009-06-11

The endosperm in plants is a major source of human nutrition and industrial raw material. The genetic study of endosperm poses a great challenge due to its complex genetic composition and unique physical and developmental properties. In this note, we shall revisit 2 classic mating designs—North Carolina Design III (NCIII) and triple test cross (TTC)—and demonstrate their efficiency in detecting quantitative trait loci underlying endosperm traits.

Mapping an Overdominant Quantitative Trait Locus for Heterosis of Body Weight in Mice

Ishikawa, A. — 2009-06-11

The genetic basis of heterosis has not been elucidated. Previously, a congenic mouse strain with a 44-Mb genomic region of proximal chromosome 2 containing the allele derived from wild Mus musculus castaneus at Pbwg1, a quantitative trait locus (QTL) for body weight and growth, has been developed. In this study, to fine-map and characterize body weight QTLs on the congenic region, QTL analysis of body weight at 1, 3, 6, and 10 weeks after birth was performed on a population of 265 F₂ intercross mice between the developed congenic strain and its background strain C57BL/6J. A significant QTL (named Pbwg1.10) affecting body weight at 6 and 10 weeks of age was identified within an approximately 21-Mb support interval. Surprisingly, Pbwg1.10 had an overdominance effect and caused heterosis for body weight. This result supported the overdominance hypothesis explaining heterosis.

Plant Genotyping II: SNP Technology

Hamblin, M. T. — 2009-06-11