The effect of nickel on the growth, photosynthesis, and nitrogenase activity of Anabaena inaequalis.

Anabaena inaequalis was sensitive to nickel ion in the order of decreasing sensitivity of growth, photosynthesis, and acetylene reduction. At a culture density of 9 x 10(4) cells per millilitre, growth after 12 days was completely inhibited by 0.125 ppm (microgram/mL) Ni2+. Nickel caused the increase of both the lag phase of growth and the culture doubling time, and caused the retardation phase to be sooner. Photosynthesis and acetylene reduction were completely inhibited by 10 and 20 ppm Ni2+, respectively, at a cell concentration of 1.3 x 10(6) cells per millilitre. Preincubation for 24 h in the presence of nickel ion significantly increased the sensitivity of photosynthesis and acetylene reduction. Under these conditions acetylene reduction was more sensitive than photosynthesis. Nickel ion reduced culture growth by 35% at a level of 0.05 ppm and inhibited that culture's acetylene-reducing ability by 29% while leaving photosynthesis unaffected. Nickel caused some damage to filament apical cells and induced pigment bleaching in aged cultures. Nickel toxicity was proposed to be due to poisoning of intracellular enzyme systems by nickel ions.     

Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.     

Effect of nitrogen nutrition on endosperm protein synthesis in wild and cultivated barley grown in spike culture

In normal growth conditions, total protein percent (salt soluble plus hordein fractions) in the endosperm at maturity in barley cultivar Hordeum vulgare L. cv `Ruth' was about 14%, whereas in an accession of wild barley, Hordeum spontaneum Koch line 297, it was about 28%. Spike culture experiments were conducted to ascertain whether there were basic differences between the two genotypes under conditions of widely different nitrogen supply. Spikes of each genotype were grown from 8 to 25 days after flowering in in vitro culture in a growth medium containing 0 to 4 grams per liter nitrogen supplied as NH<sub>4</sub>NO<sub>3</sub>. Spikes were pulse-labeled at intervals from 12 to 24 days after flowering with 3.7 megabecquerel of [<sup>3</sup>H]leucine to determine relative rates of synthesis of hordein-1 and hordein-2 polypeptides. At low nitrogen levels `Ruth' had a lower protein content than 297, but at increasing nitrogen levels its protein content increased rapidly and reached a maximum (35%) higher than 297 (30%). The relative contribution of the hordein fraction to total protein increased mainly with time, and hordein-1 to total hordein increased mainly with nitrogen level, in both genotypes. There appeared to be no fundamental limitations in the capacity of `Ruth' to accumulate protein; 297 appears to have a greater basal level of nitrogen availability under normal conditions.     

Molecular structure of amylopectin from Amaranth starch and its effect on physicochemical properties

The molecular structure of amylopectin and its varphi,beta-limit dextrins from starch of 13 amaranth cultivars was determined by HPAEC-PAD after debranching. Chain length profiles of amylopectins showed bimodal distributions. The molar-based ratios of the average chain lengths of amylopectins (CLap) ranged from 17.41 to 18.22. The molar-based average chain lengths (CLld) and average B-chain lengths (BCLld) of varphi,beta-limit dextrins varied from 7.68 to 8.05, and from 14.10 to 14.73, respectively. Correlation analysis indicated that most structural parameters were positively correlated with thermal properties with few exceptions, whereas the content of fraction fa' ("'" stands for molar-based chain length ratio) was negatively correlated with the thermal properties. Pasting properties of cold paste viscosity (CPV) and setback were also correlated with amylopectin structural parameters.     

Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice ( Oryza sativa L.)

Rice starch is composed of amylose and amylopectin. Amylose content, an important determinant of rice starch quality, is primarily controlled by the waxy gene, encoding granule-bound starch synthase (GBSS). The starch branching enzyme (SBE) and soluble starch synthase (SSS) play major roles in the synthesis of amylopectin. Microsatellite polymorphisms in the three genes, the wx gene encoding granule-bound starch synthase I, the SBE gene encoding starch branching enzyme I and the SSS gene encoding soluble starch synthase I, were studied for 56 accessions of waxy rice ( Oryza sativa L.). Four (CT)(n) microsatellite alleles, (CT)(16), (CT)(17), (CT)(18) and (CT)(19), at the wx locus were detected in this set of waxy rice, of which (CT)(17) was the most frequent. Three (CT)(n) microsatellite allele classes were found at the SBE locus, (CT)(8) or (CT)(10) together with an insertion sequence of CTCTCGGGCGA, and (CT)(8) alone without the insertion. There were multiple microsatellites clustered at the SSS locus. However, these alleles can also be grouped into three classes, i.e. the allele class SSS-A = (AC)(2) em leader TCC(TC)(11) em leader (TC)(5)C(ACC)(11), the allele class SSS-B = (AC)(3) em leader TCT(TC)(6) em leader (TC)(4)C(ACC)(9), and the allele class SSS-C = (AC)(3) em leader TCT(TC)(6) em leader (TC)(4)C(ACC)(8). The analyses of starch physicochemical properties among different microsatellite genotypes indicated that the waxy rice group with the (CT)(19) allele, the SBE-A allele and the SSS-B allele was quite different from other groups. Nine out of 15 accessions with a high gelatinization temperature (GT) belonged to the wx (CT)(19) group, all of them belonged to the SBE-A group and 13 of them belonged to the SSS-B group. These microsatellites might be useful in marker-assisted breeding for the improvement of rice grain quality.     

μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives

Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end‐use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the three‐dimensional (3D) characteristics of grains, we combine X‐ray microcomputed tomography (μCT) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape vary across wild and domesticated wheat and barley. We find that grain depth and, to a lesser extent, width are major drivers of shape change and that these traits are still relatively plastic in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes.     

Characterization of mutants in Arabidopsis showing increased sugar-specific gene expression, growth, and developmental responses

Sugars such as sucrose serve dual functions as transported carbohydrates in vascular plants and as signal molecules that regulate gene expression and plant development. Sugar-mediated signals indicate carbohydrate availability and regulate metabolism by co-coordinating sugar production and mobilization with sugar usage and storage. Analysis of mutants with altered responses to sucrose and glucose has shown that signaling pathways mediated by sugars and abscisic acid interact to regulate seedling development and gene expression. Using a novel screen for sugar-response mutants based on the activity of a luciferase reporter gene under the control of the sugar-inducible promoter of the ApL3 gene, we have isolated high sugar-response (hsr) mutants that exhibit elevated luciferase activity and ApL3 expression in response to low sugar concentrations. Our characterization of these hsr mutants suggests that they affect the regulation of sugar-induced and sugar-repressed processes controlling gene expression, growth, and development in Arabidopsis. In contrast to some other sugar-response mutants, they do not exhibit altered responses to ethylene or abscisic acid, suggesting that the hsr mutants may have a specifically increased sensitivity to sugars. Further characterization of the hsr mutants will lead to greater understanding of regulatory pathways involved in metabolite signaling.     

Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.)

Starch characteristics determine the quality of various products of rice, e.g., eating, cooking and processing qualities. Our previous study indicated that molecular markers inside or close to starch synthesizing genes can differentiate the starch properties of 56 waxy rices. Here we report microsatellite (or simple sequence repeat, SSR) polymorphism in the Waxy (Wx) gene, soluble starch synthase I gene (SS1) and starch branching enzyme 1 gene (SBE1), single nucleotide polymorphism (SNP) in Wx and starch branching enzyme 3 gene (SBE3), and a sequence tagged site (STS) in starch branching enzyme 1 gene (SBE1) among 499 nonwaxy rice samples and their relationships with starch physicochemical properties. The nonwaxy rice samples consist of landraces (n = 172) obtained from germplasm centers and cultivars and breeding lines (n = 327) obtained from various breeding programs. Ten (CT) _n microsatellite alleles, (CT)₈, (CT)₁₀, (CT)₁₁, (CT)_12, (CT)₁₇, (CT)₁₈, (CT)₁₉, (CT)₂₀, (CT)₂₁, and (CT)₂₂, were found at the Wx locus, of which (CT)₁₁ was the most frequent, and (CT)₁₂, (CT)₂₁ and (CT)₂₂ were identified for the first time. Four (CT) _n microsatellite alleles were found at the SBE1 locus, (CT)₈, (CT)₉, and (CT)₁₀ together with an insertion sequence of CTCTCGGGCGA, and (CT)₈ alone without the insertion, of which (CT)₉ and the insertion was a new allele identified in only one rice, IR1552. Multiple microsatellites clustered at the SS1 locus, and in addition to the three alleles previously detected (SSS-A = (AC)₂...TCC(TC)₁₁...(TC)₅C(ACC)₁₁, SSS-B = (AC)₃...TCT(TC)₆...(TC)₄C(ACC)₉, and SSS-C = (AC)₃...TCT(TC)₆...(TC)₄C(ACC)₈), one new allele (SSS-D = (AC)₂...TCC(TC)₁₀...(TC)₄C(ACC)₉) was found. Analysis of the starch physicochemical properties of the samples with different microsatellites, SNPs and STS groups indicated that these molecular markers can differentiate almost all the physicochemical properties examined, e.g., apparent amylose content (AAC), pasting viscosity characteristics, and gel textural properties. Wx SSR and Wx SNP alone explained more variations for all physicochemical properties than the other molecular markers. The total six markers could explain 92.2, 81 and 86% of total variation of AAC, gel hardness (HD), and gel cohesiveness (COH), respectively, and they could explain more than 40% of the total variation of hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BD), setback viscosity (SB) and gel adhesiveness (ADH). However, only 29% of the total variation of peak viscosity (PV) and 37% of pasting temperature (PT) could be explained by all the molecular markers. Some of these markers can differentiate the starch physicochemical properties among the rice samples with the same Wx allele, indicating that the variation within Wx allele classes can be explained by other starch synthesizing genes. These SSRs, SNPs and STS are useful in marker-assisted breeding for the improvement of starch quality of rice.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Structures of clusters in sweetpotato amylopectin

Sweetpotato amylopectin was subjected to partial hydrolysis by α-amylase from Bacillus amyloliquefaciens to release the clusters. Clusters were then fractionated and precipitated by methanol and structurally characterized by gel-permeation chromatography and high-performance anion-exchange chromatography. An initial stage of α-amylolysis on the amylopectin isolated mostly domains but also clusters. A second stage of α-amylolysis on the domains and clusters further isolated their respective clusters and sub-clusters. All the domains, clusters and sub-clusters were sequentially subjected to phosphorolysis and β-amylolysis to obtain their internal part. The degree of polymerization of the clusters in the form of φ,β-limit dextrins were from 58 to 86. Each domain contained 2–8 clusters. Two types of clusters were structurally identified. Type A clusters were larger and contained about 12 chains per cluster with higher degree of branching (DB), whereas those of type B were smaller and contained about eight chains per cluster with lower DB.