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The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep‐water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome‐wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole‐genome re‐sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine‐scale population genetic structure to inform the management of this species.

A total of 10 000 M4 individuals in Jao Hom Nil (JHN) mutant population was treated with high temperature (40 °C to 45 °C) during the day time (6 h) from the booting to the harvesting stages, and ambient temperature (33 °C to 35 °C) was used as the control. The results of screening and yield trials found that the mutant line M9962 had a high spikelet fertility of 78% under heat stress. In addition, the other mutant lines, including M3181 and M7988, had a spikelet fertility of approximately 70%. However, the JHN wild type, Sin Lek, RD15 and RD33 had very low spikelet fertility of 34%, 14%, 9% and 4%, respectively. The lower spikelet fertility at an elevated temperature resulted in a dramatic decrease of filled grain and contributed to a loss in 100-grain weight. M9962 is a potential genetic stock for use in a heat tolerance breeding programme. In addition, spikelet fertility at high temperature was representative of heat tolerance and can be used as a screening trait for heat tolerance during the reproductive phase on a large scale. Keywords: High temperature, Rice, Spikelet fertility, Heat tolerance, Mutant

Genetic individual assignment of river stock of origin of mixed stock catch fish offers a tool to analyze size differences among river stocks. Data on the genetically identified river stock of origin of individual fish from commercial mixed stock catches were used to compare the catch size-at-age of mature Atlantic salmon catch fish (Salmo salar) from different rivers in the Baltic Sea. In this application of genetic mixed stock modeling, individual assignments of the river stock of origin were analyzed together with length- and weight-at-age data for individual catch fish. The use of four genetic stock identification based methods was compared for defining the length distributions of caught mature salmon in different river stocks. The catch data included information on maturing salmon in the northern Baltic Sea over the years 2000–2013. DNA microsatellite data on 17 loci and information on the smoltification age were used to assign spawners to their stock of origin. All of the compared methods for using probabilistic stock of origin data in our case yielded very similar estimates of the final mean length distributions of the stocks. The Bayesian mixture model yielded slightly more conservative estimates than the direct probability method, threshold method, or the modified probability method. The catch size between spawners of a same sex and age from river stocks differed significantly and the differences were large. The mean catch weight of 1-sea-winter old mature males in different rivers varied from 1.9 kg to 2.9 kg, from 5.1 kg to 7.5 kg for 2-sea-winter old males, from 5.0 kg to 7.2 kg for 2-sea-winter old females, and from 8.2 kg to 10.8 kg for 3-sea-winter-old females. The mean size of caught wild salmon spawners in each year-class was on average smaller than that of the hatchery-reared and sea ranched stocks.

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals, but studies describing detailed workflows of GTseq panel development are rare. Here, we develop a dual-purpose GT-seq panel for walleye (Sander vitreus) and discuss trade-offs associated with different development and genotyping approaches. Our GT-seq panel was developed using restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We then conducted simulations to test the utility of loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We conducted three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. Optimization focused on reducing variation in amplification rate among loci and minimizing the proportion of off-target sequence, both of which are important considerations for developing large GT-seq panels. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (1) inexpensive Chelex extractions performed well for genotyping, (2) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was likely unnecessary, and (3) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings should aid in their construction in myriad taxa.

The objective of research was to asses the genetic variability of Hot Chili in order to increase genetic stock for plant breeding program. The research was conducted in A glass house of Plant Science Departement, Sebelas Maret University, irradiation of seed was done in BATAN Jakarta.The experimental design was Completely Randomized Design which consisted of two treatment, irradiation dosage and Chili Varieties.The research conducted that dosages of irradiation affected the genetic variability of Chili. At the higher dosage of irradiation, there was A negative effect of gamma rays irradiation to the plant height, harvest age, number of red fruit, weight of red fruit and genetic variability. The heritability was high enough on all variables measured, except age flowering. Therefore, the genetic factor was more dominant on all variables, and for flowering age was more affected by environmental factor.

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley ( Lepidochelys kempii ) and olive ridley ( L. olivacea ) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle ( Chelonia spp.; 63%), with hawksbill ( Eretmochelys imbricata ; 17%) and ridley turtles ( Lepidochelys spp . ; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle ( Caretta caretta ) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.

Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.

Potato is a highly heterozygous and tetraploid crop and therefore it was a major challenge to decipher the potato genome. This chapter highlights the developmental stories of the potato genetic stock used for the whole genome sequencing by the Potato Genome Sequencing Consortium (PGSC). Published version

Three of the 20 species in the genus Trachinotus, in the jack family, Carangidae, are found in Florida waters. These are Florida Pompano (T. carolinus), Permit (T. falcatus), and Palometa (T. goodei). Florida Pompano is a coastal pelagic species found in estuarine and marine waters; it spawns in multiple batches in offshore waters. Permit is the largest and longest lived of the three species and also spawns offshore in multiple batches, near reefs. As adults, Permit can be found nearshore and offshore and are often associated with reefs, but as juveniles they are common estuarine inhabitants. Palometa is a marine species, similar in size to Florida Pompano, and has the widest latitudinal distribution of the three species. Palometa spawn in offshore waters throughout the year with two peaks of activity. All three species support commercial or recreational fisheries on both the Gulf of Mexico coast and Atlantic coast of Florida. Very little has been done to evaluate movement patterns of Trachinotus species. Based on a few tagging studies, it appears that Pompano do not travel far from coastal waters. The only preliminary investigation of genetic stock structure for the Florida Pompano population from Tampa Bay, FL, and Puerto Rico was based on microsatellite markers developed for the Pompano. The report’s key conclusion was that Pompano from Puerto Rico and from Florida belong to two highly distinct genetic stocks. This study was conducted to re-examine, using different microsatellite markers, the genetic status of Pompano stocks in Florida and Puerto Rico. The objectives of this study, therefore, were the following: 1) to develop microsatellite markers for Permit; 2) to cross-amplify the markers in Pompano and Palometa; and 3) to use these markers to confirm the status of Puerto Rico Pompano as a novel genetic stock using the methods of Bayesian population assignment, phylogenetic clustering, and factorial correspondence analysis. ... Three methods were used to investigate the relationship among the taxa using the microsatellite genotype data obtained from the samples. The results from the three analytical methods, based on Bayesian population assignment tests, phylogenetic clustering, and factorial correspondence analysis of genetic relationships among the four Trachinotus samples, showed that Florida and Puerto Rico Pompano samples belong to two highly distinct gene pools. But other multiple molecular tools, particularly nuclear-DNA sequences from many introns, and nonmolecular tools, such as morphological and meristic data, should be used together to determine species-level categorical designation for the Puerto Rico Pompano.

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.

This paper investigates the morphological and productive characteristics of two Tsigaie ecotypes belonging to the red variety. They represent genetic stock and semen, oocytes and embryos will be harvested from them in order to be cryopreserved. The sheep belong to the hill ecotype (Jucu farm and SCD Turda) and the mountain ecotype (SCDCOC Reghin). Body dimensions and weight are characteristic for the breed and prove the superiority of the hill ecotype over the mountain ecotype. The differences between populations from the hill ecotype are an effect of the keeping and feeding, the measurements being higher for animals from the Jucu farm. Wool production of sheep from the mountain ecotype is close to that of animals form the Jucu farm. Characteristics list the sheep as part of the breeds having semi-fine wool. Milk production increases until the thirs lactation and then decreases. It is higher for the hill ecotype. Milk quality, expressed through fat and protein percentages is similar for the two ecotypes and characteristic for the breed.

We apply genetic stock identification (GSI) data and models of the catch and sampling process to describe spatial and temporal patterns in the stock composition and stock-specific catch-per-unit-effort (CPUE) of both tagged and untagged stocks encountered in California recreational ocean Chinook salmon fisheries during the period 1998-2002. Spatial and temporal distributions inferred from GSI sampling of stocks with tagged hatchery components were broadly consistent with those previously inferred from studies of tag recoveries alone, while GSI provided additional insight into untagged stocks of conservation concern. The catch in all times and areas was dominated (typically ≥90%) by the "Central Valley Fall" genetic reporting group, which is comprised primarily of Sacramento River fall run Chinook. Other contributing stocks were more spread out in space and time with the exception of Central Valley winter run Chinook, which were rarely encountered by boats fishing in port areas north of Point Reyes. Localized stock-specific CPUE appeared to increase near a stock's respective natal river while decreasing in other port areas at the time of adult return to freshwater for spawning. We describe methods for quantifying uncertainty in stock proportions, stock-specific catch, and determining the statistical support for proposed management boundaries hypothesized to represent "break points" in the spatial distributions for stocks of concern, and find at most equivocal support for a proposed delineation line at Point Reyes in north-central California. Fil: Satterthwaite, William H.. National Ocean And Atmospheric Administration; Estados Unidos Fil: Ciancio Blanc, Javier Ernesto. University of California; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Crandall, Eric. University of California; Estados Unidos Fil: Palmer Zwahlen, Melodie L.. Marine Region. Ocean Salmon Project. California Department of Fish and Wildlife; Estados Unidos Fil: Grover, Allen M.. Marine Region. Ocean Salmon Project. California Department of Fish and Wildlife; Estados Unidos Fil: O'Farrell, Michael R.. National Ocean And Atmospheric Administration; Estados Unidos Fil: Anderson, Eric C.. National Ocean And Atmospheric Administration; Estados Unidos Fil: Mohr, Michael S.. National Ocean And Atmospheric Administration; Estados Unidos Fil: Garza, John Carlos. National Ocean And Atmospheric Administration; Estados Unidos

Chinook salmon spawning was firstreported in the 1980s in the Caterina River tributaryof the Santa Cruz River basin of Patagonia, whichdrains into the Atlantic Ocean. A naturalized populationnow persists and its source has been debated.Chinook salmon from California populations wasdirectly released into the Santa Cruz River in the earlytwentieth century, but ocean ranching experiments onthe Pacific coast of Patagonia (Chile) also releasedChinook salmon of lower Columbia River origin(University of Washington hatchery stock) in the latetwentieth century. We used genetic stock identificationwith single nucleotide polymorphisms to explorethe origin of this Chinook salmon population. Thegenotypes of salmon that invaded the Santa Cruz Riverwere compared with those derived from 69 knownpopulations from the Northern Hemisphere. ChinookSalmon of the Santa Cruz River were found to be mostsimilar to those from the lower Columbia River. Thissupports the hypothesis that the Santa Cruz Riverpopulation was founded from the ocean ranching insouthern Chile and the river was invaded by fishstraying from Pacific coast basins. Moreover, we findthat the life history of these naturalized fish, as inferredfrom scale analysis, was similar to that of theprogenitor stock. We suggest that the successfulinvasion of the Caterina River in Patagonia byChinook salmon was aided by pre-adaptations ofsome of the stocks used in the ocean ranchingexperiments to conditions in the new environment,rather than a post-colonization adaptation. Fil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Anderson, Eric. University of California. Southwest Fisheries Science Center National Marine Fisheries Service; Estados Unidos Fil: Garza, John Carlos. University of California. Southwest Fisheries Science Center National Marine Fisheries Service; Estados Unidos

International audience; Grain legumes contribute significantly to total world food production. Legumes are the primary source of dietary proteins in many developing countries, where protein hunger and malnutrition are widespread. Grain legumes germplasm constitute similar to 15% of the 7.4 M accessions preserved globally. Nearly, 78% of the CGIAR's, 0.217 M accessions, have been characterized, compared to 34% of national genebank collections. Interestingly, limited data on grain quality are available as the primary focus has been on morpho-agronomic traits. Clearly, more resources should be targeted on biochemical evaluation to identify nutritionally rich and genetically diverse germplasm. The formation of core and mini core collections has provided crop breeders with a systematic yet manageable entry point into global germplasm resources. These subsets have been reported for most legumes and have proved useful in identifying new sources of variation. They may however not eliminate the need to evaluate entire collections, particularly for very rare traits. Molecular characterization and association mapping will further aid to insights into the structure of legume diversity and facilitate greater use of collections. The use of high resolution elevational climate models has greatly improved our capacity to characterize plant habitats and species' adaptive responses to stresses. Evidence suggests that there has been increased use of wild relatives as well as new resources resulting from mutagenesis to enhance the genetic base of legume cultigens.

The genes involved in the putrescine formation by Morganella morganii were investigated because putrescine is an indicator of food process deterioration. We report here on the existence of a new gene for ornithine decarboxylase (ODC) in M. morganii. The sequenced 5,311-bp DNA region showed the presence of four complete and one partial open reading frame. Putative functions have been assigned to several gene products by sequence comparison with the proteins included in the databases. The third open reading frame (speC) encoded a 722-amino acid protein showing 70.9% identity to the M. morganii ODC previously characterized (SpeF). The speC gene has been expressed in Escherichia coli, resulting in ODC activity. The presence of a functional promoter (PspeC) located upstream of speC has been demonstrated. Quantitative real-time reverse transcription PCR assay was used to quantify expression of both M. morganii ODC-encoding genes, speC and speF, under different growth conditions. This assay allows us to identify SpeF as the inducible M. morganii ODC, since it was highly expressed in the presence of ornithine., This work was supported by grants AGL2005-00470 (Comisión Interministerial de Ciencia y Tecnología), FUN-C-FOOD Consolider 25506 (Ministerio de Educación), RM03-002 (Instituto Nacional de Investigación Agraria y Alimentaría), and S- 0505/AGR/000153 (Comunidad de Madrid). We thank the E. coli Genetic Stock Center for provide the E. coli HT414 (CGSC 6856) strain. The technical assistance of M. V. Santamaría is greatly appreciated. J.M. Landete is a recipient of a postdoctoral fellowship from the Ministerio de Educación.

SummaryThe switch from keeping laying hens in a floor or free range system into a cage system led to a considerable change in the way that breeding and selection took place. In the past 40–50 years up to the present date, the increase in genetic improvement of the egg laying trait was substantial. However, cage-adapted populations of laying hens seem to have lost some of their abilities to an adequate performance when returned to the old floor\free range systems. The strong concentration of all parts of the poultry production has meant that less than 10 international breeding companies supply most hens for laying purposes in the world and they have very little interest in developing genetic material for the West-European region where there are marked consumer preferences for eggs produced in non-cage systems. A particular Danish line, of White Leghorn origin named “The Skalborg hen” seems to have survived during an era of cage production system and they seems to have a production potential at farm level.

The genetic basis for plumage color of the Blue Andalusian breed was studied. Results of crosses between Blue Andalusian females and Brown (eb/eb) tester males showed that this genetic stock was E/E and did not carry a columbian-type gene. This fact was further verified by the cross between Blue Andalusian males and Melanotic Prat (eWh/eWhCo/Co Ml/Ml) females. It is suggested that the Bl/bl+ genotype is effective in changing black to blue pigment when only one eumelanizing gene is present in the genetic background, but it is ineffective in the presence of two different genes producing eumelanin simultaneously. With an E/E genotype, Bl/bl+ does not change black pigment to blue in the areas where the melanotic (Ml) or lacing (Lg) genes produce black pigment, resulting in the laced plumage pattern of the Blue Andalusian (E/E Bl/bl+Ml-Lg/Ml-Lg). On a non-E/E genetic background, a single dosage of Bl changes the black pigment to blue in the presence of the melanotic or lacing genes. Double-laced phenotypes were not found in either cross, thereby causing the authors toquestion the role of Co in double and single-laced patterns. Linkage between Ml and Lg was estimated to be 12.2% ± 2.1 (SE).