Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species

White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species.

Nutritional status of a nereidid polychaete cultured in sand filters of mariculture wastewater

This study examined the nutritional composition of the intertidal marine polychaete Perinereis helleri (Nereididae)when artificially cultured in sand filters treating mariculture wastewater. Moisture levels in harvested P. helleri ranged from 758 to 855 g kg1, and ash, from 23 to 61 g kg1 wet matter (WM). Stocking density and graded size after harvest significantly affected their composition. Higher total lipid contents were found in large (>0.6 g) P. helleri(16–19 g kg1 WM) and those grown at the lowest density(1000 m2: 18 g kg 1 WM) than in small (≤0.6 g) ones (14 g kg1 WM) and those grown at the highest densities (4000–6000 m2: 13–16 g kg1 WM). Several fatty acids within a very broad profile (some 30 identified) reflected this pattern, yet their ARA/EPA/DHA ratios were relatively unaffected. Feeding the polychaete-assisted sand filters (PASF) with fish meal to increase worm biomass productivity significantly increased their DHA content. Other components (e.g. protein, phospholipids, cholesterol, carbohydrate, amino acids, nitrogen, minerals and bromophenols) and nutritional factors (e.g. maturity, feeding seaweed and endemic shrimp viral content) were also investigated. Results suggest that PASF-produced P. helleri have a well-balanced nutritional profile for penaeid shrimp and fish broodstock.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. Weanalyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.