Andrew P. Michel

Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity

Phenotypic diversity within cultivated tomato (Solanum lycopersicum) is particularly evident for fruit shape and size. Four genes that control tomato fruit shape have been cloned. SUN and OVATE control elongated shape whereas FASCIATED (FAS) and LOCULE NUMBER (LC) control fruit locule number and flat shape. We investigated the distribution of the fruit shape alleles in the tomato germplasm and evaluated their contribution to morphology in a diverse collection of 368 predominantly tomato and tomato var. cerasiforme accessions. Fruits were visually classified into eight shape categories that were supported by objective measurements obtained from image analysis using the Tomato Analyzer software. The allele distribution of SUN, OVATE, LC, and FAS in all accessions was strongly associated with fruit shape classification. We also genotyped 116 representative accessions with additional 25 markers distributed evenly across the genome. Through a model-based clustering we demonstrated that shape categories, germplasm classes, and the shape genes were nonrandomly distributed among five genetic clusters (P < 0.001), implying that selection for fruit shape genes was critical to subpopulation differentiation within cultivated tomato. Our data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage. Furthermore, LC, OVATE, and FAS mutations may have arisen prior to domestication or early during the selection of cultivated tomato whereas the SUN mutation appeared to be a postdomestication event arising in Europe.

Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

Background Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources. Methodology/Principal Findings Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to develop both transcriptomic and genomic resources, including expressed genes and molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 transcripts and 56,688 genomic sequences. From this data set, 635 SNPs and 1,382 microsatellite markers were identified. For each sequencing method, different soybean aphid biotypes were used which revealed potential biotype specific markers. In addition, we uncovered 39,822 bp of sequence that were related to the obligatory endosymbiont, Buchnera aphidicola, as well as sequences that suggest the presence of Hamiltonella defensa, a facultative endosymbiont. Conclusions and Significance Molecular resources for an invasive, non-model aphid species were generated. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and help provide novel targets for soybean aphid control.

Genetic mapping revealed two loci for soybean aphid resistance in PI 567301B

The soybean aphid (Aphis glycines Matsumura) is the most damaging insect pest of soybean [Glycine max (L.) Merr.] in North America. New soybean aphid biotypes have been evolving quickly and at least three confirmed biotypes have been reported in USA. These biotypes are capable of defeating most known aphid resistant soybean genes indicating the need for identification of new genes. Plant Introduction (PI) 567301B was earlier identified to have antixenosis resistance against biotype 1 and 2 of the soybean aphid. Two hundred and three F7:9 recombinant inbred lines (RILs) developed from a cross of soybean aphid susceptible cultivar Wyandot and resistant PI 567301B were used for mapping aphid resistance genes using the quantitative trait loci (QTL) mapping approach. A subset of 94 RILs and 516 polymorphic SNP makers were used to construct a genome-wide molecular linkage map. Two candidate QTL regions for aphid resistance were identified on this linkage map. Fine mapping of the QTL regions was conducted with SSR markers using all 203 RILs. A major gene on chromosome 13 was mapped near the previously identified Rag2 gene. However, an earlier study revealed that the detached leaves of PI 567301B had no resistance against the soybean aphids while the detached leaves of PI 243540 (source of Rag2) maintained aphid resistance. These results and the earlier finding that PI 243540 showed antibiosis resistance and PI 567301B showed antixenosis type resistance, indicating that the aphid resistances in the two PIs are not controlled by the same gene. Thus, we have mapped a new gene near the Rag2 locus for soybean aphid resistance that should be useful in breeding for new aphid-resistant soybean cultivars. Molecular markers closely linked to this gene are available for marker-assisted breeding. Also, the minor locus found on chromosome 8 represents the first reported soybean aphid-resistant locus on this chromosome.

Population Genetic Structure of Aphis glycines

ABSTRACT The soybean aphid (Aphis glycines Matsumura) is an invasive pest of cultivated soybean (Glycine max L.) in North America. After the initial invasion in 2000, the aphid has quickly spread across most of the United States and Canada, suggesting large-scale dispersal and rapid adaptation to new environments. Using microsatellite markers from closely related species, we compared the genetic diversity and the amount of genetic differentiation within and among 2 South Korean and 10 North American populations. Overall allelic polymorphism was low, never exceeding four alleles per locus. However, differences in genetic diversity were seen among South Korean and North American populations in terms of heterozygote excesses and genotypic richness. Within North America, two populations (Michigan and Ontario), had lower genetic diversities and exhibited high genetic differentiation compared with the remaining eight populations. The earlier collection time of Michigan and Ontario samples explained the genetic differences better than geographic subdivisions. These data indicate a pattern of small colonizing populations on soybeans, followed by rapid clonal amplification and subsequent large-scale dispersal across North America.

Detached Leaf and Whole Plant Assays for Soybean Aphid Resistance: Differential Responses Among Resistance Sources and Biotypes

ABSTRACT The soybean aphid, Aphis glycines Matsumura, is a pest of cultivated soybean, Glycine max (L.) Merr., in North America. Recent developments in host plant resistance studies have identified at least four soybean aphid resistance genes (Rog1–4) and two soybean aphid biotypes (biotype 1 and 2), defined by differential survivability on resistant soybean. Detached soybean leaves were tested as a more rapid and practical assay to assess host plant resistance and virulence. Two susceptible lines (‘Wyandot’ and ‘Williams 82’) and two resistant lines (PI 243540 and PI 567301B) were examined. Various life history characteristics were compared among aphids on whole plants and detached leaves. Results indicated that resistance to soybean aphid was lost using detached leaves of PI 567301B but retained with PI 243540. To test for aphid virulence, net fecundities were compared among biotype 1 and biotype 2 after rearing on detached leaves of the resistant ‘Jackson’ (to which biotype 2 is virulent). A significant difference was detected in net fecundities among biotypes on detached leaves of Jackson and used to predict growth rates and virulence from 30 field-collected individuals of unknown virulence. No field individuals matched biotype 2 predictions, but four individuals had higher net fecundities than biotype 2 predictions (13%) and could be considered moderately virulent. The results indicated that the retention of soybean aphid resistance in detached leaves is dependent on PI and resistant source, but if resistance is retained, detached leaves could be used to determine soybean aphid virulence.

Population structure and genetic differentiation associated with breeding history and selection in tomato ( Solanum lycopersicum L.)

Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise Fst (θ) and Neis standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an Fst-outlier method based on the deviation from the expected distribution of Fst and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato

Ecology and management of the western bean cutworm (Lepidoptera: Noctuidae) in corn and dry beans.

The western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is a native North American pest that feeds mainly on corn and dry beans. The historical geographic range of the western bean cutworm covered the western Great Plains states, including Colorado, Nebraska, and Wyoming. Since 1999, the geographic range of the western bean cutworm has rapidly expanded eastward across the United States Corn Belt, causing significant and economic damage to corn and dry beans in parts of this region. This expansion has led to a resurgence of interest in this pest, particularly in areas where it has most recently caused damage. We summarize the ecology and biology of western bean cutworm and discuss options for scouting and management, with an emphasis in the expanded geographical range.

Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species

Heteroecious holocyclic aphids exhibit both sexual and asexual reproduction and alternate among primary and secondary hosts. Most of these aphids can feed on several related hosts, and invasions to new habitats may limit the number of suitable hosts. For example, the aphid specialist Aphis glycines survives only on the primary host buckthorn (Rhamnus spp.) and the secondary host soybean (Glycine max) in North America where it is invasive. Owing to this specialization and sparse primary host distribution, host colonization events could be localized and involve founder effects, impacting genetic diversity, population structure and adaptation. We characterized changes in the genetic diversity and structure across time among A. glycines populations. Populations were sampled from secondary hosts twice in the same geographical location: once after secondary colonization (early season), and again immediately before primary host colonization (late season). We tested for evidence of founder effects and genetic isolation in early season populations, and whether or not late-season dispersal restored genetic diversity and reduced fragmentation. A total of 24 single-nucleotide polymorphisms and 6 microsatellites were used for population genetic statistics. We found significantly lower levels of genotypic diversity and more genetic isolation among early season collections, indicating secondary host colonization occurred locally and involved founder effects. Pairwise FST decreased from 0.046 to 0.017 in early and late collections, respectively, and while genetic relatedness significantly decreased with geographical distance in early season collections, no spatial structure was observed in late-season collections. Thus, late-season dispersal counteracts the secondary host colonization through homogenization and increases genetic diversity before primary host colonization.

The Crypt-Dwelling Primary Bacterial Symbiont of the Polyphagous Pentatomid Pest Halyomorpha halys (Hemiptera: Pentatomidae)

ABSTRACT A recent invader of North America, the brown marmorated stink bug (Halyomorpha halys Stål) is a polyphagous pentatomid that harbors a gammaproteobacterial mutualist in the crypts of specialized midgut gastric caeca (region V4). Histological analyses revealed a single rod-shaped morphology abundant in distal V4 midgut caecal crypts. A strong fluorescence signal was detected when thin sections of these tissues were hybridized with a fluorescently-labeled, Enterobacteriaceae-specific oligonucleotide probe. A single operational taxonomic unit (OTU) assigned to the Pantoea genus represented >99% of 3,454 16S rDNA amplicons obtained from midgut V4 tissues and egg samples. Detection of H. halys primary symbiont in DNA extracted from eggs suggested vertical maternal inheritance as the mode of intergenerational transmission. Consistent detection of the bacterial symbiont in geographically distinct H. halys populations strongly supports an intimate association between these two organisms. An inferred phylogeny of gammaproteobacterial symbionts of pentatomids placed the Pantoea-assigned OTU from H. halys within a clade distinct from primary bacterial symbionts of related stink bugs, Nezara viridula (L.) and Eurydema rugosa Motschulsky. Given these data, Candidatus “Pantoea carbekii” is proposed as the name of the primary bacterial symbiont of H. halys.

Evolution of Soybean Aphid Biotypes: Understanding and Managing Virulence to Host-Plant Resistance

The soybean aphid (Aphis glycines Matsumura) has rapidly become one of the most significant insect pests of soybean (Glycine max) worldwide (Ragsdale et al., 2007). The rise of soybean aphid in importance is in large part due to the invasion of North America ca. 2000, presumably coming from its native range in Asia (Ragsdale et al., 2004). In the first few years of the North American invasion, the soybean aphid spread across much of the NorthCentral US and the provinces of Ontario and Quebec. Its current distribution includes over 80% of the soybean growing region of the US and Canada (Vennette & Ragsdale, 2004). Worldwide, the distribution includes much of East Asia (China, Japan, The Philippines, South Korea, Indonesia, Malaysia, Thailand, Vietnam, and Russia), all of which likely represents the ancestral range (Footit et al., 2006). Options for management and control of soybean aphid are limited. As an alternative to chemical insecticides, host-plant resistance is a common method of aphid control (Van Emden, 2007), which uses plant hosts with genetically inherited traits that enable the plant to withstand pest attack better than a plant lacking these traits (Smith, 2005). Although soybean aphid resistant varieties have been studied in China (Wu et al., 2004), new soybean varieties have been developed with resistance to the soybean aphid specifically for use in North America (Hill et al., 2004, 2006a,b; Mian et al., 2008; Zhang et al., 2009; Hill et al., 2010). Varieties for North American commercial use were available for the first time in 2010. However, the host-plant resistance strategy is complicated because of rapid evolution of soybean aphid populations (i.e. biotypes) that have overcome host-plant resistance (i.e. virulence). Biotypes can be defined as “populations within an arthropod species that differ in their ability to utilize a particular trait in a particular plant genotype” (Smith, 2005). The presence of soybean aphid biotypes with virulence to host-plant resistance varieties before these varieties were commercially released suggests that the soybean aphid can rapidly adapt to these new lines and thereby threaten the effectiveness and sustainability of the host-plant resistance strategy.