Genetic analysis and phenotypic associations for drought tolerance in Hordeum spontaneum introgression lines using SSR and SNP markers

Associations between markers and drought related traits were investigated on a set of 57 advanced barley breeding lines, carrying various levels of introgression from Hordeum spontaneum lines 41-1 and 41-5, the best sources of drought tolerance in the ICARDA barley breeding program, using 74 simple sequences repeats (SSR) and 20 single nucleotide polymorphism markers. The 57 lines were evaluated for grain yield and drought related traits for three years (2003/04, 2004/05, 2005/06) in nine Mediterranean low rainfall environments. A high level of polymorphism was found with SSR markers, and the mean polymorphism information content and gene diversity values were 0.67 and 0.71, respectively. The number of alleles per locus varied from 2 to 11, with an average of 5.8 alleles per marker. Considering all the 57 lines, the linkage disequilibrium (LD) analysis was significant at a comparison-wise P?<?0.01 level in nearly 9 % of the SSR marker pairs used and a decay of LD was observed to a value of r ²?<?0.2 at a genetic distance of 40?cM. The association analysis revealed a total of 147 significant marker?Ctrait associations for grain yield and drought related traits. A total of 72 (49 %) marker?Ctrait associations showed favorable effects of the exotic germplasm where the H. spontaneum lines contributed to an improvement of the trait under drought stress conditions. The number of significant marker?Ctrait associations per trait were: 12 for growth habit; 2 for growth vigor; 11 for peduncle extrusion; 5 for number of grains per spike; 20 for peduncle length; 16 for days to heading; 20 for plant height; 8 for spike length; 17 for thousand kernel weight; 30 for grain yield; 4 for harvest index and 2 for biological yield. The phenotypic variation explained by individual marker?Ctrait associations ranged from 7.6 % to 36.2 %. The identification of genomic regions associated with grain yield and drought related traits is useful for the genetic improvement of cultivars better adapted to drought stress environments. Thus, the present study is encouraging in identifying significant marker?Ctrait associations through LD based association mapping analysis, which could complement and augment previous quantitative trait loci information for the potential use of Marker Assisted Selection for drought.     

Independent target region amplification polymorphism and single‐nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes

The independent target region amplification polymorphism (TRAP) and single‐nucleotide polymorphism (SNP) marker s were used for genetic evaluation of different selected 47 sugarcane genotypes. A total of 23 pairs of TRAP markers generated 925 alleles, of which 74% alleles were polymorphic. Polymorphism was generally high (>50%), ranging from 54 to 98%. The polymorphism information content (PIC) values 0.20 varied among the primer combination ranging from 0.17 in SAI + Arbi 2 to 0.31 in GL 2+ Arbi 1 with an average of 0.24. However, the Pearson correlation between PIC and power of discrimination (PD) was found to be less significant. Single‐nucleotide polymorphisms were used first time for the assessment of genetic diversity among different species of Saccharum and cultivated sugarcane varieties. The SNPs were detected from 454 sequencing. A total of 245 SNP markers were assayed across the 47 genotypes, and 167 SNPs were found to be polymorphic. The PIC values ranged from 0.04 to 0.38 with an average of 0.21, and their respective PD varied from 0.58 to 0.04 with an average value of 0.31. The obtained results relatively significant were compared with the other marker systems through genetic similarity and the clusters formed in different unweighted pair group method with arithmetic mean clustering dendrogram. The clustering analysis established genetic relationship in the order of Erianthus > Sclerostachya > Narenga > Saccharum spontaneum > S. robustum > S. barberi > S. officinarum/cultivars. These results ratify TRAP and SNP marker systems for assessing genetic diversity studies, and more diversified Erianthus spp. can contribute substantially towards sugarcane varietal improvement through breeding with Saccharum spp. or hybrid cultivars.     

MAGNETIC RESONANCE IMAGING OF THE CANINE ABDOMEN: EFFECT OF PULSE SEQUENCE ON DIAGNOSTIC QUALITY

Motion artifact is an important limiting factor for abdominal magnetic resonance imaging (MRI) in veterinary patients. The purpose of this study was to determine the effects of pulse sequence on abdominal MRI diagnostic quality in dogs. Ten normal dogs were each scanned using 16 MRI pulse sequences. Sequences included breath‐holding sequences, respiratory navigation sequences, and traditional spin‐echo sequences. Four observers independently scored diagnostic quality for each sequence based on the appearance of specific organs, overall diagnostic quality, and degree of artifactual interference. Signal‐to‐noise ratio and contrast‐to‐noise ratio were also calculated for each sequence. The sequence with the highest overall mean diagnostic quality score was the dorsal T2 turbo spin echo (TSE) with fat saturation and breath‐holding. The sequence with the lowest mean diagnostic quality score was the dorsal T2 fast spin echo. The sequence with the highest signal‐to‐noise ratio for all evaluated organs was the sagittal T1 spin echo. Signal‐to‐noise and contrast‐to‐noise ratios did not correlate with subjective assessment of overall diagnostic quality for the majority of the sequences evaluated (P < 0.05). The three sequences considered to have the highest diagnostic quality for the cranial abdomen were the dorsal T2 TSE with fat saturation and breath‐hold, transverse T1 turbo fast low‐angle shot gradient echo with breath‐hold, and dorsal T2 half‐Fourier acquisition single shot TSE with respiratory navigation. These sequences had short acquisition times, yielded studies of similar diagnostic quality, provided complementary information, and are therefore recommended for routine canine abdominal MRI protocols.     

Long-Term Cropping System, Tillage, and Poultry Litter Application Affect the Chemical Properties of an Alabama Ultisol

Sustainable agricultural practices have been steadily increasing in the last couple of decades. These management practices frequently involve cover crops, less or no-tillage, and organic fertilization. In this study, we evaluated the effects of cropping systems,tillage and no-tillage, and the application of poultry litter(PL) on selected soil physicochemical properties and soil test nutrients. Soil samples were collected from the topmost surface(0–5 cm) and subsurface(5–10 cm) layers. The general effect trend was PL application no-tillage cover crop cropping type. There were more statistically significant(P ≤ 0.05) correlations between the 18 soil attributes at the topmost surface than at the subsurface. This could be due to the accumulation of external C inputs and nutrients by crop residues and PL application as well as the retaining effects of no-tillage on less mobile nutrient components. Because of their high mobility and volatile nature, total nitrogen(N), ammonia-N(NH_4~+-N), and nitrate-N(NO_3~--N) levels varied greatly(high standard deviations), showing no consistent patterns among the treatments. Compared to the soybean cropping system, corn, especially with the wheat cover crop, contributed more to the total carbon(C) and sulfur(S) in the topmost surface soils(0–5 cm). Poultry litter application greatly increased pH, cation exchange capacity(CEC), base saturation, magnesium(Mg), phosphorus(P), calcium(Ca),sodium(Na), potassium(K), manganese(Mn), copper(Cu), and zinc(Zn) in both soil layers. Contrast comparisons revealed that PL application had more of an effect on these soil chemical properties than no-tillage and cropping systems. These results will shed light on developing better nutrient management practices while reducing their runoff potentials.     

Genetic diversity of ICARDA’s worldwide barley landrace collection

Twenty genic- and genomic SSR markers were used to study genetic diversity and geographical differentiation of barley from 29 countries through analysis of a worldwide collection of 304 ICARDA’s barley landraces. Of these, 19 loci were highly polymorphic in the material studied. Based on Nei-distance matrix, Principal Component Analysis (PCoA) and cluster analysis using UPGMA associated with AMOVA the data revealed countries’ grouping within regions. Three distinct germplasm pools were identified in the landraces. The first of these was from Eastern Africa (Eritrea and Ethiopia) and South America (Ecuador, Peru and Chile) suggesting that barley introduced to South America might have originated specifically from East Africa or that they share a common genetic basis for adaptation. The second was the Caucasus (Armenia and Georgia) and the third included the remaining regions of Central Asia, Near East, Northern Africa and Eastern Asia. Genetic diversity of barley subspecies (Six-rowed barley, Two-rowed barley, H. spontaneum C. Koch and H. agriocrithon Åberg) also discriminates them into three groups: cultivated barleys (Six-rowed barley and Two-rowed barley), wild barley H. spontaneum and subspecies H. agriocrithon. These results associated with parsimony analysis demonstrate that H. agriocrithon and H. spontaneum might be distinct and do not support a hybrid origin for H. agriocrithon suggesting further investigation of the basis of more intense sampling of the two subspecies H. spontaneum and H. agriocrithon.     

Otolith elemental characteristics of whitefish (Coregonus lavaretus) from brackish waters of the Gulf of Bothnia,Baltic Sea

To investigate whether European whitefish (Coregonus lavaretus) groups in the brackish (≤7%) Gulf of Bothnia (Baltic Sea) express specific otolith elemental characteristics, concentrations of elements (Ca, Ba, Sr, Zn, Mn, Fe) in whole otoliths were studied by inductively coupled plasma‐optical emission spectrometry. Whitefish (N = 67) were sampled from six different latitudinal sites; four in the sea and two in rivers along the west coast of Finland, and from a fresh water lake for comparison. The concentration of several elements showed significant differences among sampling sites. Otolith Ba concentrations were higher at the northern sampling sites compared to the southern ones, thereby showing negative association to capture‐habitat salinity. In contrast, otolith Sr and Zn concentrations were lower at the northern sampling sites, thereby associating positively to capture‐habitat salinity. Otolith Mn concentrations did not associate with latitude or salinity but markedly varied between sampling sites. Elevated Fe concentrations occurred in fish otoliths from the two northernmost sites. Ca concentrations were at the same levels in otoliths from all whitefish samples. Otoliths of whitefish from the lake had very high Ba and low Sr concentrations compared to concentrations in otoliths from whitefish in the sea and rivers. Our results show that otolith elemental characteristics of whitefish vary considerably at various geographic scales showing high potential for population identification using elemental fingerprints. Analysis of otolith elemental characteristics may therefore provide an efficient tool for the identification of main areas of residence, spawning locations, and migration routes, thus contributing towards the sustainable management of whitefish stocks.     

Cold temperature/Biodur®/S10/von Hagens'—Silicone plastination technique

Plastination is a late 20th century preservation methodology which replaces tissue fluid within a specimen with a curable polymer, such as silicone. Plastination yields superb, beautiful, well‐preserved specimens each with their own unique qualities. Silicone polymer is used around the world to preserve macroscopic cadavers or portions/organs thereof. Plastination was conceived by Dr. Gunther von Hagens, Universität Heidelberg, Heidelberg, Germany prior to 1977. Silicone polymer was the primary polymer which emerged initially for plastination. The Biodur^® line of silicone polymer and additives was chosen and manufactured because it has consistently produced the best plastinates since the inception of plastination. Since the discovery of silicone, generic and similar silicone polymers are known and used around the World by many industries and used in numerous products. The plastination process has four steps: Specimen preparation, Specimen dehydration and degreasing, Vacuum‐forced impregnation of specimens and Specimen hardening.