Genetic studies on saline and sodic tolerances in soybean

Salt-affected soils are generally classified into two main categories: saline and sodic (alkaline). Developing and using soybean (Glycine max (L.) Merr) cultivars with high salt tolerance is an effective way of maintaining sustainable production in areas where soybean growth is threatened by salt stress. Early classical genetics studies revealed that saline tolerance was conditioned by a single dominant gene. Recently, a series of studies consistently revealed a major quantitative trait locus (QTL) for saline tolerance located on linkage group N (chromosome 3) around the SSR markers Satt255 and Sat_091; other minor QTLs were also reported. In the case of sodic tolerance, most studies focused on iron deficiency caused by a high soil pH, and several QTLs associated with iron deficiency were identified. A wild soybean (Glycine soja Sieb. & Zucc.) accession with high sodic tolerance was recently identified, and a significant QTL for sodic tolerance was detected on linkage group D2 (chromosome 17). These studies demonstrated that saline and sodic tolerances were controlled by different genes in soybean. DNA markers closely associated with these QTLs can be used for marker-assisted selection to pyramid tolerance genes in soybean for both saline and sodic stresses.     

Detection of stapylococcal enterotoxin,methicillin-resistant and Panton–Valentine leukocidin genes in coagulase-negative staphylococci isolated from cows and ewes with subclinical mastitis

Coagulase-negative staphylococci (CNS) are the most prevalent mastitis pathogens. However, virulence characteristics of CNS have not been well determined. The presence of genes for enterotoxins (sea-sej), toxic shock syndrome toxin-1 (tst), the exfoliative toxins (eta, etb), Panton–Valentine leukocidin (pvl) and mecA of CNS species isolated from cows and ewes with subclinical mastitis was investigated in this study. A total of 121 CNS (81 cows, 40 ewes) representing 18 different Staphylococci species were examined by PCR, and 38.1% (33 cows and 13 ewes) of CNS isolates had one or more se genes. The difference between percentages for SE toxin genes of CNS strains isolated from cows (40.7%) and ewes (32.5%) was not statistically significant (P > 0.05; χ ² = 0.380). It was found that S. simulans isolates had the highest prevalent se genes. Furthermore, the most common SE gene types was seh-sej. In this study, none of the isolates harbored the toxic shock syndrome toxin gene (tsst) and the exfoliative toxin genes (eta, etb). Five cow (6.17%) and three ewe CNS (7.5%) isolates had mecA gene. Three cow (3.7%) and two ewe CNS (5.0%) isolates had pvl gene. In conclusion, the present study showed that CNS species isolated from cows and ewes could serve as potential reservoir of se, mecA, and pvl genes.     

Study of the genetic variability of porcine circovirus type 2 detected in Serbia and Slovenia

Recent variants of porcine circovirus type 2 (PCV2) were obtained from tissues of domestic pigs with porcine circovirus associated disease and from randomly selected wild boar samples from Serbia and Slovenia. A 450-base-pair nucleotide sequence was obtained by PCR from the ORF2. The derived nucleotide and amino acid sequences were aligned and compared to the corresponding region of closely related PCV2 sequences determined in previous years and retrieved from the GenBank. The 30 Serbian and 17 Slovenian PCV2 sequences clustered into three previously determined genotypes (PCV2a: 7), (PCV2b: 38) and (PCV2d: 2). Three major variable regions, concerning 29 amino acid position substitutions within the ORF2, were observed, which further supports the segregation of the detected strains into three separate genotypes. This study indicates that PCV2b is the predominant genotype in Serbia and Slovenia and the detected PCV2 strains are closely related to those previously described in Europe and in other parts of the world.     

Growth and wood basic density of acacia hybrid clones at three locations in Vietnam

Field trials testing a total of 27 clones of the interspecific hybrid Acacia mangium × A. auriculiformis and seedling controls of the parental species were established at Ba Vi and Yen Thanh in the north of Vietnam and Long Thanh in the south. At both Ba Vi and Yen Thanh there were significant (P < 0.001) differences in height and diameter at breast height (DBH) among 22 tested clones at 4 years. At Long Thanh, twelve hybrid clones did not differ significantly in DBH at age 3 years, but did (P < 0.001) at age 5 years. At the two northern sites the acacia hybrid clones had significantly greater DBH than control seedlots of the parental species. At Long Thanh, DBH of the hybrid clones and A. mangium was similar, with a genetically improved seedlot of A. mangium displaying the best DBH. Mean wood basic density at breast height of the acacia hybrid clones was 539 kg m⁻³ at Yen Thanh at age 8 years, and 473 kg m⁻³ at Long Thanh at age 5 years; density for A. mangium at Long Thanh was only slightly lower than the hybrid clones at 461 kg m⁻³. Linear regressions of Pilodyn penetration (PP) at breast height on wood basic density explained 60% of the variance in density of treatments (clones and control seedlots) at Yen Thanh and 36% at Long Thanh. There were significant differences between hybrid clones in PP at all three trial sites. Clonal DBH performance was not strongly correlated across the three trial sites; Pearson correlations of clone mean DBH between pairs of sites ranged from −0.47 to 0.20. Clonal rankings for PP were more stable, with Pearson correlations between pairs of sites ranging from r = 0.71 to 0.78.     

Armillaria ostoyae associated with dying 60‐year‐old Scots pines in northern Turkey

We investigated an Armillaria root disease centre in a 60‐year‐old, naturally regenerated Pinus sylvestris stand located at 1250 m altitude in Sinop province in northern Turkey. Based on sequence analysis of the internal transcribed spacer region of the rDNA, the mycelial fans sampled from the infected trees were Armillaria ostoyae. Multilocus genotyping indicated that the fans belonged to a single genet, at least 0.2 ha in size. Drought as a predisposing factor is discussed. The study area received 50–70 and 25–50% of the normal precipitation in May, June and August in 2009 and in August and September in 2010, respectively. Moreover, earlier excavation work to prepare a forest road had probably disrupted the water table in the affected stand.     

Development of EST‐SSR markers for diversity and breeding studies in opium poppy

All publicly available opium poppy expressed sequence tag (EST) sequences, totalling 20 885, were assembled into unigenes and examined for simple sequence repeats (SSRs). Nearly 19% of the 14 957 unigenes contained SSRs with 4% harbouring more than one SSR. Average density of the SSRs was 1 SSR per 3.6 kb of non‐redundant EST sequence. Trinucleotide SSRs were most frequently identified (39%), and many of the most prevalent motifs were AT‐rich. Flanking primers were designed for 86% of the SSRs and 67 primer pairs were tested on 37 opium poppy accessions and seven related species. All markers were transferable to the related species. Polymorphism information content (PIC) values for the markers were intermediate for comparisons within opium poppy (average of 0.27) and slightly higher for comparisons across species (average of 0.29). The markers were found to be useful for diversity analysis as they successfully distinguished among Turkish opium poppy accessions and land races.     

Potential of indigenous Bacillus spp. as probiotic feed supplements in an extruded low‐fish‐meal diet for juvenile olive flounder,Paralichthys olivaceus

A 12‐week feeding trial was designed to assess the probiotic potential of indigenous Bacillus amyloliquefaciens and/or Bacillus subtilis singly or in combination with Bacillus licheniformis in an extruded feed for olive flounder (Paralichthys olivaceus) juveniles. A high fish meal (FM) diet (control) and a low‐FM diet containing an alternative protein blend (30% FM replacement, FM30) were formulated. Three other experimental diets were prepared by inclusion of B. amyloliquefaciens (BA), B. subtilis (BS), or a mixture of B. amyloliquefaciens, B. subtilis, and B. licheniformis (BASL) into FM30 diet, with a final concentration of 10⁶ CFU/g diet. Results indicated that the FM30 diet was well tolerated by flounder, and the overall performance was not affected by dietary treatments. Lysozyme activity and total immunoglobulin level were significantly reduced in flounders when fed with the FM30 diet compared with the BASL and BA diets, respectively. The Bacillus additives neither enriched the relative abundance of the corresponding Bacillus spp. in the relevant gut microbiota of olive flounder nor modulated the presumptive gene functions of the gut microbiome. Despite the absence of growth‐promoting effect, the tested probiotics could still be economically viable for use as immunostimulants in commercial flounder diets with partial FM replacement.     

Preliminary assessment of large‐scale co‐culture of sandfish (Holothuria scabra) with the Babylon snail (Babylonia areolata) in earthen ponds and in raceways

Holothuria scabra (sandfish) and Babylonia areolata were trialed in two large‐scale co‐culture experiments. Experiment 1 assessed co‐culture in 4 × 400 m² earthen ponds where Babylonia were cultured in a central pen at a density of 400 individuals/m² with sandfish occupying the remaining pond space at 1.1 individuals/m². Sandfish grew from 18.20 ± 6.67 g to 119.03 ± 17.74 g in 92 days and Babylonia (fed trash fish in both experiments) grew from 0.90 ± 0.38 g to 4.93 ± 1.44 g, but Babylonia growth was not increased in co‐culture compared to monoculture. Water and sediment quality varied between co‐culture and monoculture ponds. Neither showed clear improvement due to sandfish culture. Experiment 2 compared non‐segregated sandfish‐Babylonia co‐culture with Babylonia monoculture in 20 m² concrete raceways. Sandfish were cultured at 2 individuals/m² and Babylonia at 300 individuals/m². Sandfish grew up to 1.91 g.day^?1 with 100% survival. Babylonia weight gain was significantly greater in co‐culture raceways (3.35 ± 0.64 g over 61 days), which was double that of Babylonia in monoculture. Substrate total N was reduced by 20% in co‐culture compared with monoculture (p = .032). This provisional study of commercial scale sandfish‐Babylonia co‐culture demonstrates culture compatibility, providing a basis for further system development.     

Growth performance,carcass quality characteristics and colonic microbiota profiles in finishing pigs fed diets with different inclusion levels of rice distillers’ by‐product

The aim of this study was to evaluate the effects of diets containing rice distillers’ by‐product (RDP) on growth performance, carcass characteristics, meat quality, and gut microbiota of fattening pigs. Twenty‐four crossbred finishing pigs (Duroc × Landrace × Yorkshire), 56.9 ± 3.1 kg initial body weight, were randomly allocated to three groups. For 56 days, pigs were fed one of three diets including RDP0 (control), RDP15 (15% RDP in DM), and RDP30 (30% RDP in DM). With RDP level in diet, average daily gain and backfat thickness linearly increased (p < 0.05), and drip loss tended to increase (p ≤ 0.08). In addition, 16S ribosomal RNA gene amplicon profiling showed that RDP was associated with modulation of colonic microbiota composition, especially at family and genus levels. Relative abundance of Porphyromonadaceae and Erysipelotrichaceae families in colonic digesta increased with inclusion of RDP, while that of Enterobacteriaceae decreased. The proportion of genera unclassified Erysipelotrichaceae, and Butyrivibrio increased as inclusion of RDP. These results indicate that up to 30% inclusion in diet of finishing pigs, RDP can modulate colonic microbiota composition, and induces an improvement of animal growth and fat deposition.     

Developing socioeconomic indicators for an ecosystem-based fisheries management approach: An application to the Korean large purse seine fishery

Developing socioeconomic indicators for ecosystem-based fisheries management is particularly important. This is because socioeconomic factors have direct effects on ecosystems, and ecosystems have direct effects on socioeconomic factors. Therefore, it is imperative that socioeconomic indicators are developed and evaluated in order to predict changes in ecosystems and to provide advice for effective fisheries management. In this study, socioeconomic indicators have been developed to be combined with biological and ecological indicators, in order to conduct the ecosystem-based fisheries assessment. In terms of socioeconomic indicators, five socioeconomic criteria were considered as important attributes of socioeconomic changes. These were economic production, business conditions, levels of income, the state of the market, and levels of employment. In order to establish reference points for the evaluation of indicators, target reference points and limit reference points were set through a comparison with other industries or other fisheries rather than by using the Traffic Light System (TLS) method, which has been used in many previous studies. In addition, on the basis of the application of developed indicators and reference points to the Korean large purse seine fishery, the socioeconomic conditions of the fishery and the usefulness of the indicators were evaluated and management implications were discussed.