Australian Uromyces viciae-fabae: Host and nonhost interaction among cultivated grain legumes

Uromyces viciae-fabae, rust of faba bean, parasitizes other legume crops such as lentils (Lens culinaris) and field peas (Pisum sativum) in some environments. In this study we examined the host range of two Australian isolates of U. viciae-fabae collected and purified from a faba bean crop and classified as U. viciae-fabae ex V. faba. Field pea (P. sativum), chickpea (Cicer arientinum), lupin (Lupinus spp.), lentil (L. culinaris), and mung bean (Vigna radiata) genotypes were tested with these isolates, as well as resistant and susceptible genotypes of the faba bean host. Race specificity for these two pathogen isolates was observed on Vicia faba, with two faba bean genotypes showing partial resistance. Both U. viciae-fabae isolates also colonized field pea seedlings and successfully produced uredinia under glasshouse conditions, despite this fungus not being known as a pathogen of Australian field pea crops. No sporulation of either isolate of U. viciae-fabae ex V. faba was observed on any of the remaining legume species tested. However, obvious differences in fungal growth were observed, ranging from small infection sites with very rare haustorium formation in mung bean to more extensive growth and the development of potential uredinial structures in chickpea. These observations are discussed in relation to the phylogenetic relationship of these host and nonhost species.     

Assessing seed desiccation responses of native trees in the Caribbean

New Forests - Native trees from the Caribbean were tested for seed desiccation responses, by adapting the “100-seed test” protocol. Ninety-seven seed lots of 91 species were collected...     

Body shape variation in two species of darters (Etheostoma,Percidae) and its relation to the environment

Environmental variation can shape phenotypic variation in organisms, but most evidence for trait differentiation comes from analyses of dichotomous habitat types that differ in only one or few key environmental factors. In reality, environmental variation is often more subtle, gradual and multifarious. Here, we investigated geographic variation in body shape of two darter species (Etheostoma spectabile and Etheostoma flabellare; Percidae) that occur along river gradients. This study addressed three specific questions: Is there intraspecific geographic variation in the two species across different sites in the Ozark Highlands of Oklahoma (USA)? Is phenotypic variation across sites correlated with abiotic environmental conditions? Do the two species share site‐specific (i.e. convergent) phenotypic variation in areas where they occur together? Our results indicated significant body shape variation in both species. Population differences in body shape were particularly correlated with variation in substrate composition. The combined analysis of both species indicated a small but significant effect of convergence on body shape wherever they are sympatric; shared variation, however, was not related to any environmental variables included in the analysis. While it remains unclear whether phenotypic variation in these species is due to heritable differentiation or environmentally induced plasticity, our results indicate that even subtle and gradual environmental variation can induce substantial variation in phenotypes on a relatively small spatial scale.     

Forecasting the Genetic Impacts of Net Pen Failures on Gulf of Mexico Cobia Populations Using Individual‐based Model Simulations

Offshore net pen fish farming provides a cost‐efficient means for production of marine finfish, and there is great interest in development of net pen operations in domestic waters. However, there are concerns over the possible genetic and ecological impacts that escaped fish may have on wild populations. We used individual‐based simulations, with parameter values informed by life history and genetic data, to investigate the short‐term (50 yr) impacts of net pen failures on the genetic composition of cobia, Rachycentron canadum, stocks in the Gulf of Mexico. Higher net pen failure rates resulted in greater genetic impacts on the wild population. Additionally, the use of more genetically differentiated source populations led to larger influxes of non‐native alleles and greater temporal genetic change in the population as a result of net pen failure. Our results highlight the importance of considering the appropriate source population for broodstock collection in net pen aquaculture systems and help to provide a general set of best management practices for broodstock selection and maintenance in net pen aquaculture operations. A thorough understanding of the genetic diversity, stock structure, and population demography of target species is important to determine the impact escapees can have on wild populations.     

Winter movement activity patterns of anadromous Arctic charr in two Labrador lakes

Anadromous Arctic charr, Salvelinus alpinus, feed in the marine environment for several months during the summer and migrate back to fresh water in late summer to spawn and/or overwinter. While overwintering, anadromous Arctic charr are generally believed to reduce or cease feeding, and they are poorly described in their winter movement activity. This study used telemetry data collected from two locations to describe overwintering movement activity, including interindividual variation. Movement activity declined markedly during the ice‐covered period, suggesting opportunistic maintenance feeding was used as an energy conservation strategy. Fall and spring movement was correlated with daylight hours, and ice break‐up had a significant effect on the timing of outmigration. Movement activity was negatively correlated with body length, with smaller individuals being more active than larger fish. Although general activity patterns were evident, there were significant differences among individuals, particularly during spring immediately prior to lake departure. Lake size and individual differences in metabolic rate may account for some of this variation.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.