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1.
Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications 总被引：1，自引：0，他引：1
Michael J. Thomson Namrata Singh Maria S. Dwiyanti Diane R. Wang Mark H. Wright Francisco Agosto Perez Genevieve DeClerck Joong Hyoun Chin Geraldine A. Malitic-Layaoen Venice Margarette Juanillas Christine J. Dilla-Ermita Ramil Mauleon Tobias Kretzschmar Susan R. McCouch 《Rice》2017,10(1):40
Background
Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.Results
Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.Conclusions
The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.2.
Stphanie Fontagn Laurent Burtaire Genevive Corraze Pierre Bergot 《Aquaculture (Amsterdam, Netherlands)》2000,190(3-4):289-303
The present study investigated the interaction of dietary medium-chain fatty acids (MCFA) and phospholipids (PL) on survival, growth and lipid metabolism in common carp larvae. Nine diets based on casein and dextrin and with a variable lipid part were tested in triplicate for 22 days post first feeding. The 3×3 design consisted of three triacylglycerols (3% of diet) combined with three different lipid supplements. Tested triacylglycerols were triolein (TOL), tricaprylin (TC8) and tricaproin (TC6), and lipid supplements were 2% soybean oil (low-fat diets without PL), 2% soybean lecithin (low-fat diets with 2% PL) or both 2% soybean lecithin and 6% TOL (high-fat diets with 2% PL).
In the first step, both TC6 and TC8 resulted in improved survival and growth rates compared to TOL, irrespective of the PL supply. In the second step, TC8 decreased survival and growth rates, whereas the difference between TC6 and TOL became less. Histological signs of impaired intestinal absorption of neutral lipids were evidenced in larvae fed TOL without PL and also in high-fat diets with 2% PL. The latter diets also resulted in poorer growth rates compared to low-fat diets with 2% PL. These results suggest that the quantitative PL requirement of larvae increases as the dietary level of long-chain triacylglycerols increases. Larvae fed TC6 or TC8 showed enlarged liver and hepatocyte volume and a decreased level of body neutral lipids. Based on β-hydroxybutyrate (β-HBA) measurements in whole larvae, TC8 was found to be more ketogenic than TC6. TC6 and TC8 affected differently the fatty acid profile of larval body neutral lipids. TC6 did not induce the appearance of MCFA, whereas TC8 feeding resulted in a low level of 8:0 and relatively high levels of 10:0 (3.8% of total fatty acids). Neither 8:0 nor 10:0 were found in larval polar lipids.
This study confirmed the essentiality of PL in common carp larval diets and underlines differences in the utilization of TC6 and TC8, which both initially stimulate growth during the first week, but only temporarily in the case of TC8. 相似文献
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Choi KS Nah JJ Choi CU Ko YJ Sohn HJ Libeau G Kang SY Joo YS 《Veterinary microbiology》2003,96(1):1-16
An experimental competitive enzyme-linked immunosorbent assay (morbillivirus cELISA) using a recombinant N antigen (rRPV N) expressed in a baculovirus and a ruminant morbillivirus (RPV and PPRV)-specific monoclonal antibody (P-13A9) was developed for simultaneous detection of rinderpest virus (RPV) and peste des petits ruminants virus (PPRV) antibodies and its diagnostic performance was evaluated. A set of known reference antisera against RPV and PPRV belonging to different lineages, experimental sera from cattle vaccinated for a RPV of Asian lineage, and field sera from cattle and sheep/goat populations known to be positive (West Africa) and negative (Korea) for RPV and PPRV were used for the evaluation. Morbillivirus cELISA results on the panel of experimental RPV and PPRV antisera showed high correlation (r=0.97) between the whole virus and the rRPV N antigens, suggesting that the rRPV N contains a ruminant morbillivirus-specific antigenic determinant recognized by the P-13A9 and it may be suitable as an ELISA antigen in place of the whole virus. Morbillivirus cELISA detected anti-RPV and anti-PPRV antibodies in all reference RPV and PPRV antisera containing VN titers >/=1:8, suggesting that the assay can simultaneously detect antibodies against RPV and PPRV. Anti-RPV antibody was detected by morbillivirus cELISA in vaccinated cattle as early as the VNT and continued to be detectable by both the cELISA and the VNT until termination of the study. When applied to field samples from Africa, morbillivirus cELISA showed good agreement with a RP cELISA kit (kappa value of 0.86) in bovine sera and with a peste des petits ruminant cELISA kit (kappa value of 0.81) in caprine/ovine sera. Usefulness of morbillivirus cELISA using the rRPV N protein was discussed. 相似文献
4.
Dietary lipid level affects fatty acid composition and hydrolase activities of intestinal brush border membrane in seabass 总被引：2，自引：0，他引：2
C.L. Cahu J.L. Zambonino Infante G. Corraze D. Coves 《Fish physiology and biochemistry》2000,23(2):165-172
Triplicate groups of juvenile seabass (initial weight of 241 g) were fed during 13 weeks three isonitrogenous experimental diets containing different lipid levels, 12% (LL group), 21% (ML group) and 30% (HL group). At the end of the experiment, fish weight gain was similar among the 3 dietary groups. Intestinal brush border membranes were purified for each dietary group; one part of the brush border fraction was dedicated to enzyme assays, the remaining fraction being used for lipid extraction followed by fatty acid analysis. The fatty acid composition of the brush border membrane differed among the 3 groups, although the 3 experimental diets had the same fatty acid composition. The increase in dietary lipid level resulted in a lowering in (n-3) polyunsaturated fatty acid (PUFA) paralleled with an increase in monounsaturated fatty acid. A significant reduction in the brush border enzyme activities, namely alkaline phosphatase, aminopeptidase N, -glutamyl transpeptidase and maltase, was also observed with the elevation of the dietary lipid level. The change in activity of intestinal digestive enzymes, which are membrane-bound proteins, could be attributed to the modification of fatty acid composition and fluidity of the brush border membranes (BBM). Such lowering in PUFA and increase in monounsaturated fatty acid in BBM, concomitant with a decline in membrane enzymatic activity, has been described as a malnutrition indicator in mammals. It raises the question of possible disorders of gut functions in fish fed increasing lipid levels. 相似文献
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The distribution of seabirds west of Scotland was studied relative to water masses in August 1988. Surface salinity was used to indicate the ship's position relative to the water masses described in the literature. Comparisons were made between seabird densities in Inshore Water, the Northern Coastal Current, the Southern Coastal Current and Atlantic/Hebridean Water. Seabird density varied with water mass; some species distributions suggested strong habitat associations. Water masses represent marine habitats, with different physical regimes supporting different marine life; patterns in bird distribution are likely to reflect prey distribution and availability. Manx shearwaters Puffinus puffinus, razorbills Alca torda, guillemots Uria aalge, and kittiwakes Rissa tridactyla were found mostly in Inshore Water, with lower densities in the Northern and Southern Coastal Current water. Only trace numbers of these species occurred in Atlantic/Hebridean Water. Storm petrels Hydrobates pelagicus, fulmars Fulmarus glacialis and puffins Fratercula arctica were found in very low densities in Inshore Water, and were dispersed in higher densities throughout the more oceanic areas. These data suggest that in late summer the Inshore Water of southwestern Scotland has the highest densities of seabirds potentially vulnerable in the event of an oil incident. 相似文献
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Genevieve Patrick Andrea M. Tarnecki Nicole Rhody Ryan Schloesser Kevan Main Roy Yanong Ruth Francis‐Floyd 《Aquaculture Research》2019,50(12):3793-3801
Almaco jack (Seriola rivoliana Valenciennes) is an excellent candidate for aquaculture due to its fast growth rate and high market value. While S. rivoliana have adapted well to captivity, survival at early life stages can be improved to increase profitability during production. A wide range of variables cause larval mortalities but high bacterial loads in rearing tanks are often correlated with these losses. The aim of this study was to investigate the effect of egg disinfection on bacterial load and hatch rate of S. rivoliana. Disinfectants tested included formalin (F100 and F200; 100 and 200 mg/L, respectively, for 60 min), hydrogen peroxide (HPO; 300 mg/L for 10 min) and peracetic acid/hydrogen peroxide (PAA/HPO; 15.7 mg/L/39.6 mg/L for 1 min). Concentrations and contact times were determined based on current use in marine aquaculture and preliminary trials. Eggs treated with HPO and F100 had significantly higher hatch rates than the untreated control group. All treatments significantly decreased total Vibrio counts compared to untreated eggs; however, total bacterial counts were only decreased following treatments with PAA/HPO and F200. To prevent egg mortality due to bacterial overgrowth, consideration should be given to the use of surface disinfection using HPO or F100. Future studies should investigate the use of peracetic‐based products at lower doses. 相似文献
10.
Carolina Castro Amalia Peréz-Jiménez Filipe Coutinho Geneviève Corraze Stéphane Panserat Helena Peres Aires Oliva Teles Paula Enes 《Fish physiology and biochemistry》2018,44(3):911-918
The aim of the present study was to assess the impact of an acute handling stress on hepatic oxidative status of European sea bass (Dicentrarchus labrax) juveniles fed diets differing in lipid so urce and carbohydrate content. For that purpose, four diets were formulated with fish oil (FO) and vegetable oils (VO) as lipid source and with 20 or 0% gelatinized starch as carbohydrate source. Triplicate groups of fish with 74 g were fed each diet during 13 weeks and then subjected to an acute handling stress. Stress exposure decreased hematocrit (Ht) and hemoglobin (Hb) levels. Independent of dietary treatment, stress exposure increased hepatic lipid peroxidation (LPO). Stressed fish exhibited lower glucose 6-phosphate dehydrogenase (G6PD), catalase (CAT), and superoxide dismutase (SOD) activities, independent of previous nutritional history. In the VO groups, stress exposure increased glutathione peroxidase (GPX) activity. Diet composition had no effect on Ht and Hb levels. In contrast, dietary carbohydrate decreased hepatic LPO and CAT activity and increased glutathione reductase (GR) and G6PD activities. Dietary lipids had no effect on LPO. Fish fed the VO diets exhibited higher G6PD activity than fish fed the FO diets. In conclusion, dietary carbohydrates contributed to the reduction of oxidative stress in fish. However, under the imposed handling stress conditions, liver enzymatic antioxidant mechanisms were not enhanced, which may explain the overall increased oxidative stress. 相似文献