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.

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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.

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Advances in breeding for high grain Zinc in Rice.

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.

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Daphnia as an emerging model for toxicological genomics

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R2 of 31.7 %, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.

QTL Mapping and Confirmation for Tolerance of Anaerobic Conditions During Germination Derived From the Rice Landrace Ma-Zhan Red

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.).

ツユクサ科の一年生雑草であるマルバツユクサについて, 地上部および地下部にそれぞれ生産される大小両種子の大きさについて調査した。また, 3月から9月の異なる時期に出芽した場合, および遮光下で生育した場合におけるマルバツユクサの生育および種子生産についても調査した。地上部および地下部に生産されたさく果は前後2心皮となって中央で裂けるが, 前方心皮中の2～4粒の種子とそれよりも大型となる後方心皮中の1粒の種子の大きさについて比較したところ, 地下部の大種子が長径, 短径および厚さのいずれも大きく, 次いで地上部の大種子, 地下部の小種子となり, 地上部の小種子のそれらは最も小さかった。3月から9月にかけて出芽したマルバツユクサの中で, 6月に出芽した個体において草丈および一次分枝数がいずれも最も大きく推移し, 9月に出芽した個体のそれらは, いずれも最も小さかった。出芽から開花までの日数は, 5月出芽の個体で21日と最も短く, 9月出芽の個体で42日と最も長かった。また, 種子の落下期間は5月出芽の個体で80日と最も長くなり, 9月出芽の個体では種子を生産しなかった。地上部および地下部における花序数および大小種子粒数は, 4月に出芽した個体の場合に共に最も多くなったが, それ以降に出芽した個体のそれらは減少した。82%, 50%および14%の相対照度下で生育したマルバツユクサの草丈は, 100%の相対照度下の場合よりも高く推移したが, 個体当たりの一次分枝数に有意差は見られなかった。地上部における花序数および大小種子粒数は, 82%の相対照度下で生育した個体において最も多くなったが, 相対照度の低下とともにそれらは減少した。一方, 地下部に生産された花序数および大小種子粒数は, 各相対照度間で有意差を示さなかった。

Tsugufumi Ogawa

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.).

Effect of emergence times and shading conditions on growth, seed production, and seed size of tropical spiderwort (Commelina benghalensis L.)

Mapping of quantitative trait loci for gibberellic acid response at rice (Oryza sativa L.) seedling stage

Molecular Genetic Mapping of QTLs for Tiller Angle in Rice (Oryza sativa L.)