Mark G. Wright

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

Background The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Biological control of invasive species: solution or pollution?

Biological control of invasive species using co-evolved natural enemies has long been considered a safe, cost effective, and environmentally benign tool for pest management. However, recent work has questioned the extent to which these imported natural enemies have negative impacts on populations of non-target species. The result has been a vociferous debate about the safety and proper role of biological control, often without convincing evidence on either side. The issues are particularly well focused in Hawaii, with its high numbers of both endemics and invasive pest species. We review the data concerning environmental impacts from past biocontrol projects, discuss the patterns and generalizations that emerge from retrospective analyses, and consider some new techniques for risk assessment. We then emphasize the need for a federal regulatory framework that is rational, efficient, transparent, and ecologically meaningful.

Insect species richness tracking plant species richness in a diverse flora: gall-insects in the Cape Floristic Region, South Africa

Abstract The Cape Floristic Region (CFR) is one of the most plant-species-rich regions in the world. It is also a warm temperate region and hypothetically should have high gall-insect species richness, making it interesting to investigate the relationship between the insects of the region and the rich flora. The relationship between gall-insect species richness (GSR) and plant richness was investigated for the Fynbos and for representatives of vegetation of the whole CFR. Samples (of up to 600 plants per transect for Fynbos) of woody shrubs were investigated for the presence of galls. The species richness of these insects was quantified, as well as plant species richness for each transect. GSR for Fynbos was compared to global figures for GSR. Fynbos harboured significantly more gall-insect species than other CFR vegetation types. GSR was positively correlated with CFR plant richness. GSR also closely tracked plant richness in Fynbos. GSR was not significantly influenced by other variables (elevation and aspect), suggesting that plant richness per se was an important factor in generating GSR. Fynbos GSR is comparable to other sclerophyllous regions of high GSR globally, corroborating that this vegetation type is conducive to gall-insect diversification. There is likely to be a high percentage of gall-insect endemism in the Fynbos, as might be expected from the high host fidelity of this insect group.

Inoculative releases of Trichogramma ostriniae for suppression of Ostrinia nubilalis (European corn borer) in sweet corn: field biology and population dynamics

Abstract The effectiveness of inoculative releases of Trichogramma ostriniae Pang and Chen for suppression of Ostrinia nubilalis (Hubner) in sweet corn was assessed. Early-season, low-density (75,000 females ha −1 ) releases were made, and establishment, levels of parasitism and sex ratios of emerging T. ostriniae quantified. T. ostriniae established effectively for each season that they were released, but appeared to be unable to overwinter. Parasitism levels tracked egg mass numbers closely, and T. ostriniae persisted in fields even where insecticides were applied. Parasitism by indigenous Trichogramma species was ∼3%. Field populations of T. ostriniae were distinctly female biased (∼78%), with males produced in the majority of broods. Numbers of males did not increase linearly with number of O. nubilalis eggs parasitized, but appeared to remain constant above an egg mass size of about 20 eggs. A Type-I functional response to increasing egg and egg mass density was found under field conditions, where the proportion of egg masses parasitized remained constant with increasing egg mass density. A relatively consistent percentage of eggs per egg mass was parasitized, with a linear increase in number of eggs parasitized with increasing number of eggs per egg mass. These results show that T. ostriniae established viable reproductive populations in sweet corn following inoculative release, with the potential to contribute to reduced dependence on insecticides for the control of O. nubilalis in an integrated pest management program.

Super-Genotype: Global Monoclonality Defies the Odds of Nature

The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae) with differing global (North American and African) patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (FST = 0.0) and is supported by extreme low quantitative trait variance (QST = 0.00065–0.00952). The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010.

This article documents the addition of 205 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Bagassa guianensis, Bulweria bulwerii, Camelus bactrianus, Chaenogobius annularis, Creontiades dilutus, Diachasmimorpha tryoni, Dioscorea alata, Euhrychiopsis lecontei, Gmelina arborea, Haliotis discus hannai, Hirtella physophora, Melanaphis sacchari, Munida isos, Thaumastocoris peregrinus and Tuberolachnus salignus. These loci were cross‐tested on the following species: Halobaena caerulea, Procellaria aequinoctialis, Oceanodroma monteiroi, Camelus ferus, Creontiades pacificus, Dioscorea rotundata, Dioscorea praehensilis, Dioscorea abyssinica, Dioscorea nummularia, Dioscorea transversa, Dioscorea esculenta, Dioscorea pentaphylla, Dioscorea trifida, Hirtella bicornis, Hirtella glandulosa, Licania alba, Licania canescens, Licania membranaceae, Couepia guianensis and 7 undescribed Thaumastocoris species.

Life Table Studies of European Corn Borer (Lepidoptera: Crambidae) with and without Inoculative Releases of Trichogramma ostriniae (Hymenoptera: Trichogrammatidae)

Abstract Life table studies of European corn borer, Ostrinia nubilalis (Hübner), populations with and without inoculative releases of Trichogramma ostriniae (Peng & Chen) were conducted in sweet corn and field corn. Inoculative releases of T. ostriniae (at 72,000 females per hectare) provided relatively high parasitism of European corn borer eggs (≈37%) throughout the season. The increase in egg parasitism was not offset by compensatory changes in other mortality rates such as egg predation, eggs not hatching, and death of early instars after egg hatch. Early instar disappearance was a key mortality factor accounting for >70% of total mortality from egg deposition to established larvae. Egg parasitism by T. ostriniae was also a key mortality factor. Releases of T. ostriniae increased total egg and larval mortality of O. nubilalis from 61 to 92% in sweet corn and from 80 to 93% in field corn.

Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps

Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here, we have analyzed expressed sequence tag (EST) data from 4 species (Pinus pinaster, Pinus taeda, Picea glauca, and Pseudotsuga menziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positive selection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species that was not included in the EST data set. The estimates of branch-specific Ka/Ks (nonsynonymous/synonymous substitution rates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. There was no evidence for the traditional indication of positive selection, Ka/Ks above 1. However, several lines of evidence based on polymorphism patterns suggest that genes with high Ka/Ks (0.20-0.52) in the EST data set are in fact more affected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01-0.04). The high Ka/Ks genes have a lower level of polymorphism and more negative Tajimas D than the low Ka/Ks genes. Further, in the high Ka/Ks group, the Hudson-Kreitman-Aguade test is significant. This suggests that the EST data set is a good starting point for finding genes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A group of 5 genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.

New record for the coffee berry borer, Hypothenemus hampei, in Hawaii

Abstract The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae) is endemic to Africa and is the most devastating pest of coffee worldwide. The female bores a hole in the coffee berry and deposits her eggs inside. Upon hatching, larvae feed on the seeds, thus reducing both quality and yields of the marketable product. The coffee berry borer was found in the district of Kona on the island of Hawaii in August 2010 and appears to be restricted to that area.