Flight Synchrony among the Major Moth Pests of Cranberries in the Upper Midwest, USA.

The cranberry fruitworm (Acrobasis vaccinii Riley), sparganothis fruitworm (Sparganothis sulfureana Clemens), and blackheaded fireworm (Rhopobota naevana Hübner) are historically significant pests of cranberries (Vaccinium macrocarpon Aiton) in the Upper Midwest (Wisconsin), USA. Their respective natural histories are well documented but correlations between developmental benchmarks (e.g., larval eclosion) and degree-day accruals are not yet known. Treatment timings are critical to the optimization of any given control tactic, and degree-day accrual facilitates optimization by quantifying the developmental status of pest populations. When key developmental benchmarks in the pest life cycle are linked to degree-days, real-time weather data can be used to predict precise treatment timings. Here, we provide the degree-day accumulations associated with discrete biological events (i.e., initiation of flight and peak flight) for the three most consistent moth pests of cranberries in Wisconsin. Moths were trapped each spring and summer from 2003 to 2011. To characterize flight dynamics and average timing of flight initiation, pheromone-baited trap-catch data were tallied for all three pest species within each of seven growing seasons. These flight dynamics were then associated with the corresponding degree-day accumulations generated using the cranberry plant's developmental thresholds. Finally, models were fit to the data in order to determine the peak flight of each species. The initiation of the spring flight among all three moth species was highly synchronous, aiding in the timing of control tactics; however, there were substantial differences in the timing of peak flight among the moth species. Characterization of the relationship between temperature and pest development allows pest management professionals to target specific life stages, improving the efficacy of any given pest control tactic.

Microbes are trophic analogs of animals.

In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen ((15)N:(14)N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals). Here, we report that patterns of intertrophic (15)N-discrimination were remarkably similar among bacteria, fungi, and animals, which permitted unambiguous measurement of consumer trophic position, independent of phylogeny or ecosystem type. The observed similarities among bacterial, fungal, and animal consumers suggest that within a trophic hierarchy, microbiota are equivalent to, and can be interdigitated with, macrobiota. To further test the universality of this finding, we examined Neotropical fungus gardens, communities in which bacteria, fungi, and animals are entwined in an ancient, quadripartite symbiosis. We reveal that this symbiosis is a discrete four-level food chain, wherein bacteria function as the apex carnivores, animals and fungi are meso-consumers, and the sole herbivores are fungi. Together, our findings demonstrate that bacteria, fungi, and animals can be integrated within a food chain, effectively uniting the macro- and microbiome in food web ecology and facilitating greater inclusion of the microbiome in studies of functional diversity.

Temperature-Mediated Development Thresholds of Sparganothis sulfureana (Lepidoptera: Tortricidae) in Cranberries.

Larvae of Sparganothis sulfureana Clemens frequently attack cranberries, often resulting in economic damage to the crop. Because temperature dictates insect growth rate, development can be accurately estimated based on daily temperature measurements. To better predict S. sulfureana development across the growing season, we investigated the temperature range within which S. sulfureana larvae can feed and grow. Larvae were reared at 13 constant temperatures ranging from 6.5-38.6 °C. Larval growth rate was determined by the rate of change of larval weight across time. The respective growth rates among these temperatures were modeled using simple linear, cubic, and Lactin nonlinear development functions. These models isolated the lower temperature threshold at which growth became nonzero and the upper temperature at which growth was maximized. All three models were significantly predictive of S. sulfureana growth, but the cubic model best represented the observed growth rates, effectively isolating lower and upper thresholds of 9.97 and 29.89 °C, respectively. We propose that these thresholds be used to create a degree-day model of temperature-mediated S. sulfureana development.

Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops?

As the world population grows and resources and climate conditions change, crop improvement continues to be one of the most important challenges for agriculturalists. The yield and quality of many crops is affected by abscission or shattering, and environmental stresses often hasten or alter the abscission process. Understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality and greater sustainability. As plant scientists, we have learned significant amounts about this process through the study of model plants such as Arabidopsis, tomato, rice, and maize. While these model systems have provided significant valuable information, we are sometimes challenged to use this knowledge effectively as variables including the economic value of the crop, the uniformity of the crop, ploidy levels, flowering and crossing mechanisms, ethylene responses, cultural requirements, responses to changes in environment, and cellular and tissue specific morphological differences can significantly influence outcomes. The value of genomic resources for lesser-studied crops such as cranberries and grapes and the orphan crop fonio will also be considered.

Degree-Day Benchmarks for Sparganothis sulfureana (Lepidoptera: Tortricidae) Development in Cranberries.

Sparganothis sulfureana Clemens is a severe pest of cranberries in the Midwest and northeast United States. Timing for insecticide applications has relied primarily on calendar dates and pheromone trap-catch; however, abiotic conditions can vary greatly, rendering such methods unreliable as indicators of optimal treatment timing. Phenology models based on degree-day (DD) accrual represent a proven, superior approach to assessing the development of insect populations, particularly for larvae. Previous studies of S. sulfureana development showed that the lower and upper temperature thresholds for larval development were 10.0 and 29.9°C (49.9 and 85.8°F), respectively. We used these thresholds to generate DD accumulations specific to S. sulfureana, and then linked these DD accumulations to discrete biological events observed during S. sulfureana development in Wisconsin and New Jersey cranberries. Here, we provide the DDs associated with flight initiation, peak flight, flight termination, adult life span, preovipositional period, ovipositional period, and egg hatch. These DD accumulations represent key developmental benchmarks, allowing for the creation of a phenology model that facilitates wiser management of S. sulfureana in the cranberry system.

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences.

The application of next-generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome-wide and gene-based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high-throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.

Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences.

Switchgrass (Panicum virgatum), a central and Eastern USA native, is highly valued as a component in tallgrass prairie and savanna restoration and conservation projects and a potential bioenergy feedstock. The purpose of this study was to identify regional diversity, gene pools, and centers-of-diversity of switchgrass to gain an understanding of its post-glacial evolution and to identify both the geographic range and potential overlap between functional gene pools. We sampled a total of 384 genotypes from 49 accessions that included the three main taxonomic groups of switchgrass (lowland 4x, upland 4x, and upland 8x) along with one accession possessing an intermediate phenotype. We identified primary centers of diversity for switchgrass in the eastern and western Gulf Coast regions. Migration, drift, and selection have led to adaptive radiation in switchgrass, creating regional gene pools within each of the main taxa. We estimate that both upland-lowland divergence and 4x-to-8x polyploidization within switchgrass began approximately 1.5-1 M ybp and that subsequent ice age cycles have resulted in gene flow between ecotype lineages and between ploidy levels. Gene flow has resulted in "hot spots" of genetic diversity in the southeastern USA and along the Atlantic Seaboard.

A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.).

BACKGROUND: A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). RESULTS: Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. CONCLUSIONS: Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).

The extent of hybridization and its impact on the genetic diversity and population structure of an invasive tree, Ulmus pumila (Ulmaceae).

Ulmus pumila is considered an invasive tree in 41 of the United States. In this study, we examined the extent of hybridization in naturalized populations of U. pumila, its impact on genetic diversity and genetic structure and its potential role in explaining the invasion process of U. pumila. Genetic analyses indicated widespread hybridization with native Ulmus rubra in naturalized U. pumila populations. Hybridization increased the genetic diversity of U. pumila populations and affected their genetic structure. The level of genetic diversity in 'mature' accessions, many of which may represent original plantings throughout the USA, was high and similar to the diversity of East Asian accessions. Hybridization with the native red elm may play an important role in the success of Siberian elm as an invader in temperate regions of the USA.

Patterns of hybridization and introgression between invasive Ulmus pumila (Ulmaceae) and native U. rubra.

Natural hybridization between introduced species and their native congeners occurs frequently and can create serious conservation concerns. Ulmus pumila (Siberian elm) is an introduced Asian elm species that has naturalized in the United States and is now considered invasive in 41 states. Red elm (U. rubra), a native to the eastern United States, often occurs in sympatry with Siberian elm, and the two species are thought to hybridize. Here, we genetically characterized reference populations of the two elm species to identify species-specific microsatellite alleles. These markers were used to classify individuals in putative hybrid zones as parental species or hybrids, assess the extent of hybridization, and track patterns of introgression. We identified nine U. rubra, 32 U. pumila, and 51 hybrid individuals in our hybrid zones. Of the 51 hybrids, 35 were classified as first-generation hybrids and 16 as backcrosses. The majority of the backcrosses (88%) were introgressed toward U. pumila. Our classification of genotypes was consistent whether we used manual classification, principal coordinate analyses or Bayesian clustering. We observed greater genetic diversity and new combination of alleles in the hybrids. Our study indicates widespread hybridization between U. pumila and U. rubra and an asymmetric pattern of introgression toward U. pumila.

Genetic diversity and relationships among Dutch elm disease tolerant Ulmus pumila L. accessions from China.

Elm breeding programs worldwide have relied heavily on Asian elm germplasm, particularly Ulmus pumila, for the breeding of Dutch elm disease tolerant cultivars. However, the extent and patterning of genetic variation in Asian elm species is unknown. Therefore, the objective of this research was to determine the extent of genetic diversity among 53 U. pumila accessions collected throughout the People's Republic of China. Using 23 microsatellite loci recently developed in the genus Ulmus, a total of 94 alleles were identified in 15 polymorphic and 4 monomorphic loci. The average number of alleles per locus was 4.9, with a range of 1-11 alleles. Gene diversity estimates per locus ranged from 0.08 to 0.87, and the non-exclusion probability for the 15 polymorphic loci combined was 0.7 x 10(-9). Nineteen region-specific alleles were identified, and regional gene diversity estimates were moderately high (0.48-0.57). The genetic relationships among accessions and regions were estimated by UPGMA and principal coordinate analysis. Both techniques discriminated all accessions and regions. Two microsatellite markers (UR175 + UR123 or Ulm-3) were sufficient to discriminate up to 99.7% of the accessions studied. This research provides useful information for DNA-based fingerprinting, breeding, ecological studies, and diversity assessment of elm germplasm.