Journal of Heredity - recent issues

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

Species Delineation and Evolutionary History of the Globally Distributed Spotted Eagle Ray (Aetobatus narinari)

Richards, V. P., Henning, M., Witzell, W., Shivji, M. S. — 2009-04-14

The spotted eagle ray (Aetobatus narinari), a large coral reef–associated batoid of conservation concern, is currently described as a single, circumglobally distributed species. However, geographic differences in its morphology and parasite diversity have raised unconfirmed suspicions that A. narinari may constitute a species complex. We used 1570 bp of mitochondrial and nuclear sequence data (cytochrome b, cytochrome c oxidase subunit I, and internal transcribed spacer 2) to assess the validity of A. narinari as a single cosmopolitan species and infer its evolutionary history. Specimens from 4 major geographic regions were examined: the Central Atlantic, Eastern Pacific, Western Pacific, and Central Pacific. Phylogenies described 3 distinct, reciprocally monophyletic lineages with no genetic exchange among regions. Based on combined genealogical concordance and genetic distance criteria, we recommend that the Western/Central Pacific lineage be recognized as a distinct species from lineages in the Central Atlantic and Eastern Pacific. The latter 2 lineages, separated by the Isthmus of Panama, are proposed as subspecies. A basal position in phylogenetic analyses and statistical parsimony results support an Indo-West Pacific origin for the A. narinari species complex, with subsequent westerly dispersal around the southern tip of Africa into the Atlantic and then into the Eastern Pacific.

The Comparative Phylogeography of East Coast Estuarine Fishes in Formerly Glaciated Sites: Persistence versus Recolonization in Cyprinodon variegatus ovinus and Fundulus heteroclitus macrolepidotus

Haney, R. A., Dionne, M., Puritz, J., Rand, D. M. — 2009-04-14

Species distributions may be dramatically affected by climatic variability, such as occurred during Pleistocene glaciation. Populations of coastal organisms could have been affected directly by ice movement or through sea level change. Response could involve shifts in distribution southwards or persistence through the full range or in limited high-latitude refugia. Comparative studies of the response of ecologically similar species can provide a useful complement to those examining response across disparate species in defining what parameters influence persistence. Patterns of mitochondrial genetic variation in 2 estuarine fish subspecies from the Northwest Atlantic, Fundulus heteroclitus macrolepidotus and Cyprinodon variegatus ovinus, indicate that ecological similarity does not necessarily predict propensity for glacial persistence. Fundulus heteroclitus macrolepidotus is highly diverse in glaciated regions, with isolated populations whose origins predate the last glacial maximum and may have recently expanded it's range to the south from New England. However, within glaciated regions, signals of population growth and distributional shifts indicate a dynamic Pleistocene history for F. h. macrolepidotus, in contrast with recent studies involving microsatellites. A different pattern is found in C. v. ovinus, which is depauperate in formerly glaciated sites, with a clear signal of recent recolonization of glaciated regions from the south. Genetic differentiation in glaciated areas is consistent with isolation after glacial withdrawal. In C. v. ovinus, rapidly evolving microsatellite loci show a similar pattern to mitochondrial DNA but may be reaching equilibrium on small spatial scales. These contrasting patterns of variation illustrate how ecologically similar species can respond to large-scale environmental change in distinct ways.

Genetic Structure of the Asiatic Black Bear in Japan Using Mitochondrial DNA Analysis

Yasukochi, Y., Nishida, S., Han, S.-H., Kurosaki, T., Yoneda, M., Koike, H. — 2009-04-14

The genetic structure of the Asiatic black bear (Ursus thibetanus) in Japan was studied to understand the events that occurred during its evolution. The left domain of the mitochondrial control region (about 240 bp) was sequenced, defining 27 haplotypes that consisted of 23 haplotypes from 333 bears in Japan and 22 bears in the Asian continent. The network tree of the control region indicated that the Japanese population formed a distinct clade from the continental population. The phylogeographic analysis of the haplotypes indicated that the Shikoku and Kii Hanto populations had diverged during the initial phase from the ancestral population. After the 3 dominant haplotypes were rapidly distributed throughout Japan in the early stage of the population dispersal, the Japanese population diverged into eastern and western populations. Using the entire mitochondrial cytochrome b sequence, divergence time between the Japanese and the Continental populations suggested that the Japanese population might have colonized into Japan through the land bridge from the Korean Peninsula around 500 ka, which is consistent with paleontological evidence. Our finding that bears in western Japan exhibit lower genetic diversity and higher levels of genetic differentiation than bears in eastern Japan provides a vital contribution to conservation policy for these isolated populations.

Phylogenetic and Phylogeographic Patterns in Sigmodontine Rodents of the Genus Oligoryzomys

2009-04-14

The sigmodontine South American rodent genus Oligoryzomys was first described as a subgenus of the genus Oryzomys to group together species distinguished by morphological measurements. To describe the dispersion patterns of this genus in South America, in this study, a total of 100 sequences were analyzed and compared with sequences of 9 Oligoryzomys species from GenBank. The sequences comprised 90 mitochondrial cytochrome b genes and 10 nuclear interphotoreceptor retinoid-binding protein genes, from 75 individuals of 7 species from 27 localities. Topologies of different phylogenetic trees revealed Oligoryzomys as a monophyletic genus containing 2 main species groups, one designated as the "Amazon–Cerrado" assemblage and the second as the "Pampa–Andean" clade. The north-to-south geographic pattern observed supports the hypothesis that the genus started from the northern Andes, occupied the Amazon and the Cerrado, and later inhabited the more southern regions of South America.

Divergence in Zygodontomys (Rodentia: Sigmodontinae) and Distribution of Amazonian Savannas

2009-04-14

Northern South America presents a diverse array of nonforest or savanna-like ecosystems that are patchily distributed. The distribution of these open habitats has been quite dynamic during Quaternary glacial–interglacial cycles; yet, the relevance of climatically driven vicariance events to the diversification of nonforest Amazonian vertebrates remains poorly known. We analyzed karyologic and mitochondrial DNA sequence data of the genus Zygodontomys, a small cricetid rodent distributed throughout nonforest habitats of northern Amazonia. Samples analyzed represented 4 Brazilian Amazonian localities and 2 French Guiana localities. Karyologic variation among Amazonian Brazilian Zygodontomys populations is high, with, at least, 3 karyomorphotypes. Molecular phylogenetic analyses recovered 3 major clades congruent with known karyotypes, a finding that suggests the existence of 3 species, 2 of which currently undescribed. The French Guiana and Surumú clade, identified as Zygodontomys brevicauda microtinus, is characterized by 2n = 86 and is sister to the clade formed by the 2 nondescribed forms. The Rio Negro–Rio Branco form is characterized by 2n = 82, and the Ferreira Gomes–Itapoá form is characterized by 2n = 84. The distribution of the 3 Zygodontomys lineages identified is in accordance with the geography of the open vegetation patches in Northern Amazonia, and divergence time estimates relate speciation events to the middle-upper Pleistocene, supporting the prominent role of Quaternary climatically driven vicariance events in the diversification of the genus.

Microsatellite Characterization and Marker Development from Public EST and WGS Databases in the Reef-Building Coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia)

Wang, S., Zhang, L., Matz, M. — 2009-04-14

Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.

Genetic Diversity of Amaranthus Species from the Indo-Gangetic Plains Revealed by RAPD Analysis Leading to the Development of Ecotype-Specific SCAR Marker

Ray, T., Roy, S. C. — 2009-04-14

Genetic diversity and relationships among 6 Amaranthus species from 8 phytogeographic regions of the Indo-Gangetic plains were analyzed using a random amplified polymorphic DNA (RAPD) marker. RAPD primers yielded a total of 262 amplicons, ranging from ~250 to ~3000 bp in size with an average of 13.1 amplicons per primer, of which 254 amplicons (96.94%) were polymorphic. The genetic similarity coefficient among all the Amaranthus species ranged from 0.16 to 0.97 with a mean similarity coefficient of 0.56, indicating that variation existed in the genetic diversity of different populations. In the unweighted pair group method with arithmetic average dendrogram, populations of the same species clustered together. A unique 1371-bp RAPD band specific for Amaranthus gangeticus (syn. tricolor) of a particular phytogeographic region was converted to a sequenced characterized amplified region (SCAR) marker. The translated marker sequence showed homology with hemagglutinin protein. This SCAR marker is potentially useful for germplasm conservation and identification of amaranth ecotype.

Temperature Affects Expression of Symptoms Induced by Soybean Mosaic Virus in Homozygous and Heterozygous Plants

Li, D., Chen, P., Shi, A., Shakiba, E., Gergerich, R., Chen, Y. — 2009-04-14

Seven strains (G1 to G7) of soybean mosaic virus (SMV) and 3 resistance loci (Rsv1, Rsv3, and Rsv4) have been identified in soybean. The interaction of SMV strains and host resistance genes results in resistant (symptomless), susceptible (mosaic), or necrotic (leaf and stem necrosis) reactions. The necrotic reaction may be gene dosage dependent and influenced by temperature. Using a set of soybean isolines and hybrids containing homozygous or heterozygous alleles of rsv, Rsv1, Rsv1-n, Rsv3, or Rsv4, this study has explored the relationship of SMV-induced symptoms and resistance gene dosage at different temperatures. Results showed that SMV-inoculated plants carrying Rsv3 or Rsv4 were symptomless at both homozygous and heterozygous states at all temperature regimes. Threshold temperatures for symptoms changing from stem tip necrosis (STN) to mosaic were 30, 33, and 33 °C in G7-inoculated homozygous genotypes V94-3971(Rsv1) and PI 96983 (Rsv1) and G1-inoculated V262 (Rsv1-n), respectively. However, at the heterozygous state, threshold temperature was 30 °C in G7-inoculated V94-3971 x Essex F₁ for the symptom change from STN to mosaic, 31 °C in G7-inoculated Essex x PI 96983 F₁ from STN to mixture of necrosis and mosaic (N-M), and 32 °C in G1-inoculated V262 x Essex F₁ from N-M to mosaic. Incomplete necrosis was observed in the heterozygous state in G1-inoculated V262 x Essex F₁ and G7-inoculated PI 96983 x Essex F₁ where necrotic and mosaic symptoms were mixed. High temperature (37 °C) tends to mask the expression of mosaic symptoms in both homozygous and heterozygous plants. STN expression in response to temperature was affected by resistance gene, gene dosage, host genetic background, and specific SMV strains. Thus, Rsv3 and Rsv4 are a better choice as source of genetic resistance for breeding SMV-resistant cultivars.

The CArG-Box Located Upstream from the Transcriptional Start of Wheat Vernalization Gene VRN1 Is Not Necessary for the Vernalization Response

Pidal, B., Yan, L., Fu, D., Zhang, F., Tranquilli, G., Dubcovsky, J. — 2009-04-14

In diploid wheat (Triticum monococcum), and likely in other Triticeae species, the VRN1 gene is essential for the initiation of the reproductive phase, and therefore, a detailed characterization of its regulatory regions is required to understand this process. A CArG-box (MADS-box–binding site) identified in the VRN1 promoter upstream from the transcription initiation site has been proposed as a critical regulatory element for the vernalization response. This hypothesis was supported by the genetic linkage between CArG-box natural deletions and dominant Vrn1 alleles for spring growth habit and by physical interactions with VRT2, a MADS-box protein proposed as a putative flowering repressor regulated by vernalization. Here, we describe a T. monococcum accession with a strong vernalization requirement and a 48-bp deletion encompassing the CArG-box in the VRN1 promoter. Genetic analyses of 2 segregating populations confirmed that this VRN1 allele is completely linked with a strong winter growth habit (vrn-A^m1b). Transcript levels of the VRN1 allele with the 48-bp deletion were very low in unvernalized plants and increased during vernalization to levels similar to those detected in other wild-type vrn-A^m1 alleles. Taken together, these results indicate that the CArG-box found upstream of the VRN1 transcription initiation site is not essential for the vernalization response.

Male Reproductive Success and Multiple Paternity in Wild, Low-Density Populations of the Adder (Vipera berus)

Ursenbacher, S., Erny, C., Fumagalli, L. — 2009-04-14

We studied for the first time the occurrence of multiple paternity, male reproductive success, and neonate survival in wild, low-density adder (Vipera berus) populations using 13 microsatellite loci. Paternity was assigned for 15 clutches, collected during 3 years. Our data demonstrated that multiple paternity can occur at a high level (69%) in natural populations of V. berus, even if the density of adults is low. The high proportion of multiple sired clutches was comparable to the proportion observed in captive populations. Male reproductive success significantly increased with body length, and only the largest males successfully sired entire clutches. Finally, no relationship was detected between the number of fathers per clutch and neonate survival. These results suggest that multiple matings could be beneficial in populations with high level of inbreeding or low male fecundity.

Genes for "Reverse" Fruit Striping in Squash (Cucurbita pepo)

Paris, H. S. — 2009-04-14

Longitudinal striping is a common fruit color pattern in Cucurbita pepo and is conferred by any of several alleles at the light coloration-1 locus. Normally, dark stripes appear over the fruit surface areas between the 10 main subepidermal vein tracts with the lighter background color over and adjacent to these vein tracts. Less commonly, the striping is "reversed," that is, lighter than the background color. The present work was conducted to elucidate the mode of inheritance of reverse striping. The results indicated that reverse striping is conferred by the complementary interaction of an allele for striping with a heretofore unidentified allele at the light coloration-2 locus which is hereby designated l-2^R. Fruits of plants carrying an allele for striping and that are homozygous for l-2^R have completely reversed striping, whereas those heterozygous for l-2^R have striping that is completely normal or that is partially normal and partially reversed.

A Novel Growth Retardation and Abnormal Gonad Morphology Locus on Mouse Chromosome 4

Suto, J.-I. — 2009-04-14

Mutant mice exhibiting a growth retardation phenotype arose spontaneously in the inbred NC/Sgn mouse strain. The mode of inheritance of this mutation was autosomal recessive, and I named this mutation growth deficit (gd). The gd locus was mapped to the proximal part of chromosome 4, between microsatellite markers D4Mit139 and D4Mit178. Histologic abnormalities were detected in the mutant testis and ovary. Degeneration and/or necrosis were found in the seminiferous epithelium, particularly in the spermatocytes; therefore, mutant males were thought to be sterile owing to defective spermatogenesis. Mutant ovaries were generally atrophied. Necrosis of granulosa cells and increased number of atretic follicles were remarkable. The gd locus is suggested to be syntenic to human chromosome segment 9q32–q34, to which no similar mutations had been mapped. Although the molecular nature of this mutation is unclear, gd promises to make future contribution to relevant diseases in human beings.

Identification of Novel Single Nucleotide Polymorphisms in Promoter III of the Acetyl-CoA Carboxylase-{alpha} Gene in Goats Affecting Milk Production Traits

2009-04-14

Acetyl-CoA carboxylase- (ACACA) is the major regulatory enzyme of fatty acid biosynthesis. We have sequenced a fragment of Promoter III of the ovine ACACA gene in 211 goats of 5 breeds. The caprine sequence showed a high nucleotide identity (99%) with the ovine. We have identified 3 novel single nucleotide polymorphisms (SNPs) that fall in the core sequence of putative binding sites of transcription factors and have lower allele frequency than the wild type in all breeds. We evaluated the allele substitution effect of the SNPs on milk traits in the Saanen and the Local Grey breeds. Results from this study show that the mutations are associated with fat yield.

AFLP Fragment Isolation Technique as a Method to Produce Random Sequences for Single Nucleotide Polymorphism Discovery in the Green Turtle, Chelonia mydas

Roden, S. E., Dutton, P. H., Morin, P. A. — 2009-04-14

The green sea turtle, Chelonia mydas, was used as a case study for single nucleotide polymorphism (SNP) discovery in a species that has little genetic sequence information available. As green turtles have a complex population structure, additional nuclear markers other than microsatellites could add to our understanding of their complex life history. Amplified fragment length polymorphism technique was used to generate sets of random fragments of genomic DNA, which were then electrophoretically separated with precast gels, stained with SYBR green, excised, and directly sequenced. It was possible to perform this method without the use of polyacrylamide gels, radioactive or fluorescent labeled primers, or hybridization methods, reducing the time, expense, and safety hazards of SNP discovery. Within 13 loci, 2547 base pairs were screened, resulting in the discovery of 35 SNPs. Using this method, it was possible to yield a sufficient number of loci to screen for SNP markers without the availability of prior sequence information.

MsatAllele_1.0: An R Package to Visualize the Binning of Microsatellite Alleles

Alberto, F. — 2009-04-14

MsatAllele is a computer package built on R to visualize and bin the raw microsatellite allele size distributions. The method is based on the creation of an R database with exported files from the open-source electropherogram peak-reading program STRAND. Contrary to other binning programs, in this program, the bin limits are not fixed and are automatically defined by the data stored in the database. Data manipulation and graphical functions allow to 1) visualize raw allele size variation, allowing the detection of potential scoring errors, strange bin distributions, and unexpected spacing between the bins; 2) bin raw fragment sizes and write bin summary statistics for each locus; and 3) export genotype files with the resulting binned data.

Announcements

2009-04-14

Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae

Janes, D. E., Ezaz, T., Marshall Graves, J. A., Edwards, S. V. — 2009-02-12

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 ( = 4N_eµ) 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 ( = 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, L. S., Beadell, J. S., McClung, A., McIntosh, C. E., Fleischer, R. C. — 2009-02-12

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, M. C. T. — 2009-02-12

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 more 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. — 2009-02-12

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, J. I., Hundertmark, K. J., Bowyer, R. T., McCracken, K. G. — 2009-02-12

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 (H_E = 0.483–0.612), and private alleles ranged from 0 to 6. Both F_ST and R_ST indicated significant population structure (P < 0.001) with F_ST < 0.109 and R_ST < 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 moose, 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, B. N. — 2009-02-12

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, S. P. — 2009-02-12

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, K. M., Koblmuller, S. — 2009-02-12

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 (H_e ≤ 0.68) yielded only slow improvement of the results, but all 3 methods performed well with 5–7 markers of H_e = 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, A. C. S., De Lemos-Filho, J. P., Lovato, M. B. — 2009-02-12

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, P. S., Kermicle, J. L., Sachs, M. M. — 2009-02-12

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.)

2009-02-12

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 achieved 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

2009-02-12

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 long-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, E. N., Seabury, C. M., Elliott, J. S., Womack, J. E. — 2009-02-12

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 immunity.

Simultaneous Extraction of High-Quality RNA and DNA from Small Tissue Samples

Triant, D. A., Whitehead, A. — 2009-02-12

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 µg of DNA and 1.1 µg 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, D. L. — 2009-02-12

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. — 2009-02-12

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 with 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. — 2009-02-12

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 F_2:3 and 157 F_2:4 lines derived from the cross of SS-516 (low calcium) x Camp (high calcium). The F_2:3 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%, 16.3%, 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

2009-02-12