Diversity among landraces of Indian snapmelon (<Emphasis Type="Italic">Cucumis melo</Emphasis> var. <Emphasis Type="Italic">momordica</Emphasis>)

Diversity among 36 snapmelon landraces, collected from 2 agro-ecological regions of India (9 agro-climatic sub-regions), was assayed using RAPD primers, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance and biochemical composition (TSS, ascorbic acid, titrable acidity). Typical differences among accessions were observed in plant and fruit characteristics and snapmelon germplasm with high titrable acidity and possessing resistance to downy mildew, Cucumber mosaic virus, Zucchini yellow mosaic virus, Papaya ringspot virus, Aphis gossypii and Meloidogyne incognita was noticed in the collection. RAPD based grouping analysis revealed that Indian snapmelon was rich in genetic variation and region and sub-region approach should be followed across India for acquisition of additional melon landraces. Accessions of var. agrestis and var. momordica clustered together and there was a separate cluster of the accessions of var. reticulatus. Comparative analysis of the genetic variability among Indian snapmelons and an array of previously characterized reference accessions of melon from Spain, Israel, Korea, Japan, Maldives, Iraq, Pakistan and India using SSRs showed that Indian snapmelon germplasm contained a high degree of unique genetic variability which was needed to be preserved to broaden the genetic base of melon germplasm available with the scientific community. N. P. S. Dhillon and Ranjana contributed equally to this work and are considered the first authors.     

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.     

Handling missingness when modeling the force of infection from clustered seroprevalence data

Modeling infectious diseases data is a relatively young research area in which clustering and stratification are key features. It is not unlikely for these data to have missing values. If values are missing completely at random, the analysis on the complete cases is valid. However, in practice this assumption is usually not fulfilled. This article shows the effect of ignoring missing data in modeling the force of infection of the bovine herpesvirus-1 in Belgian cattle and proposes the use of weighted generalized estimating equations with constrained fractional polynomials as a flexible modeling tool.     

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.     

Molecular genetics of race non-specific rust resistance in wheat

Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat or introgressed into wheat from related species. A few of these genes from the ‘slow-rusting’ adult plant resistance (APR) class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes, particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications, and the eventual cloning of the encoding genes.     

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.     

Identification of QTLs for phenolic compounds in oilseed rape (<Emphasis Type="Italic">Brassica napus L.</Emphasis>) by association mapping using SSR markers

Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected, five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection.