Spatial patterns of diversity and genetic erosion of traditional cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz) in the Peruvian Amazon: An evaluation of socio-economic and environmental indicators

This study evaluates quantitatively the suitability of the use of site-specific socio-economic and environmental data as indicators to rapidly assess patterns of diversity and genetic erosion risk in cassava. Socio-economic data as well as farmers’ estimation of genetic erosion were collected in the study area, the Ucayali region of the Peruvian Amazon, through interviews with 285 cassava farmers in 50 communities, while diversity was assessed based on agromorphological characterization of 295 cassava accessions. Using multivariate regression analyses, 50 and 45% of the variation in respectively diversity and genetic erosion estimation could be explained by a selected set of socio-economic and environmental indicators. In both regression models four out of the total of 38 variables proved to contribute significantly (at p < 0.10 level). Additionally, the study revealed that farmers are a good direct source of information on the diversity present at community level, which can contribute to the development of methodologies to assess diversity more rapidly. The results of this study are valuable for the development of models to rapidly assess diversity dynamics in large areas.     

Genetic diversity of potato landraces from northwestern Argentina assessed with simple sequence repeats (SSRs)

Andean potato varieties are cultivated in the northwest of Argentina and constitute the most important staple food for the local farmers. The genetic diversity of 155 accessions conserved at the Genebank of Balcarce (INTA) was tested using four microsatellites. Three commercial potato varieties of Tuberosum group and one accession of Curtilobum group were used as outgroups. The presence of bands was scored for each microsatellite and for each accession and the data were analysed by principal coordinate analysis. The polymorphism information content was obtained for each molecular marker from banding patterns. Analysis of molecular variance was carried out with a variable number of accessions for each landrace, from different departments and sites within departments. More than one genotype was detected in the majority of the potato landraces. Some accessions within each landrace did not differentiate. AMOVA revealed that most of the genetic variation occurred among sites within departments and among local varieties. These findings are discussed considering the agricultural practices carried out in the Andean farming system.     

Composition and transformation of 1.4 nm minerals in cutan and matrix of alfisols in central China

Background, Aims, and Scope  Hydroxy interlayered vermiculite (HIV) and vermiculite are commonly referred to as 1.4 nm minerals. In the subtropical soils of central China, the concentration of vermiculites decreased while that of HIVs increased gradually from north to south as the intensity of soil formation or eluviation increases in the same direction. The cutans in these soils closely interact with air, roots, microbes, water and dissolved ions in soils. Cutans may therefore be expected to exert an important influence on the formation of 1.4 nm minerals relative to the matrix soils. However, little is known about the transformation of 1.4 nm minerals in Alfisols in central China. Here, we investigate the compositional differences of 1.4 nm minerals in cutans and matrix soils, and the probable transformation of vermiculite to HIV or vice versa when sodium citrate and sodium acetate are added to matrix Alfisols. Methods  Cutans and matrix soils were separated from three soils in the northern subtropical zone in China. The samples were analyzed for Fe, Mn, exchangeable cations, organic matter(O.M.), pH, and clay minerals. To 10 mL of matrix soil, suspensions containing about 250 mg (oven-dry weight) of clay was added with 5 mL of 0.4 mol/dm³ or 2 mol/dm³ of sodium citrate or sodium acetate solution and 5 mL of 0.2 mol/dm³ mixed solutions of CaCl₂, Mg(NO₃)₂ and KCl. After its pH was adjusted to 6.0, the mixture was ‘incubated’ for 120 or 210 days (more than one season or half a year) during which period it was shaken for 1 hour every day. The clay mineral composition of the samples was determined after incubation. Results  Both vermiculites and HIVs were present in matrix soils, but only vermiculties were detected in cutans. The addition of organic ligands (citrate and acetate) promoted the transformation of HIV to vermiculite. This transformation was obvious for the matrix soils that had been incubated with 0.5 mol/dm³ sodium citrate for 210 days while sodium acetate was less effective in this regard. The promoting effect of organic ligands is dependent on type and concentration as well as incubation time. This would suggest the reverse transformation occurred in the formation of cutans compared with a vermiculite-to-HIV transformation in the subtropical soils of central China from north to south. Discussion  The position and environment of cutans in the B horizon together with the pH, organic matter and exchangeable base status in cutans seem conducive to the co-existence of vermiculite and HIV in the soils, but only vermiculite is found in cutans. The transformation of HIV to vermiculite in incubation experiments could be divided into two steps: 1) Cheluviation of organic matter to the interlayer hydroxy-aluminums from HIVs. 2) Rebasification of hydrated cations into the interlayers of vermiculites. Conclusions  The clay minerals in cutans can interact with organic ligands and nutrient elements excreted by roots. Under conditions of frequent wetting and drying and high pH, and when the concentrations of exchangeable bases, iron-manganese oxides, clays, and organic matter are high, the exchangeable cations can be incorporated into the interlayers of HIV, thereby promoting the partial transformation of HIV to vermiculite in rhizosphere soils. Recommendations and Perspectives  Cutan is at the interface of material and energy exchange involved in physical, chemical and biochemical reactions in the rhizosphere. These factors strongly affect the compositions of cutans. HIVs in (upper or adjacent) matrix soils may transform to vermiculites during cutan formation in these special soil environments. ESS-Submission Editor: Jizheng (Jim) He (jzhe@rcees.ac.cn)     

Assessment of genetic relationships between <Emphasis Type="Italic">Rhus</Emphasis> L. species using RAPD markers

Genetic diversity of seven Rhus L. species was assessed using random amplified polymorphic DNA (RAPDs) markers. Initially, 90 primers were screened, of which 25 produced reproducible amplification products. These primers generated a total of 296 bands, with an average of 11.8 bands per primer. Out of 296 bands scored, 236 (80%) were polymorphic and 62 (20%) were monomorphic. Primers OPC-05 and OPD-05 generated 100% polymorphic bands. The resolving power of primers ranged from 9.4 to 26.8. Similarity matrix values ranged from 0.45 to 0.63. The dendrogram generated using Unweighted Pair Group Method using Arithmetic Averages (UPGMA) grouped all the species of Rhus in one major group with two sister groups, whilst R. pyroides Burch. and R. dentata Thunb. were outliers. R. gerrardii (Harv. ex Engl.) Diels, R. glauca Thunb. and R. pentheri Zahlbr. constituted one sister group, while R. natalensis Bernh. ex C. Krauss and R. gueinzii Sond. were included in the other. The degree of genetic diversity observed between seven species of Rhus with RAPD markers suggest that this approach could be used for studying the phylogeny of the genus.     

Application of high-temperature gas chromatography-mass spectrometry to the investigation of glycosidically bound components related to cashew apple (Anacardium occidentale L. Var. Nanum) volatiles

Free and bound volatile components of a Brazilian cashew apple variety (Anacardium occidentale L. var. nanum) were obtained by simultaneous distillation-extraction (SDE) and XAD-2 adsorption. According to gas chromatography-mass spectrometry (GC-MS) analyses and retention indices, 62 free volatile constituents were characterized and quantified. They were esters (40%), terpenes (20%), hydrocarbons (14%), fatty acids (9%), aldehydes (8%), alcohols (3%), lactones (3%), ketones (1%), phenols (1%), and norisoprenoids (1%). The glycosidically bound volatile precursors were analyzed by high-temperature GC-MS, after room temperature silylation. Several conjugated alcohols and cinnamic acids were detected and reported as cashew apple glycosyl constituents for the first time.     

Incorporating parameter uncertainty into prediction intervals for spatial data modeled via a parametric variogram

In spatial predictions, researchers usually treat the estimated theoretical variogram parameters as known without error and ignore the variability of the parameter estimators. Although the prediction is still unbiased, the prediction error is usually underestimated. Therefore, the coverage probability of the prediction interval usually is lower than the nominal probability. A simulation study is performed to show how the coverage probability for prediction relates to the true range and sill of an exponential variogram. This article proposes two parametric bootstrap methods to incorporate the variability of the corresponding parameter estimators. A simulation study is performed to evaluate the coverage probability of these proposed methods. Finally, we apply the parametric bootstrap methods to a real dataset and compare the results with those from naive (i.e., treating estimated parameters as known) and Bayesian methods.     

QTL mapping of sheath blight resistance in a deep-water rice cultivar

Sheath blight, caused by the pathogen Rhizoctonia solani Kühn, is one of the most serious diseases of rice and leads to severe yield loss worldwide. A recombinant inbred line (RIL) population consisting of 121 lines was constructed from a cross between HH1B and RSB03, the latter of which is a deep-water rice variety. Five traits were used to evaluate sheath blight resistance, namely disease rating (DR), lesion length (LL), lesion height (LH), relative lesion length [RLL, the ratio of LL to plant height (PH)], and relative LH (RLH, the ratio of LH to PH). Using the RIL population and 123 molecular markers, we identified 28 quantitative trait loci (QTLs) for the five traits in two environments. These QTLs are located on nine chromosomes and most of them are environment specific. A major QTL for DR (qSBR1) on chromosome 1 was identified with contributions of 12.7% at Shanghai and 42.6% at Hainan, and it collocated with a QTL for PH. The allele at this locus from RSB03 enhances sheath blight resistance and increases PH. Another QTL for DR on chromosome 7 was adjacent to QTLs for heading date (HD) and four other disease traits. RSB03 also carries the resistant allele at this locus and shortens HD. The susceptible parent, HH1B, provides the resistance allele at the locus qSBR8, where QTLs for four other disease traits were identified. QTL mapping results showed that most QTLs for LL, LH, RLL, and RLH are collocated with QTLs for DR. Three QTLs for DR are independent from HD, PH, and four other disease traits, while four QTLs are closely related to HD and PH. Four QTLs for LL, LH, RLL, and RLH are independent from DR, HD, and PH, while there is only one region harboring QTLs for these four traits and HD. Correlation analysis and QTL mapping results indicated that LL, LH, RLL, and RLH might be important indices, like DR, for evaluating the level of resistance to rice sheath blight.     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Development of simple PCR-based markers linked to the <Emphasis Type="Italic">Ms</Emphasis> locus,a restorer-of-fertility gene in onion (<Emphasis Type="Italic">Allium cepa</Emphasis> L.)

In order to implement reliable marker-assisted selection systems for the restorer-of-fertility locus (Ms) in onions (Allium cepa L.), simple PCR-based codominant markers linked to the Ms locus were developed. Based on the EST probe sequences of previously reported RFLP markers, full-length genomic sequences of the gene encoding putative oligopeptide transporter (OPT) was obtained by RACE. The first intron contained two 108 and 439-bp indel polymorphisms between the two Ms allele-linked OPT alleles. A simple PCR marker for OPT was developed by designing a primer pair on the flanking regions of the 108-bp indel which is created by two tandem repeats. The second simple PCR marker was developed from the EST probe encoding photosystem I subunit O (PsaO). Two 14 and 39-bp tandem repeats were identified from the 5′ upstream sequences of the PsaO-coding gene, which were isolated by genome walking. Three different compositions of these tandem repeats were identified from diverse onion germplasm. A primer set binding to the flanking sequence of these polymorphic repeats was used to amplify three different marker haplotypes. The OPT marker was tightly linked to the Ms locus at a distance of 1.5 cM, but the analysis of the linkage relationship showed little linkage disequilibrium between the marker and the Ms locus. Even so, these simple PCR markers are valuable tools for the marker-assisted selection of segregating individuals in onion F₁ hybrid breeding programs.     

Rust-proofing wheat for a changing climate

This paper offers projections of potential effects of climate change on rusts of wheat and how we should factor in a changing climate when planning for the future management of these diseases. Even though the rusts of wheat have been extensively studied internationally, there is a paucity of information on the likely effects of a changing climate on the rusts and their influence on wheat production. Due to the lack of published empirical research we relied on the few published studies of other plant diseases, our own unpublished work and relevant information from the vast literature on rusts of wheat to prepare this overview. Three broad areas of potential risks from a changing climate were described: increased loss from wheat rusts, new rust pathotypes evolving faster and the reduced effectiveness of rust resistances. Increased biomass of wheat crops grown in the presence of elevated CO₂ concentrations and higher temperatures will increase the leaf area available for attack by the pathogen leading to increased inoculum production. If changed weather conditions were to accelerate the life cycle of a pathogen, the increased inoculum can lead to severe rust epidemics in many environments. Likewise should the effects of climate change result in more conducive conditions for rust development there will also be a corresponding increase in the rate of evolution of new pathotypes which could increase the rate of appearance of new virulences. The effectiveness of some rust resistance genes is influenced by temperature and crop development stage. Climate change may directly or indirectly influence the effectiveness of some resistance genes but this can not be ascertained due to a complete lack of knowledge. Since disease resistance breeding is a long term strategy it is important to determine if any of the important genes may become less effective due to climate change. Studies must be made to acquire new information on the rust disease triangle to increase the adaptive capacity of wheat under climate change. Leadership within the Borlaug Global Rust Initiative (BGRI) is needed to broker research on rust evolution and the durability of resistance under climate change.