Varietal differences in shoot and rooting parameters of pearl millet on sandy soils in Niger

Root parameters are important traits for the acquisition of nutrients and water under resource-limited conditions. In order to investigate the extent of varietal differences in rooting parameters in pearl millet, we compared a total of eight pearl millet varieties in two experiments (ridging and traditional sowing) over four years at the ICRISAT Sahelian Centre, Niger. We found substantial genotypic variation for root length density (RLD), root dry matter, and total root length (RL), but not for specific root length, depth of rooting, or partitioning of roots between topsoil and subsoil (>20 cm depth). RL showed a highly dynamic pattern over the growing season. RL and shoot dry matter were positively correlated over P supplies and contrasting levels of field productivity. The relationship between RL and grain yield as well as harvest index were less clear. The root fraction responded to variation in soil productivity, increasing from roughly 20% under high productivity to more than 40% at low productivity, but we found no evidence of varietal differences in this trait despite pronounced differences in maturity and plant stature. Identification of pearl millet varieties suited for growth under low input conditions in south-west Niger can potentially make use of existing genotypic variability in root parameters, but we suggest that, due to high variability for root traits, indirect selection for shoot parameters (e.g., number of stems) is more promising than direct selection for RLD or RL.     

Natural variants of pearl millet (Pennisetum typhoides) with altered levels of set II alcohol dehydrogenase activity

Two linked genes, Adh1 and Adh2, specify three sets of ADH isozymes in pearl millet. Set I is a homodimer specified by Adh1, Set III is a homodimer specified by Adh2, and Set II is a heterodimer consisting of one ADH1 subunit and one ADH2 subunit. Dry seeds exhibit only Sets I and II. Anaerobic treatment of seeds greatly increases the activity of Sets I and II and causes the Set III isozymes to be expressed. In the investigation reported here, the ADH zymogram phenotypes of 112 inbred pearl millet lines were analyzed. Two kinds of naturally occurring ADH variant strains were observed: in the low-activity variant, Set II activity is low in the dry seed, and no Set III activity is present upon anaerobic treatment. In the high-activity variant, Set II activity is high and Set III isozymes are expressed in the dry seed. The mutation in the high-activity strain appears to affect the product of Adh2 and not the product of Adh1. Dominance tests show that the mutations in both types of variant strains act in cis. These observations and linkage tests indicate that the mutations are closely linked to or at the Adh2 locus.This work was supported by a PHS National Research Service Award Training Grant in Genetics to the Biology Department of the University of Oregon.     

A novel approach to the establishment of dual cultures of pearl millet and Sclerospora graminicola

Dual cultures were successfully established using malformed florets of pearl millet infected with Sclerospora graminicola, the downy mildew pathogen. A higher proportion (86%) of calli from malformed florets formed dual cultures on Murashige and Skoog's (MS) medium with 2 mg 1^-1 of 2,4-dichlorophenoxy acetic acid (2,4-d), compared to shoot tips (25%). Fungal mycelium covered the entire surface of the callus within 30 days of placement of explants on the MS medium with 2 mg 1^-1 of 2,4-d. The infected calli also differentiated and produced plantlets when transferred to MS medium without 2,4-d.     

Genetic analysis of phytic acid content in pearl millet

Summary The genetics of phytic acid content in pearl millet (Pennisettum typhoides (Burm) S & H) was studied using a 12 parent diallel. The analysis of variance of diallel progenies exhibited significant genotypic differences. Different analyses, i.e., combining ability analysis, analysis of variance of diallel tables and genetic component analysis, showed that both additive and non additive gene effects were significant. It is suggested that a population improvement is possible by breeding for low phytic acid cultivars of pearl millet.     

Influence of A1 cytoplasmic substitution on the downy-mildew incidence of pearl millet

Large-scale cultivation of pearl millet [Pennisetum glaucum (L.) R. Br. F₁ hybrids in India has led to increased incidence of downy-mildew (Sclerospora graminicola). There is concern that the A₁ male-sterile cytoplasm used in all the hybrids released so far is responsible for this increase. The influence of A₁ malesterile cytoplasm on downy-mildew incidence in pearl millet was studied by comparing the disease reaction of 40 pairs of F₁ hybrids, each pair carrying respectively a₁ male-sterile and normal B cytoplasm. Mean downy-mildew incidence was similar in the hybrids carrying either A₁ male-sterile or B cytoplasm. The general combining ability of lines with and without A₁ cytoplasm was found to be similar for downy-mildew incidence. These results indicated that in pearl millet A₁ cytoplasm is not associated with increased downymildew incidence. The possible danger of using only one source of cytoplasm has been briefly discussed.     

Tuareg, a novel miniature-inverted repeat family of pearl millet (Pennisetum glaucum) related to the PIF superfamily of maize

Miniature-inverted repeat transposable elements (MITEs) are abundantly repeated in plant genomes and are especially found in genic regions where they could contribute regulatory elements for gene expression. We describe with molecular and cytological tools the first MITE family reported in pearl millet: Tuareg. It was initially detected in the pearl millet ortholog of Teosinte-branched1, an important developmental gene involved in the domestication of maize. The Tuareg family was amplified recently in the pearl millet genome and elements were found more abundant in wild than in domesticated plants. We found that they shared similarity in their terminal repeats with the previously described mPIF MITEs and that they are also present in other Pennisetum species, in maize and more distantly related grasses. The Tuareg family may be part of MITEs activated by PIF-like transposases and it could have been mobile since pearl millet domestication. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users. O. Robin contributed the FISH and fiber-FISH hybridizations.     

Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife

There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called ‘adverse outcome pathway’ (AOP) constructs. The AOP approach provides a framework for organizing information at the chemical and biological level, allowing evidence from both in silico and in vitro studies to be rationally combined to fill gaps in knowledge concerning toxicological events. Fundamental to this new paradigm is a greater understanding of the mechanisms of toxicity and, in particular, where these mechanisms may be conserved across taxa, such as between model animals and related wild species. This presents an opportunity to make predictions across diverse species, where empirical data are unlikely to become available as is the case for most species of wildlife.     

Acetylene reduction activity of pearl millet inbred lines grown in soil

Pearl millet inbred lines previously selected for differences in acetylene reduction activity (ARA) in seedling agar tubes were found to support low soil ARA. Lines selected for high ARA gave better performance than lines selected for low ARA. None of the high ARA lines was found to approach the ARA of alfalfa with their average rates over 40 fold lower.     

The role of matrix proteins in the control of nacreous layer deposition during pearl formation

To study the function of pearl oyster matrix proteins in nacreous layer biomineralization in vivo, we examined the deposition on pearl nuclei and the expression of matrix protein genes in the pearl sac during the early stage of pearl formation. We found that the process of pearl formation involves two consecutive stages: (i) irregular calcium carbonate (CaCO(3)) deposition on the bare nucleus and (ii) CaCO(3) deposition that becomes more and more regular until the mature nacreous layer has formed on the nucleus. The low-expression level of matrix proteins in the pearl sac during periods of irregular CaCO(3) deposition suggests that deposition may not be controlled by the organic matrix during this stage of the process. However, significant expression of matrix proteins in the pearl sac was detected by day 30-35 after implantation. On day 30, a thin layer of CaCO(3), which we believe was amorphous CaCO(3), covered large aragonites. By day 35, the nacreous layer had formed. The whole process is similar to that observed in shells, and the temporal expression of matrix protein genes indicated that their bioactivities were crucial for pearl development. Matrix proteins controlled the crystal phase, shape, size, nucleation and aggregation of CaCO(3) crystals.     

The past, present, and future of embryo selection in in vitro fertilization: Frontiers in Reproduction Conference

Assisted reproductive technology (ART) has been recognized for its success in treating infertility, a condition that affects 15 percent of couples in the United States. The most popular option is in vitro fertilization (IVF), which relies on embryo culture, selection, and transfer for implantation, with the ultimate aim of pregnancy. Previous embryo selection methods relied on morphological factors to select for greatest viability. At Yale's Frontiers in Reproduction Conference on April 29, 2011, at the New Haven Lawn Club, Dr. Denny Sakkas of Yale's Department of Obstetrics, Gynecology, and Reproductive Sciences presented a paradigm shift: using morphological factors along with metabolic, protein, and genetic markers in culture media to enhance embryo selection and IVF success rates.     

In vitro Osteogenic impulse effect of Dexamethasone on periodontal ligament stem cells

Periodontium is a complex organ composed of mineralized epithelial and connective tissue. Dexamethasone could stimulateproliferation of osteoblast and fibroblasts. This study aimed to assess the osteogenic effect of dexamethasone on periodentalligament (PDL) stem cells. PDL stem cells were collected from periodontal ligament tissue of root of extracted premolar of youngand healthy people. The stem cells were cultured in α-MEM Medium in three groups, one group with basic medium contains (α-MEM and FBS 10 % and 50 mmol of β_ gelisrophosphat and L_ ascorbic acid µg/ml), the second group: basic medium withdexamethasone and the third one: basic medium without any osteogenic stimulant. Mineralization of cellular layer was analyzedwith Alizarin red stain method. Osteogenic analysis was done by Alkaline phosphates and calcium test. These analysis indicatedthat the amount of intra-cellular calcium and alkaline phosphates in the Dexamethasone group was far more than the control andbasic group (P<0.05). The results of Alizarin red stain indicated more mineralization of cultured cells in Dexamethasone group(P<0.05). The study results showed that Dexamethasone has significant osteogenic effect on PDL stem cells and further studies arerecommended to evaluate its effect on treatment of bone disorders.     

Alfalfa (Medicago sativa) Somatic Embryogenesis: Genetic Control and Introduction of Favourable Alleles into Elite Argentinean Germplasm

The objectives of this work were to isolate regenerative genotypes from the alfalfa Canadian cultivar Rambler to perform the genetic analysis of somatic embryogenesis in this species and to introgress regeneration favourable alleles into Argentinean alfalfa elite germplasm. For regeneration inheritance studies, greenhouse established plants from a cross between a Rambler derived regenerative clone and a non-regenerative Argentinean clone as well as self-pollinated progenies of these clones were analyzed. The results showed that somatic embryogenesis is under the control of two complementary genes. The introgression of somatic embryogenesis favourable alleles was performed using two populations derived from crosses between regenerative clones, obtained in the first step of this work, and non-regenerative clones of Argentinean alfalfa elite populations. Twenty-seven plants obtained through this process showed somatic embryogenesis ability. Two of them, designated as INTA R1 and INTA R2, exhibited a high regeneration capacity as well as high regeneration multiplicity. Our results demonstrate that Rambler derived somatic embryogenesis favourable alleles are successfully expressed in Argentinean elite alfalfa genetic background rendering it suitable for tissue culture-based breeding methodologies.     

An in vitro perspective on the molecular mechanisms underlying mutant huntingtin protein toxicity

Huntington''s disease (HD) is a devastating neurodegenerative disorder whose main hallmark is brain atrophy. However, several peripheral organs are considerably affected and their symptoms may, in fact, manifest before those resulting from brain pathology. HD is of genetic origin and caused by a mutation in the huntingtin gene. The mutated protein has detrimental effects on cell survival, but whether the mutation leads to a gain of toxic function or a loss of function of the altered protein is still highly controversial. Most currently used in vitro models have been designed, to a large extent, to investigate the effects of the aggregation process in neuronal-like cells. However, as the pathology involves several other organs, new in vitro models are critically needed to take into account the deleterious effects of mutant huntingtin in peripheral tissues, and thus to identify new targets that could lead to more effective clinical interventions in the early course of the disease. This review aims to present current in vitro models of HD pathology and to discuss the knowledge that has been gained from these studies as well as the new in vitro tools that have been developed, which should reflect the more global view that we now have of the disease.     

Effect of crop residues on root growth and phosphorus acquisition of pearl millet in an acid sandy soil in Niger

The effect of long-term (1983–1988) applications of crop residues (millet straw, 2–4 t ha^-1 yr^–1) and/or mineral fertilizer (30 kg N, 13 kg P and 25 kg K ha^-1 yr^-1) on uptake of phosphorus (P) and other nutrients, root growth and mycorrhizal colonization of pearl millet (Pennisetum glaucum L.) was examined for two seasons (1987 and 1988) on an acid sandy soil in Niger. Treatments of the long-term field experiment were: control (–CR–F), mineral fertilizer only (–CR+F), crop residues only (+CR–F), and crop residues plus mineral fertilizer (+CR+F).In both years, total P uptake was similar for +CR–F and –CR+F treatments (1.6–3.5 kg P ha^-1), although available soil P concentration (Bray I P) was considerably lower in +CR–F (3.2 mg P kg^-1 soil) than in –CR+F (7.4) soil. In the treatments with mineral fertilizers (–CR+F; +CR+F), crop residues increased available soil P concentrations (Bray I P) from 7.4 to 8.9 mg kg^-1 soil, while total P uptake increased from 3.6 to 10.6 kg P ha^-1. In 1987 (with 450 mm of rainfall), leaf P concentrations of 30-day-old millet plants were in the deficiency range, but highest in the +CR+F treatment. In 1988 (699 mm), leaf P concentrations were distinctly higher, and again highest in the +CR+F treatment. In the treatments without crop residues (–CR–F; –CR+F), potassium (K) concentrations in the leaves indicated K deficiency, while application of crop residues (+CR–F; +CR+F) substantially raised leaf K concentrations and total K uptake. Leaf concentrations of calcium (Ca) and magnesium (Mg) were hardly affected by the different treatments.In the topsoil (0–30 cm), root length density of millet plants was greater for +CR+F (6.5 cm cm^-3) than for +CR–F (4.5 cm cm^-3) and –CR+F (4.2 cm cm^-3) treatments. Below 30 cm soil depth, root length density of all treatments declined rapidly from about 0.6 cm cm^-3 (30–60 cm soil depth) to 0.2 cm cm^-3 (120–180 cm soil depth). During the period of high uptake rates of P (42–80 DAP), root colonization with vesicular-arbuscular mycorrhizal (VAM) fungi was low in 1987 (15–20%), but distinctly higher in 1988 (55–60%). Higher P uptake of +CR+F plants was related to a greater total root length in 0–30 cm and also to a higher P uptake rate per unit root length (P influx). Beneficial effects of crop residues on P uptake were primarily attributed to higher P mobility in the soil due to decreased concentrations of exchangeable Al, and enhancement of root growth. In contrast, the beneficial effect of crop residues on K uptake was caused by direct K supply with the millet straw.     

Effect of A1 cytoplasm on the combining ability for smut severity in pearl millet

Among the various available sources of male-sterile cytoplasm in pearl millet [Pennisetum glaucum (L.) R.Br.], the A₁ source has been exploited the most for the breeding of commercial F₁ hybrids. The effect of this source on the combining ability (CA) for smut severity was studied since it is the CA that determines the performance of hybrids. The effect was estimated by comparing the CA estimates of 5 pairs of lines and 35 pairs of crosses with and without A₁ cytoplasm. The cytoplasm showed either a significantly desirable or at least no adverse effect on the CA of 4 out of the 5 line pairs and 56 out of 70 pairs of comparison of crosses in two environments. The differential effect of cytoplasm in some pairs might be due to its interaction with nuclear genes. These results further substantiated that the A₁ cytoplasm is not linked with increased smut severity in pearl millet hybrids.     

Genetic analysis of auditory neuropathy spectrum disorder in the Korean population

Auditory neuropathy spectrum disorder (ANSD) is caused by dys-synchronous auditory neural response as a result of impairment of the functions of the auditory nerve or inner hair cells, or synapses between inner hair cells and the auditory nerve. To identify a causative gene causing ANSD in the Korean population, we conducted gene screening of the OTOF, DIAPH3, and PJVK genes in 19 unrelated Korean patients with ANSD. A novel nonsense mutation (p.Y1064X) and a known pathogenic mutation (p.R1939Q) of the OTOF gene were identified in a patient as compound heterozygote. Pedigree analysis for these mutations showed co-segregation of mutation genotype and the disease in the family, and it supported that the p.Y1064X might be a novel genetic cause of autosomal recessive ANSD. A novel missense variant p.K1017R (c.3050A>G) in the DIAPH3 gene was also identified in the heterozygous state. In contrast, no mutation was detected in the PJVK gene. These results indicate that no major causative gene has been reported to date in the Korean population and that pathogenic mutations in undiscovered candidate genes may have an effect on ANSD.     

Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database

Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.     

Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D''Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D''Urville birds among extant LSK. The N_e/N_C ratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size.