Molecular characterisation of the amino- and carboxyl-domains in different Glu-A1x alleles of Triticum urartu Thum. ex Gandil.

The wild diploid wheat (Triticum urartu Thum. ex Gandil.) is a potential gene source for wheat breeding, as this species has been identified as the A-genome donor in polyploid wheats. One important wheat breeding trait is bread-making quality, which is associated in bread wheat (T. aestivum ssp. aestivum L. em. Thell.) with the high-molecular-weight glutenin subunits. In T. urartu, these proteins are encoded by the Glu-A1x and Glu-A1Ay genes at the Glu-A ^u 1 locus. The Glu-A1x genes of 12 Glu-A ^u 1 allelic variants previously detected in this species were analysed using PCR amplification and sequencing. Data showed wide diversity for the Glu-A1x alleles in T. urartu, which also showed clear differences to the bread wheat alleles. This variation could enlarge the high-quality genetic pool of modern wheat and be used to diversify the bread-making quality in durum (T. turgidum ssp. durum Desf. em. Husn.) and common wheat.     

Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring

Key message

An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring.

Abstract

Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4–63.0 % for spike length, 48.2–79.6 % for spikelet number per spike, 13.1–48.1 % for plant architecture, and 12.2–26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A ^m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.

     

Effects of take-all (Gaeumannomyces graminis var. tritici) on crop N uptake and residual mineral N in soil at harvest of winter wheat

Background and aims

Take-all, caused by the fungus Gaeumannomyces graminis var. tritici, is the most damaging root disease of wheat. A severe attack often leads to premature ripening and death of the plant resulting in a reduction in grain yield and effects on grain quality (Gutteridge et al. in Pest Manag Sci 59:215–224, 2003). Premature death of the plant could also lead to inefficient use of applied nitrogen (Macdonald et al. in J Agric Sci 129(2):125–154, 1997). The aim of this study was to determine crop N uptake and the amount of residual mineral N in the soil after harvest where different severities of take-all had occurred.

Methods

Plant and soil samples were taken at anthesis and final harvest from areas showing good and poor growth (later confirmed to be caused by take-all disease) in three winter wheat crops grown on the same soil type on Rothamsted Farm in SE England in 1995, 2007 and 2008 (harvest sampling only). All crops received fertiliser N in spring at recomended rates (190–200?kg?N ha^?1). On each ocassion crops were assessed for severity of take-all infection (TAR) and crop N uptakes and soil nitrate plus ammonium (SMN) was determined. Grain yields were also measured.

Results

Grain yields (at 85% dry matter) of crops with moderate infection (good crops) ranged from 4.3 to 13.0?t ha^?1, compared with only 0.9–4.5?t ha^?1 for those with severe infection (poor crops). There were significant (P?<?0.05) negative relationships between crop N uptake and TAR at anthesis and final harvest. At harvest, good crops contained 129–245?kg?N ha^?1 in grain, straw and stubble, of which 85–200?kg?N ha^?1 was in the grain. In contrast, poor crops contained only 46–121?kg?N ha^?1, of which only 22–87?kg?N ha^?1 was in the grain. Positive relationships between SMN and TAR were found at anthesis and final harvest. The SMN in the 0–50?cm layer following harvest of poor crops was significantly (P?<?0.05) greater than that under good crops, and most (73–93%) was present as nitrate.

Conclusions

Localised patches of severe take-all infection decreased the efficiency with which hexaploid wheat plants recovered soil and fertiliser derived N, and increased the subsequent risk of nitrate leaching. The risk of gaseous N losses to the atmosphere from these areas may also have been enhanced.     

Identification of the molecular genetic basis of the low palmitic acid seed oil trait in soybean mutant line RG3 and association analysis of molecular markers with elevated seed stearic acid and reduced seed palmitic acid

The fatty acid composition of vegetable oil is becoming increasingly critical for its ultimate functionality and utilization in foods and industrial products. Partial chemical hydrogenation of soybean [Glycine max (L.) Merr.] oil increases oxidative stability and shelf life but also results in the introduction of trans fats as an unavoidable byproduct. Due to mandatory labeling of consumer products containing trans fats, conventional soybean oil has lost the ability to deliver the most appropriate economical functionality and oxidative stability, particularly for baking applications. Genetic improvement of the fatty acid profile of soybean oil is one method of meeting these new requirements for oil feedstocks. In this report, we characterized three mutant genetic loci controlling the saturated fatty acid content of soybean oil: two genes additively reduce palmitic acid content (fap1 and fap3-ug), and one gene independently elevates stearic acid content (fas). We identified a new null allele of fap3-ug/GmFATB1A (derived from line ELLP2) present in line RG3. The splicing defect mutation in a beta-ketoacyl-[acyl-carrier-protein] synthase III candidate gene located in the region mapped to fap1, derived originally from ethyl methane sulphonate mutant line C1726 (Cardinal et al. in Theor Appl Genet 127:97–111, 2014), was also present in line RG3. We also utilized the elevated stearic acid line RG7, which has previously been shown to contain novel mutant fas/SACPD-C alleles encoding stearoyl-acyl carrier protein desaturase (Boersma et al. in Crop Sci 52:1736–1742, 2012). Molecular marker assays have been developed to track these causative mutations and understand their contributions to seed oil fatty acid profiles in a recombinant inbred line population segregating for fap1, fap3-ug, and fas alleles.     

Molecular characterization and diversity of the Pina and Pinb genes in cultivated and wild diploid wheat

Grain hardness is one of the most important characteristics of wheat quality. Soft endosperm is associated with the presence of two proteins in the wild form, puroindoline a and b. The puroindoline genes and their derived proteins are present in the putative wheat diploid ancestors which are thought to be the donors of the A, B and D genomes in common and durum wheat. In this study, we investigated the variability of grain hardness in einkorn, along with the nucleotide diversity of Pina and Pinb genes in a collection of einkorn wheat and T. urartu, in addition to studying the neutrality and linkage disequilibrium of these genes. Various alleles were detected for Pina and Pinb genes including three novel alleles for the Pinb locus: Pinb-A ^m 1i, Pinb-A ^m 1j and Pinb-A ^m 1k. Some differences were found in grain hardness between the different genotypes. The neutrality test showed a different pattern of variation between the two Pin genes. The genetic analysis of a diploid wheat collection has demonstrated that these species are a potential source of novel puroindoline variants. Our data suggest that, although further studies must be carried out, these variants could be used to expand the range of grain texture in durum and common wheat, which would permit the development of new materials adapted to novel uses in the baking and pasta industry.     

Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region

The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A^uA^u) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A^mA^m), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A^u genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A^u genome. The difference in the compared region between A^u and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A^u than to A^m. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A^u sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.     

Anther structure and pollen ontogeny of Hosta Tratt. and its systematic significance

Anther structure and pollen ontogeny of six species of Hosta Tratt. was studied to provide additional data for its classification. Microscopic observation found that their male gametogenesis has the following structural characteristics: (1) the four microsporangia are linearly arranged on introrse side of anther connective tissue; (2) mature anther wall is composed of an epidermis, endothecium, middle layer(s), and tapetum; (3) microsporogenesis is successive; (4) mature pollen grains are three-celled at anthesis, with a vegetative cell filled with large amounts of starch grains; (5) pollen ontogeny is obviously asynchronous; (6) each tepal has about 9?C13 vascular traces in cross-section view. The above observations suggest that genus H. Tratt. should be classified as family Hostaceae, in agreement with Dahlgren and Clifford (1982), Takhtajan (1997), and Wu et?al. (2003).     

Wx gene in diploid wheat: molecular characterization of five novel alleles from einkorn (Triticum monococcum L. ssp. monococcum) and T. urartu

The Wx gene encodes the granule-bound starch synthase I or waxy protein, which is the sole enzyme responsible for amylose synthesis in wheat seeds. Triticum urartu and einkorn (T. monococcum L. ssp. monococcum), which are related to the A genome of bread wheat, could be important sources of variation for this gene. This study evaluated the Wx gene variability in 52 accessions of these species and compared their nucleotide sequences with the Wx-A1a allele of bread wheat. The level of polymorphism found was high, although not distributed equally between the two species. Five different alleles were found in T. urartu, of which four were novel (Wx-A ^u 1b, -A ^u 1c, -A ^u 1d and -A ^u 1e). All einkorn accessions had the same allele, which was also novel and was named Wx-A ^m 1a. A comparison between the proteins deduced from the novel alleles and the Wx-A1a protein showed that there were up to 33 amino acid changes in both the transit peptide and the mature protein. These results showed that these species, especially T. urartu, are a potential source of novel waxy variants.     

Dynamic analysis of competition and complementarity for light and N use to understand the yield and the protein content of a durum wheat–winter pea intercrop

In a previous paper [Bedoussac L, Justes E (2009) Plant Soil, doi: 10.1007/s11104-009-0082-2], we showed that intercropping of durum wheat and winter pea increased the yield and protein concentration of durum wheat when early N availability was less than 120 kg N ha^?1. The aim of the present work was to understand these results by analysing intercrop species dynamics for growth, light and N acquisition. A 2-year field experiment was carried out in southwest France with different fertilizer-N levels in order to compare wheat (Triticum turgidum L.) and pea (Pisum sativum L.) grown as sole crops and as an intercrop in a row substitutive design. The advantages of intercropping in low N conditions were due mainly to: (1) better light use (up to 10%), thanks to species dynamic complementarity for leaf area index and height; (2) growth complementarity over time (higher growth rate of wheat until pea flowering and then of pea until wheat flowering); and (3) dynamic complementary N acquisition associated with better wheat N status throughout growth. Disadvantages, underlining poorer complementarity within the intercrop stand, were observed with ample available N in early growth. This induced higher cereal growth during winter, which led to increase interspecies competition by reducing pea light absorption and, consequently, its biomass production.     

Studies of the morphology of chromosomes of some selected species

Karyotypes of twelve species from twenty-four localities in southern Moravia and one locality in Slovakia were investigated. Their counts or karyotypic formulae are as follows:Chenopodium foliosum (Moench) Ascherson: K (2n)=18=16 A^m+2 B^sm;Astragalus austriacus Jacq.: K (2n)=16=8 A^m+8 B^sm;Astragalus exscapus L.: K (2n)=16=10 A^m+4 B^sm+2 C^st;Astragalus cicer L.: K (2n)=64;Astragalus onobrychis L.: K (2n=64 and K (2n)=64+1;Vicia dumetorum L.: K (2n=14=10 A^m+4 B^sm;Vicia sylvatica L.: K (2n)=14=2 A^m+10 B^sm+2 C^st;Vicia pisiformis L.: K (2n)=12=8 A^m+4 B^sm;Vicia cassubica L.: K (2n)=12=4 A^m+6 B^sm+2 C^st;Vicia cracca L. (from five localities in southern Moravia): K (2n)=28=4 A^m+12 B^sm+12 C^st and K (2n)=28+1=5 A^m+12 B^sm+12 C^st;Vicia cracca L. (from one locality in Slovakia): K (2n)=14=2 A^m+6 B^sm+6 C^st;Vicia tenuifolia Roth: K (2n)=24=4 A^m+16 B^sm+4 C^st;Serratula lycopifolia (Vill.) Kern.: K (2n)=60.     

A model of direction selectivity in the starburst amacrine cell network

Displaced starburst amacrine cells (SACs) are retinal interneurons that exhibit GABA _A receptor-mediated and Cl ^? cotransporter-mediated, directionally selective (DS) light responses in the rabbit retina. They depolarize to stimuli that move centrifugally through the receptive field surround and hyperpolarize to stimuli that move centripetally through the surround (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006). They also play a key role in the activity of DS ganglion cells (DS GC; Amthor et al, Vis Neurosci 19:495–509 2002; Euler et al, Nature 418:845–852, 2002; Fried et al, Nature 420:411– 414, 2002; Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799 2006; Yoshida et al, Neuron 30:771–780, 2001). In this paper we present a model of strong DS behavior of SACs which relies on the GABA-mediated communication within a tightly interconnected network of these cells and on the glutamate signal that the SACs receive from bipolar cells (a presynaptic cell that receives input from cones). We describe how a moving light stimulus can produce a large, sustained depolarization of the SAC dendritic tips that point in the direction that the stimulus moves (i.e., centrifugal motion), but produce a minimal depolarization of the dendritic tips that point in the opposite direction (i.e., centripetal motion). This DS behavior, which is quantified based on the relative size and duration of the depolarizations evoked by stimulus motion at dendritic tips pointing in opposite directions, is robust to changes of many different parameter values and consistent with experimental data. In addition, the DS behavior is strengthened under the assumptions that the Cl^? cotransporters Na^?+?-K^?+?-Cl^?? and K^?+?-Cl^?? are located in different regions of the SAC dendritic tree (Gavrikov et al, PNAS 103(49):18793–18798, 2006) and that GABA evokes a long-lasting response (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799, 2006). A possible mechanism is discussed based on the generation of waves of local glutamate and GABA secretion, and their postsynaptic interplay as the waves travel between cell compartments.     

Nitrogen transfer from forage legumes to nine neighbouring plants in a multi-species grassland

Legumes play a crucial role in nitrogen supply to grass-legume mixtures for ruminant fodder. To quantify N transfer from legumes to neighbouring plants in multi-species grasslands we established a grass-legume-herb mixture on a loamy-sandy site in Denmark. White clover (Trifolium repens L.), red clover (Trifolium pratense L.) and lucerne (Medicago sativa L.) were leaf-labelled with ¹⁵N enriched urea during one growing season. N transfer to grasses (Lolium perenne L. and xfestulolium), white clover, red clover, lucerne, birdsfoot trefoil (Lotus corniculatus L.), chicory (Cichorium intybus L.), plantain (Plantago lanceolata L.), salad burnet (Sanguisorba minor L.) and caraway (Carum carvi L.) was assessed. Neighbouring plants contained greater amounts of N derived from white clover (4.8?g?m^-2) compared with red clover (2.2?g?m^-2) and lucerne (1.1?g?m^-2). Grasses having fibrous roots received greater amounts of N from legumes than dicotyledonous plants which generally have taproots. Slurry application mainly increased N transfer from legumes to grasses. During the growing season the three legumes transferred approximately 40?kg?N ha^-1 to neighbouring plants. Below-ground N transfer from legumes to neighbouring plants differed among nitrogen donors and nitrogen receivers and may depend on root characteristics and regrowth strategies of plant species in the multi-species grassland.     

A new species of the sleeper goby (Gobioidei,Eleotridae) from the České Středohoří Mountains (Czech Republic,Oligocene) and analysis of the validity of the family Pirskeniidae

A new species of gobioid fish Pirskenius Obrhelová, 1961 (P. radoni sp. nov.) is described from Oligocene strata of the ?eské St?edoho?í Mountains and compared with related species. The new species is characterized by a unique combination of characters that allow it to be separated from P. diatomaceus Obrhelová, 1961. The taxonomic position of the genus Pirskenius is discussed, and its affinity to the family Eleotridae is indicated. The new record documents, together with P. diatomaceus, the oldest known skeletal record of the Eleotridae.     

Leucothoid and Maerid Amphipods (Crustacea) from deep regions of the North Atlantic

From amphipod collections from the deep Norwegian Sea, three species are here redescribed: Maera loveni (Bruzelius 1859) (Maeridae), Leucothoe aff. spinicarpa (Abildgaard, 1789) and L. uschakovi Gurjanova, 1951 (Leucothoidae). A key to all Atlantic and Mediterranean Leucothoe species (males only) is provided.     

Leges sine moribus vanae: does language make moral thinking possible?

Does language make moral cognition possible? Some authors like Andy Clark have argued for a positive answer whereby language and the ways people use it mark a fundamental divide between humans and all other animals with respect to moral thinking (Clark, Mind and morals: essays on cognitive science and ethics. MIT Press, Cambridge, MA, 1996; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000a; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000b; Philosophy of mental representation. Oxford University Press, Oxford, pp 37–43 and discussion, 44–61, 2002). I take issue with Clark’s view and argue that language is probably unnecessary for the emergence of moral cognition. I acknowledge, however, that humans unlike other animals seem to posses what Haugeland in Philosophy of mental representation. Oxford University Press, Oxford (2002) terms ‘norm-hungriness’: an idiosyncratic need or desire to create and abide by a multitude of norms. Our peculiar norm-hungriness, I suggest, depends on what can be called florid control rather than on language.     

Reply to: “Comment on root orientation can affect detection accuracy of ground-penetrating radar”

Introduction

We showed that root orientation affected a parameter of ground penetrating radar (GPR), amplitude area (A) (Tanikawa et al. Plant Soil 373:317–327, 2013). The aims of this reply to Wu et al. (2014) are (i) to correct the two inaccuracies in Tanikawa et al. (2013) and (ii) to improve our method of estimating A(90°) using A(x) of root angle x.

Methods

Measured A values of Tanikawa et al. (2013) were analyzed with the modified equations.

Results

The first inaccuracy was the use of incorrect units for the coefficient b (the phase shift) in the sinusoidal waveform of A(x). The units should have been radians instead of degrees. The second inaccuracy was the mis-derivation of A(x) into A(x?+?90°). In the modified method, A(90°) was estimated by A(x) from two orthogonally intersecting transect lines and a transect line at a diagonal to them.

Conclusions

The two inaccuracies did not affect the previous main conclusions that the parameter T was suitable for estimating root diameter and that grid transects are likely to identify clear hyperbolas reflecting roots in radar profiles (Tanikawa et al. 2013). By the improved method, we could accurately estimate root diameter by scanning using three transect lines intersecting at angles of x, x?+?45°, and x?+?90°.     

A intervarietal genetic map and QTL analysis for yield traits in wheat

A new genetic linkage map was constructed based on recombinant inbred lines (RILs) derived from the cross between the Chinese winter wheat (Triticum aestivum L.) varieties, Chuang 35050 and Shannong 483 (ChSh). The map included 381 loci on all the wheat chromosomes, which were composed of 167 SSR, 94 EST-SSR, 76 ISSR, 26 SRAP, 15 TRAP, and 3 Glu loci. This map covered 3636.7 cM with 1327.7 cM (36.5%), 1485.5 cM (40.9%), and 823.5 cM (22.6%) for A, B, and D genome, respectively, and contained 13 linkage gaps. Using the RILs and the map, we detected 46 putative QTLs on 12 chromosomes for grain yield (GY) per m², thousand-kernel weight (TKW), spike number (SN) per m², kernel number per spike (KNS), sterile spikelet number per spike (SSS), fertile spikelet number per spike (FSS), and total spikelet number per spike (TSS) in four environments. Each QTL explained 4.42–70.25% phenotypic variation. Four QTL cluster regions were detected on chromosomes 1D, 2A, 6B, and 7D. The most important QTL cluster was located on chromosome 7D near the markers of Xwmc31, Xgdm67, and Xgwm428, in which 8 QTLs for TKW, SN, SSS and FSS were observed with very high contributions (27.53–67.63%).     

Chromosome morphology of the czechoslovak species of the genusScorzonera

Karyotypic formulae of theScorzonera L. species are as follows:S. purpurea L.: K (2n)=14=8 A^m+6 B^sm and K (2n)=14+1=9 A^m+6 B^sm;S. austriaca Willd.: K (2n)=14=6 A^m+6 B^sm+2 C^st;S. humilis L.: K (2n)=14=12 A^m+2 B^sm;S. parviflora Jacq.: K (2n)=14=10 A^m+4 B^sm;S. hispanica L.: K (2n)=12 A^m+2 B^sm. The results of the study of the karyotypes of the generaScorzonera L.,Tragopogon L. andPodospermum DC. are summarized.     

Heckerocrinus, a new substitute generic name for fossil crinoid Bockia Hecker 1940 (Echinodermata: Crinoidea) non Reisinger 1924 (Vermes: Turbellaria)

Heckerocrinus nom. nov., a new generic name of fossil Ordovician crinoid, is proposed for preoccupied fossil generic name Bockia Hecker 1940 non Reisinger 1924 [Vermes: Turbellaria??Typhloplanidae-Protoplanellinae]. Illegitimate family name Bockiidae Ubaghs 1972 is replaced with a new valid family name Heckerocrinidae nom. nov.