The potential of microarrays to assist shrimp breeding and production: a review

The shrimp aquaculture industry is a relatively new livestock industry, having developed over the past 30 years. Thus, it is poised to take advantage of new technologies from the outset of selective breeding programs. This contrasts with long established livestock industries, where there are already highly specialised breeds. This review focuses specifically on the potential application of microarrays to shrimp breeding. Potential applications of microarrays in selective breeding programs are summarised. Microarrays can be used as a rapid means to generate molecular markers for genetic linkage mapping, and genetic maps have been constructed for yeast, Arabidopsis and barley using microarray technology. Microarrays can also be used in the hunt for candidate genes affecting particular traits, leading to development of perfect markers for these traits (i.e. causative mutations). However, this requires that microarray analysis be combined with genetic linkage mapping, and that substantial genomic information is available for the species in question. A novel application of microarrays is to treat gene expression as a quantitative trait in itself and to combine this with linkage mapping to identify quantitative trait loci controlling the levels of gene expression; this approach may identify higher level regulatory genes in specific pathways. Finally, patterns of gene expression observed using microarrays may themselves be treated as phenotypic traits in selection programs (e.g. a particular pattern of gene expression might be indicative of a disease tolerant individual). Microarrays are now being developed for a number of shrimp species in laboratories around the world, primarily with a focus on identifying genes involved in the immune response. However, at present, there is no central repository of shrimp genomic information, which limits the rate at which shrimp genomic research can be progressed. The application of microarrays to shrimp breeding will be extremely limited until there is a shared repository of genomic information for shrimp, and the collective will and resources to develop comprehensive genomic tools for shrimp.

Ecological factors associated with the breeding and migratory phenology of high-latitude breeding western sandpipers

Environmental conditions influence the breeding and migratory patterns of many avian species and may have particularly dramatic effects on long-distance migrants that breed at northern latitudes. Environment, however, is only one of the ecological variables affecting avian phenology, and recent work shows that migration tactics may be strongly affected by changes in predator populations. We used long-term data from 1978 to 2000 to examine the interactions between snowmelt in western Alaska in relation to the breeding or migration phenologies of small shorebirds and their raptor predators. Although the sandpipers' time of arrival at Alaskan breeding sites corresponded with mean snowmelt, late snowmelts did delay breeding. These delays, however, did not persist to southward migration through British Columbia, likely due to the birds' ability to compensate for variance in the length of the breeding season. Raptor phenology at an early stopover site in British Columbia was strongly related to snowmelt, so that in years of early snowmelt falcons appeared earlier during the sandpipers' southbound migration. These differential effects indicate that earlier snowmelt due to climate change may alter the ecological dynamics of the predator-prey system.

Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

Plant breeders use many different breeding methods to develop superior cultivars. However, it is difficult, cumbersome, and expensive to evaluate the performance of a breeding method or to compare the efficiencies of different breeding methods within an ongoing breeding program. To facilitate comparisons, we developed a QU-GENE module called QuCim that can simulate a large number of breeding strategies for self-pollinated species. The wheat breeding strategy Selected Bulk used by CIMMYT's wheat breeding program was defined in QuCim as an example of how this is done. This selection method was simulated in QuCim to investigate the effects of deviations from the additive genetic model, in the form of dominance and epistasis, on selection outcomes. The simulation results indicate that the partial dominance model does not greatly influence genetic advance compared with the pure additive model. Genetic advance in genetic systems with overdominance and epistasis are slower than when gene effects are purely additive or partially dominant. The additive gene effect is an appropriate indicator of the change in gene frequency following selection when epistasis is absent. In the absence of epistasis, the additive variance decreases rapidly with selection. However, after several cycles of selection it remains relatively fixed when epistasis is present. The variance from partial dominance is relatively small and therefore hard to detect by the covariance among half sibs and the covariance among full sibs. The dominance variance from the overdominance model can be identified successfully, but it does not change significantly, which confirms that overdominance cannot be utilized by an inbred breeding program. QuCim is an effective tool to compare selection strategies and to validate some theories in quantitative genetics.

Seed viability and dormancy mechanisms of Leucopogon melaleucoides Cunn. ex DC. (Epacridaceae)

Leucopogon melaleucoides, a flowering shrub, is desired by floricultural markets but is difficult to propagate. Seed viability was tested and dormancy mechanisms were studied to develop a commercial propagation system. Although around 56% of seed were viable, germination was completely inhibited unless the endocarp was removed. After-ripened seed (8 months after collection) germinated faster than fresh seed (2 days after collection), but germination occurred over a prolonged period (155 days). Germination of after-ripened seed was promoted with GA(3) or a commercial smoke product containing unknown plant growth regulators. All viable seed treated with GA(3) at 1000 mg L-1 had germinated after 24 days. The results suggest that both a physical and physiological dormancy mechanism occur for this species, with removal of the endocarp and pretreatment with 1000 mg L-1 GA(3) promoting complete germination of viable seed.

Adventitious root formation in cuttings of Backhousia citriodora F. Muell: 1. Plant genotype, juvenility and characteristics of cuttings

Backhousia citriodora is a commercially valuable Australian woody species that has a reputation for being recalcitrant in forming adventitious roots from cuttings. A study was carried out to determine whether maturation and plant genotype influenced rooting. It also tried to establish whether genotypic differences in rooting ability were related to characteristics of the cutting material. The rooting of cuttings in B. citriodora declines after maturation and is strongly influenced by genotype. The cutting characteristics of actively growing axillary buds, wide stems and mature leaves are associated with rooting and survival but not related to genotype. Furthermore, the 8-24 weeks required by B. citriodora to form roots from cuttings makes it difficult to distinguish between the characteristics that increase rooting and those characteristics that enhance survival. A subsequent disbudding experiment demonstrated that axillary buds per se have an inhibitory effect on rooting. This suggests that the presence of actively growing axillary buds are an indication of overall growth and condition of the stock plant unrelated to the formation of adventitious rooting. The effects of other cutting characteristics on rooting are also discussed. (C) 2004 Elsevier B.V. All rights reserved.

The utility and limitations of chloroplast DNA analysis for identifying native British oak stands and for guiding replanting strategy

We report a method using variation in the chloroplast genome (cpDNA) to test whether oak stands of unknown provenance are of native and/or local origin. As an example, a sample of test oaks, of mostly unknown status in relation to nativeness and localness, were surveyed for cpDNA type. The sample comprised 126 selected trees, derived from 16 British seed stands, and 75 trees, selected for their superior phenotype (201 tree samples in total). To establish whether these two test groups are native and local, their cpDNA type was compared with that of material from known autochthonous origin (results of a previous study which examined variation in 1076 trees from 224 populations distributed across Great Britain). In the previous survey of autochthonous material, four cpDNA types were identified as native; thus if a test sample possessed a new haplotype then it could be classed as non-native. Every one of the 201 test samples possessed one of the four cpDNA types found within the autochthonous sample. Therefore none could be proven to be introduced and, on this basis, was considered likely to be native. The previous study of autochthonous material also found that cpDNA variation was highly structured geographically and, therefore, if the cpDNA type of the test sample did not match that of neighbouring autochthonous trees then it could be considered to be non-local. A high proportion of the seed stand group (44.2 per cent) and the phenotypically superior trees (58.7 per cent) possessed a cpDNA haplotype which matched that of the neighbouring autochthonous trees and, therefore, can be considered as local, or at least cannot be proven to be introduced. The remainder of the test sample could be divided into those which did not grow in an area of overall dominance (18.7 per cent of seed stand trees and 28 per cent of phenotypically superior) and those which failed to match the neighbouring autochthonous haplotype (37.1 per cent and 13.3 per cent, respectively). Most of the non-matching test samples were located within 50 km of an area dominated by a matching autochthonous haplotype (96.0 per cent and 93.5 per cent, respectively), and potentially indicates only local transfer. Whilst such genetic fingerprinting tests have proven useful for assessing the origin of stands of unknown provenance, there are potential limitations to using a marker from the chloroplast genome (mostly adaptively neutral) for classifying seed material into categories which have adaptive implications. These limitations are discussed, particularly within the context of selecting adaptively superior material for restocking native forests.