Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.

Zinc in plants

During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudo-chromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.

/pdf/rice-root-genetic-architecture-meta-analysis-from-a-drought-cbkqa7wl1m.pdf

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

Zinc (Zn) is one of the most essential micronutrients required for the growth and development of human beings. More than one billion people, particularly children and pregnant women suffer from Zn deficiency related health problems in Asia. Rice is the major staple food for Asians, but the presently grown popular high yielding rice varieties are poor supplier of Zn in their polished form. Breeding rice varieties with high grain Zn has been suggested to be a sustainable, targeted, food-based and cost effective approach in alleviating Zn deficiency. The physiological, genetic and molecular mechanisms of Zn homeostasis have been well studied, but these mechanisms need to be characterized from a biofortification perspective and should be well integrated with the breeding processes. There is a significant variation for grain Zn in rice germplasm and efforts are being directed at exploiting this variation through breeding to develop high Zn rice varieties. Several QTLs and gene specific markers have been identified for grain Zn and there is a great potential to use them in Marker-Assisted Breeding. A thorough characterization of genotype and environmental interactions is essential to identify key environmental factors influencing grain Zn. Agronomic biofortification has shown inconsistent results, but a combination of genetic and agronomic biofortification strategies may be more effective. Significant progress has been made in developing high Zn rice lines for release in target countries. A holistic breeding approach involving high Zn trait development, high Zn product development, product testing and release, including bioefficacy and bioavailability studies is essential for successful Zn biofortification.

/pdf/advances-in-breeding-for-high-grain-zinc-in-rice-16lpv649vx.pdf

Advances in breeding for high grain Zinc in Rice.

Ophiopogon japonicus--A phytochemical, ethnomedicinal and pharmacological review.

Daphnia are already an established model species in toxicology. This freshwater crustacean is used commonly for environmental monitoring of pollutants around the globe and plays an important role in establishing regulatory criteria by government agencies (e.g., US EPA, Environment Canada organization for Economic Cooperation and Development, Environment Agency of Japan). Consequently, daphniids represent 8% of all experimental data for aquatic animals within the toxicological databases (Denslow et al., 2007). As such, their incorporation within the new field of toxicological genomics is limited only by the advancement of genomic resources. Because the development of these technologies requires the input and feedback of a large research community that extends far beyond the boundaries of any one discipline, the Daphnia Genomics Consortium (DGC) was formed in 2001 to: (i) provide the organizational framework to coordinate efforts at developing the Daphnia genomic toolbox; (ii) facilitate collaborative research and (iii) develop bioinformatics strategies for organizing the rapidly growing database. This chapter reviews the progress in establishing Daphnia as model species for genomic studies, with emphasis on toxicological applications. As the goals of the DGC are defined largely by extending the boundaries of current biological research in light of genomic information, this chapter first reviews Daphnia's unique biological attributes that make it ideal for such an expansion of research efforts. These attributes include a long tradition of ecological, evolutionary and toxicological study, culminating in the benefits provided by emerging genomic tools.

/pdf/daphnia-as-an-emerging-model-for-toxicological-genomics-4p4ns5jox9.pdf

Daphnia as an emerging model for toxicological genomics

Molecular mapping of quantitative trait loci for zinc toxicity tolerance in rice seedling (Oryza sativa L.)

Leaf developmental behavior in rice (Oryza sativa L.) is one of the important agronomic characteristics, which not only determines vegetative growth but also influences grain yield. This study was conducted to identify quantitative trait loci (QTLs) for total number of leaves (TNL), days to the emergence of flag-leaf (DEF) and the leaf emergence rates (LER) on main stem, which mainly represent leaf developmental behavior, using recombinant inbred lines (RILs) derived from a cross between a japonica variety, Asominori and an indica variety, IR24, cultivated in 2001 and 2002. The transgressive segregations in both parental directions and continuous variations of all three tested traits were observed. Significant correlations among these traits were detected. A total of fourteen QTLs for leaf development behavior were detected with 289 RFLP markers. Six QTLs controlling TNL were mapped to chromosomes 3, 5, 6, 8, 9, 12, and accounted for 5.6∼15.7% of the total phenotypic variations, and three QTLs for DEF were mapped to chromosome 3, 6, 8 and accounted for 10.7∼35.4% of total phenotype variation and five QTLs for LER were mapped to chromosome 1(two QTLs), 2, 4, 9 and explained 6.2∼17.5% of phenotype variation. The identification of QTLs for leaf developmental behavior in rice may be useful for selection of ‘fast growing genotype’ before heading using maker-assisted selection.

Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.).

Dwarf lilyturf (Ophiopogon japonicus K.), used as a weed-suppressing cover crop and a medicinal plant, was suggested to be a promising natural herbicide to control weeds in the rice field through its allelopathic potential. Allelopathic chemicals from the dwarf lilyturf were identified and their growth-inhibiting effects on two major weeds in the rice field in Japan were examined. High pressure liquid chromatograph (HPLC) analysis showed the existence of at least six allelopathic chemicals, viz., salicylic acid, syringic acid, syringaldehyde, vanillic acid, ρ-hydroxybenzoic acid and sinapic acid in dwarf lilyturf plant. The chemical detected at the highest concentration was salicylic acid (251.04 ¼g g-1), which occupied more than half of total allelopathic chemicals detected (317.16 ¼g g-1), followed by syringic acid (37.30 ¼g g-1), syringaldehyde(13.30 ¼g g-1) and sinapic acid (11.03 ¼g g-1). The chemicals detected at the lowest concentration was vanillic acid (1.69 ¼g g-1). Salicylic acid displa...

Elementary identification of phenolic allelochemicals from dwarf lilyturf plant (Ophiopogon japonicus K.) and their growth-inhibiting effects for two weeds in paddy rice field

Dwarf lilyturf (Ophiopogonjaponicus Ker-Gawl), a medicinal plant, hasbeen used for sore throat therapy andinhibition of physiological thirst sinceancient times. Experimental studies wereconducted to determine the allelopathic effectsof dwarf lilyturf plants on germination andgrowth of three main weed species, viz.,barnyardgrass (Echinochloa crusgalli L.),monchoria (Monocharia vaginalis P.) andsmallflower umbrella (Cyperus difformisL.), in rice production and on emergence andgrowth of weeds in rice fields in Japan. Theseresults showed that all aqueous extracts (1, 2,4, 8%, w/v) from the dried powders ofunderground parts of dwarf lilyturf containedwater-soluble substances that significantlyinhibited seed germination and seedling growthfor monchoria and smallflower umbrella. Withrespect to barnyardgrass, all aqueous extractshad less effect on germination, but lowconcentrations ( 4%, w/v) had significantinhibitory effects. In a glasshouse experiment,all treatments (50, 100, 150 g m−2) of thedried powders significantly inhibited theemergence and dry weights of weeds in ricepaddy fields and the inhibition became strongeras the concentration increased, except that50 g m−2 concentration had slightstimulatory effects on the emergence ofbarnyardgrass. The 150 g m−2 concentrationmarkedly inhibited emergence (77.6%) and dryweight (91.1%) of rice field weeds. Inaddition, all treatments had no inhibition oninitial rice plant growth. Dwarf lilyturfplants may have inhibitory potential on weedsas a natural rice field herbicide.

https://link.springer.com/content/pdf/10.1023/B:BICO.0000017363.11530.58.pdf

Potential biological control of weeds in rice fields by allelopathy of dwarf lilyturf plants

The development of molecular genetic maps has accelerated the identification and mapping of genomic regions controlling quantitative trait loci (QTL) in rice (Oryza sativa L.). Minimizing embryo size in rice would increase proportion of edible endosperm. This study was conducted to determine the genetic basis controlling embryo size of rice grains in a recombinant inbred (RI) population derived from cross of a japonica cultivar, Asominori, with an indica cultivar, IR24, by means of 289 restriction fragment length polymorphism (RFLP) markers. Two parameters, embryo length and embryo width, which represent embryo size in rice, were estimated for each RI line and their parental varieties. Continuous distributions and transgressive segregations of embryo length and embryo width in rice were observed in the RI population, suggesting that embryo size was quantitative in grains of conventional varieties. Three QTL for embryo length were detected on chromosomes 1, 2, and 3 and explained 17.9, 25.7, and 9.2%, respectively, of the total phenotypic variation. Three QTL for the embryo width were observed on chromosome 2, 8, and 10 and accounted for 13.5, 15.7, and 15.0% of total phenotypic variation, respectively. In addition, alleles with increasing and decreasing effects were detected from the both parents. The results and the tightly linked molecular markers that flank the QTL will be useful in breeding for embryo improvement in rice.

Dongzhi Lin

Papers

Molecular mapping of quantitative trait loci for zinc toxicity tolerance in rice seedling (Oryza sativa L.)

Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.).

Elementary identification of phenolic allelochemicals from dwarf lilyturf plant (Ophiopogon japonicus K.) and their growth-inhibiting effects for two weeds in paddy rice field

Potential biological control of weeds in rice fields by allelopathy of dwarf lilyturf plants

Mapping of QTL for Embryo Size in Rice