Zooplankton and epibenthic fauna in shrimp ponds: factors influencing assemblage dynamics

The assemblage composition, biomass and dynamics of zooplankton and epibenthos were examined in a commercial shrimp (penaeid prawn) pond in subtropical Australia. Physicochemical characteristics of the pond water were measured concurrently. Numbers and biomass of zooplankton in the surface tows (140 μm mesh) varied from 111.7 ind. L^?1 (324 μg L^?1) to 8.3 ind. L^?1 (44.2 μg L^?1). Immediately after the ponds were stocked with shrimp postlarvae there was a rapid decline in zooplankton numbers, particularly the dominant larger copepods. We attributed this to predation by the shrimp postlarvae. Subsequent peaks in zooplankton numbers were principally due to barnacle nauplii. Changes in abundance and biomass of the zooplankton assemblage were not correlated with physicochemical characteristics. Epibenthic faunal abundance in the beam trawls (1 mm mesh) peaked at 14 ind. m^?2 and the biomass at 0.8 g m^?2. Unlike zooplankton, the peaks in abundance of epibenthos did not correspond to the peaks in biomass. This was due to the large differences in the size of the dominant taxa across the season. Sergestids (Acetes sibogae) and amphipods were the most abundant taxa in beam trawl samples, with amphipods abundance increasing towards the end of the growout. Negative correlations were found between epibenthos abundance and pH and temperature. These relationships were strongly influenced by the high abundances of amphipods and may reflect an effect on the growth of macroalgae in the pond rather than a direct effect on the epibenthos. No correlations were found between epibenthic fauna biomass and physicochemical parameters. Abundances of epibenthic fauna were not related to zooplankton densities, indicating that this source of food was not likely to be a limiting factor. Neither the pond water exchange regime nor moon phase could explain changes in abundances of zooplankton or epibenthos assemblages. Zooplankton clearly contribute to the nutrition of shrimp postlarvae immediately after stocking. The establishment of an abundant assemblage of zooplankton before stocking shrimp postlarvae would appear to be beneficial, if not essential. Later in the season, zooplankton and epibenthos apparently contribute little to shrimp biomass. Owing to their relatively low biomass, the consumption of shrimp feeds by epibenthos is likely to be insignificant compared with that of the shrimp.     

Genome-wide association studies in a barley (Hordeum vulgare) diversity set reveal a limited number of loci for resistance to spot blotch (Bipolaris sorokiniana)

Spot blotch caused by Bipolaris sorokiniana is an important disease in barley worldwide, causing considerable yield losses and reduced grain quality. In order to identify QTL conferring resistance to spot blotch, a highly diverse worldwide barley set comprising 449 accessions was phenotyped for seedling resistance with three isolates (No 31, SH 15 and SB 61) and for adult plant resistance at two locations (Russia and Australia) in two years. Genotyping with the 50 k iSelect barley SNP genotyping chip yielded 33,818 informative markers. Genome-wide association studies (GWAS) using a compressed mixed linear model, including population structure and kinship, revealed 38 significant marker-trait associations (MTA) for spot blotch resistance. The MTA corresponded to two major QTL on chromosomes 1H and 7H and a putative new minor QTL on chromosome 7H explaining between 2.79% and 13.67% of the phenotypic variance. A total of 10 and 14 high-confidence genes were identified in the respective major QTL regions, seven of which have a predicted involvement in pathogen recognition or defence.     

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.     

De Novo Next Generation Sequencing of Plant Genomes

The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequencing technologies have brought about great improvements in sequencing throughput and cost, but do not yet allow for de novo sequencing of large repetitive genomes as found in most crop plants. We present a strategy that combines cutting edge next generation sequencing with “old school” genomics resources and allows rapid cost-effective sequencing of plant genomes.