Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Quantifying northward movement rates of eastern king prawns along eastern Australia

Movement rates of eastern king prawns, Melicertus plebejus (Hess), were estimated from historical and recent conventional tag-recapture information collected across eastern Australia. Data from three studies and 2,656 tag recaptures were used. Recaptured males and females both moved east–north-east in central Queensland and north–north-east in southern Queensland and New South Wales. Over a period of one year, the estimated transition matrix reflected the species strong northerly movement and the more complex longitudinal movement, showing a very high probability of eastern movement in central Queensland and almost negligible eastern or western movement in northern New South Wales. The high exchange probability between New South Wales and Queensland waters indicated that spatial assessment models with movement rates between state jurisdictions would improve the management of this single-unit stock.

Quantifying northward movement rates of eastern king prawns along eastern Australia

Movement rates of eastern king prawns, Melicertus plebejus (Hess), were estimated from historical and recent conventional tag-recapture information collected across eastern Australia. Data from three studies and 2,656 tag recaptures were used. Recaptured males and females both moved east-north-east in central Queensland and north-north-east in southern Queensland and New South Wales. Over a period of one year, the estimated transition matrix reflected the species strong northerly movement and the more complex longitudinal movement, showing a very high probability of eastern movement in central Queensland and almost negligible eastern or western movement in northern New South Wales. The high exchange probability between New South Wales and Queensland waters indicated that spatial assessment models with movement rates between state jurisdictions would improve the management of this single-unit stock.

New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)

Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172837 raw reads (17.4Mbp) were retrieved, 95500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST=0.0025) can be resolved with a likely power 67% by using standard sample sizes of 50 and validated subsets of available markers.

Generalised growth models for aquatic species with an application to blacklip abalone (Haliotis rubra)

This paper presents a maximum likelihood method for estimating growth parameters for an aquatic species that incorporates growth covariates, and takes into consideration multiple tag-recapture data. Individual variability in asymptotic length, age-at-tagging, and measurement error are also considered in the model structure. Using distribution theory, the log-likelihood function is derived under a generalised framework for the von Bertalanffy and Gompertz growth models. Due to the generality of the derivation, covariate effects can be included for both models with seasonality and tagging effects investigated. Method robustness is established via comparison with the Fabens, improved Fabens, James and a non-linear mixed-effects growth models, with the maximum likelihood method performing the best. The method is illustrated further with an application to blacklip abalone (Haliotis rubra) for which a strong growth-retarding tagging effect that persisted for several months was detected. (C) 2013 Elsevier B.V. All rights reserved.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.

Performance and physiological responses of combined t-bar and PIT tagged giant mud crabs (Scylla serrata)

Mud crabs (Scylla spp.) are intensively caught throughout South-East Asia and support a very substantial commercial, recreational fishing and aquaculture industry. Identification of individual animals is important to improve understanding and management of this species. However, tagging of crustaceans is difficult as they frequently molt and internal tags can pose a hazard to consumers. In this pilot study we tested a new method combining passive integrated transponder tags and t-bar tags externally. 45 giant mud crabs (Scylla serrata) were captured from the wild and kept in tanks for a maximum of 10 months. We inserted tags into the abdomen of 35 giant mud crabs and tested a modified method where the combined t-bar/PIT-tag was inserted into the muscle tissue of the rear leg between the dorsal carapace plate and the top of the abdominal flap. Tagged crabs with the modified method showed 85% tag retention for molting crabs. We tested the same method in the field where 852 individuals were tagged with combined t-bar/PIT-tags of which 82 were recaptured showing 100% tag retention but without any evidence of molting having occurred. The tested method of combined t-bar/PIT-tags in giant mud crabs can further improve monitoring for wild and aquaculture populations and can be deployed widely with low cost.

Performance and physiological responses of combined t-bar and PIT tagged giant mud crabs (Scylla serrata)

Mud crabs (Scylla spp.) are intensively caught throughout South-East Asia and support a very substantial commercial, recreational fishing and aquaculture industry. Identification of individual animals is important to improve understanding and management of this species. However, tagging of crustaceans is difficult as they frequently molt and internal tags can pose a hazard to consumers. In this pilot study we tested a new method combining passive integrated transponder tags and t-bar tags externally. 45 giant mud crabs (Scylla serrata) were captured from the wild and kept in tanks for a maximum of 10 months. We inserted tags into the abdomen of 35 giant mud crabs and tested a modified method where the combined t-bar/PIT-tag was inserted into the muscle tissue of the rear leg between the dorsal carapace plate and the top of the abdominal flap. Tagged crabs with the modified method showed 85% tag retention for molting crabs. We tested the same method in the field where 852 individuals were tagged with combined t-bar/PIT-tags of which 82 were recaptured showing 100% tag retention but without any evidence of molting having occurred. The tested method of combined t-bar/PIT-tags in giant mud crabs can further improve monitoring for wild and aquaculture populations and can be deployed widely with low cost.