Distinct Parents Research Articles

Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil.

BackgroundWitches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm.ResultsWe developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’.ConclusionsWe combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.

Genetic analysis of rhizomatousness and its relationship with vegetative branching of recombinant inbred lines of Sorghum bicolor × S. propinquum.

Rhizomes, subterranean stems that grow horizontally, are a storage organ that is highly associated with overwintering and regrowth. This quantitative study aimed to discover genetic determinants of rhizomatousness, an important trait related to perenniality and invasiveness. A population of 161 individuals of a recombinant inbred line (RIL) derived from morphologically distinct parents, Sorghum bicolor and Sorghum propinquum, which segregates for rhizomatousness, was phenotyped and genetically mapped. Seven genomic regions influenced rhizomatousness in this population; four were "consensus" regions that correspond with previously detected quantitative trait loci (QTLs) in an F2 population of the same pedigree and with different levels of vegetative branching. Because rhizomatousness is a plastic trait that is greatly influenced by environment, overlap between regions discovered in the RIL and F2 populations validates the position and effect of QTLs. Correspondence with regions influencing vegetative branching indicates that some genes and biochemical pathways may influence both vegetative branching and rhizomatousness, while genes influencing only one trait may confer divergent aspects of development of these organs. Identifying genes conferring rhizomatousness and understanding their functions may provide opportunities to regulate plant growth for diverse applications. Increasing rhizomatousness may promote the productivity and perenniality of many grasses, especially biomass-dedicated crops, while decreasing rhizomatousness may improve monocarpic grain production and offer means to control many noxious weeds.

Overlay live video streaming with heterogeneous bitrate requirements

We study a streaming cloud formed by distributed proxies providing live video service to diverse users (e.g., smart TVs, PCs, tablets, mobile phones, etc.). The proxies form a push-based overlay network, with each proxy serving a certain video bitrate for users to join. To form a proxy overlay serving heterogeneous bitrates, we consider that the video is encoded into multiple MDC (Multiple-Description Coding) streams with the serving bitrate of proxy i being ki description streams. In order to effectively mitigate stream disruption due to node churns, proxy i also joins an additional ri redundant MDC streams (ri⩾0) in such a way that all the (ki+ri) streams are supplied by distinct parents. For live streaming, the critical issue is how to construct the parent-disjoint trees minimizing the assembly delay of the proxies.We present a realistic delay model capturing important system parameters and delay components, formulate the optimization problem and show that it is NP-hard. We propose a centralized algorithm which is useful for a centrally-managed network and serves as a benchmark for comparison (PADTrees-Centralized). For large network, we propose a simple and distributed algorithm which continuously reduces delay through overlay adaptation (PADTrees-Distributed). Through extensive simulation on real Internet topologies, we show that high stream continuity can be achieved with push-based trees in the presence of node churns. Our algorithms are simple and effective, achieving low loss and low delay.

Genetic analysis of vegetative branching in sorghum.

We identified quantitative trait loci influencing plant architecture that may be valuable in breeding of optimized genotypes for sustainable food and/or cellulosic biomass production, and advancing resilience to changing climates. We describe a 3-year study to identify quantitative trait loci (QTLs) for vegetative branching of sorghum in a recombinant inbred line population of 161 genotypes derived from two morphologically distinct parents, S. bicolor×S. propinquum. We quantify vegetative branching based on morphological position and physiological status. Different sets of QTLs for different levels of branching were identified. QTLs discovered on chromosomes 1, 3, 7 and 8 affect multiple vegetative branching variables, suggesting that these regions may contain genes that control general axillary meristem initiation. Other regions that only influence one vegetative branching trait could contain genes that influence developmental processes contributing to divergent patterns of plant architecture. We investigate the relationship between vegetative branching patterns and dry biomass, and conclude that tillers with mature panicles and immature secondary branches each show consistent positive correlation with dry biomass. Among 19 branching-related genes from rice, eight sorghum homologs of seven rice genes are in syntenic blocks within branching-related QTL likelihood intervals. Five of these eight genes are within 700kb of SNPs significantly associated with differences in branching in genome-wide association study of a diversity panel of 377 sorghum accessions, and three contain striking allelic variations between S. bicolor and S. propinquum that are likely to impact gene functions. Unraveling genetic determinants for vegetative branching may contribute to deterministic breeding of optimized genotypes for sustainable food and cellulosic biomass production in both optimal and marginal conditions, which are resilient to future climates that are more volatile and more stressful.

Heterosis profile of sunflower leaves: A label free proteomics approach

Heterosis is the superior performance of heterozygous F1-hybrid plants compared with their homozygous genetically distinct parents. The proteome of leaves of one sunflower hybrid and its parental inbred lines was analyzed by label free LC-MS/MS. A total of 1998 proteins were identified. Among them 38 proteins indicated heterosis pattern in hybrid compared with midparents. The results showed an increment of photosynthesis capacity, assimilation rate, nitrogen fixation, cell growth and reducing in some energy-consuming processes like protein production, response to stresses and respiration. These results suggest that heterosis mechanisms increase input energy of plant with reinforcement of carbon fixation pathway and reduction in consumed energy toward production of superior hybrid. This study could help to better elucidate what mechanisms are involved in heterosis of sunflower leaves and what happens at proteome level. The current work describes the first study in which gel-free shotgun proteomics was used to compare the proteome of leaves of one sunflower hybrid to its parental inbred lines. In this study 1998 proteins were identified from sunflower leaves with label free nano LC-MS/MS. The numbers of 38 proteins significantly showed heterosis pattern. The comparison between hybrid and parental inbred lines showed that hybrid vigor is actually linked by emphasizing the assimilation rate and low energy consumption.

Common and low-frequency variants associated with genome-wide recombination rate

Meiotic recombination contributes to genetic diversity by yielding new combinations of alleles. Individuals vary with respect to the genome-wide recombination counts in their gametes. Exploiting data resources in Iceland, we compiled a data set consisting of 35,927 distinct parents and 71,929 parent-offspring pairs. Within this data set, we called over 2.2 million recombination events and imputed variants with sequence-level resolution from 2,261 whole genome-sequenced individuals into the parents to search for variants influencing recombination rate. We identified 13 variants in 8 regions that are associated with genome-wide recombination rate, 8 of which were previously unknown. Three of these variants associate with male recombination rate only, seven variants associate with female recombination rate only and three variants affect both. Two are low-frequency variants with large effects, one of which is estimated to increase the male and female genetic maps by 111 and 416 cM, respectively. This variant, located in an intron, would not be found by exome sequencing.

Development of microsatellite markers in sweet passion fruit, and identification of length and conformation polymorphisms within repeat sequences

AbstractThe aim of this study was to construct and characterize an SSR‐enriched genomic library for Passiflora alata, a fruit species native to the Brazilian plateau and the eastern Amazon region. There is potential to improve this crop, as the fruit is attractive because of its pleasant aroma and flavour characteristics. Of 862 sequences, 391 (45%) were found to have SSRs. We identified 412 microsatellites: 69% were classified as perfect, 23% imperfect, 5% interrupted and 3% were compound microsatellites. The main types of repeat sequences were dinucleotide (62.5%) and trinucleotide (23%) repeats. It was possible to design 312 primer pairs, and 229 of them were synthesized and tested. The amplicons were electrophoresed using denaturing and non‐denaturing gels to screen for divergence between two phenotypically distinct parents of a mapping population of P. alata. Length and conformation polymorphisms within repeat sequences amounted to 35% and 28%, respectively. The importance of the development of SSR markers for sweet passion fruit and the effectiveness of the SSCP approach to increase the available number of polymorphic SSRs are discussed.

Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS

Heterosis is the superior performance of heterozygous F1-hybrid plants compared to their homozygous genetically distinct parents. Seminal roots are embryonic roots that play an important role during early maize (Zea mays L.) seedling development. In the present study the most abundant soluble proteins of 2-4cm seminal roots of the reciprocal maize F1-hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were quantified by label-free LC-MS/MS. In total, 1918 proteins were detected by this shot-gun approach. Among those, 970 were represented by at least two peptides and were further analyzed. Eighty-five proteins displayed non-additive accumulation in at least one hybrid. The functional category protein metabolism was the most abundant class of non-additive proteins represented by 27 proteins. Within this category 16 of 17 non-additively accumulated ribosomal proteins showed high or above high parent expression in seminal roots. These results imply that an increased protein synthesis rate in hybrids might be related to the early manifestation of hybrid vigor in seminal roots. In the present study a shot-gun proteomics approach allowed for the identification of 1917 proteins and analysis of 970 seminal root proteins of maize that were represented by at least 2 peptides. The comparison of proteome complexity of reciprocal hybrids and their parental inbred lines indicates an increased protein synthesis rate in hybrids that may contribute to the early manifestation of heterosis in seminal roots. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome.

Estimating selfing rates from reconstructed pedigrees using multilocus genotype data

Several methods have been developed to estimate the selfing rate of a population from a sample of individuals genotyped for several marker loci. These methods can be based on homozygosity excess (or inbreeding), identity disequilibrium, progeny array (PA) segregation or population assignment incorporating partial selfing. Progeny array-based method is generally the best because it is not subject to some assumptions made by other methods (such as lack of misgenotyping, absence of biparental inbreeding and presence of inbreeding equilibrium), and it can reveal other facets of a mixed-mating system such as patterns of shared paternity. However, in practice, it is often difficult to obtain PAs, especially for animal species. In this study, we propose a method to reconstruct the pedigree of a sample of individuals taken from a monoecious diploid population practicing mixed mating, using multilocus genotypic data. Selfing and outcrossing events are then detected when an individual derives from identical parents and from two distinct parents, respectively. Selfing rate is estimated by the proportion of selfed offspring in the reconstructed pedigree of a sample of individuals. The method enjoys many advantages of the PA method, but without the need of a priori family structure, although such information, if available, can be utilized to improve the inference. Furthermore, the new method accommodates genotyping errors, estimates allele frequencies jointly and is robust to the presence of biparental inbreeding and inbreeding disequilibrium. Both simulated and empirical data were analysed by the new and previous methods to compare their statistical properties and accuracies.

A Genetic Study of a Salix Germplasm Resource Reveals New Insights into Relationships Among Subgenera, Sections and Species

Genetic relationships among 154 genotypes, including 50 species, held within the UK National Willow Collection were analysed using nine primer combinations in an optimised fluorescent amplified fragment length polymorphism (AFLP®) protocol. The AFLP® data resolved relationships at all levels, from discriminating between closely related accessions to differentiating among majority of species, sections and subgenera. The neighbour-joining dendrogram split accessions into three major well-supported clusters, two of which comprised species of the subgenera Vetrix and Salix. Surprisingly, the third (98% bootstrap support) comprised only Salix triandra accessions. The genetic similarity (GS) between S. triandra and Salix or Vetrix was similar (0.39 and 0.40, respectively) and greater than the genetic similarity between Salix and Vetrix (GS = 0.57). Separate clustering of S. triandra is also supported by hierarchical analysis of molecular variance (AMOVA), that partitioned 31.4% of the total variance between these three groups, whereas only 16.3% was partitioned between the two subgenera. These results challenge all current classifications which assign S. triandra to subgenus Salix. Principal coordinate analysis gave corresponding results and facilitated interpretation of relationships among species within sections of the two subgenera, which are discussed. The study included 40 species which have been used in breeding, and the findings will facilitate the choice of parents and interpretation of the results of different crosses, on the basis of more accurate knowledge of genetic relationships. AFLPs® also detected identical genotypes (within the limits of AFLP® error) which should not be used as distinct parents in breeding programmes.

Co-inherited mutations of Fas and caspase-10 in development of the autoimmune lymphoproliferative syndrome

BackgroundAutoimmune lymphoproliferative syndrome (ALPS) is a rare inherited disorder characterized by defective function of Fas, autoimmune manifestations that predominantly involve blood cells, polyclonal accumulation of lymphocytes in the spleen and lymph nodes with lymphoadenomegaly and/or splenomegaly, and expansion of TCRαβ+ CD4/CD8 double-negative (DN) T cells in the peripheral blood. Most frequently, it is due to Fas gene mutations, causing ALPS type Ia (ALPS-Ia). However, other mutations, namely of the FasL gene (ALPS-Ib) and the caspase-10 gene (ALPS-II) are occasionally detected, whereas some patients do not present any known mutations (ALPS-III). Recently, mutations of the NRAS gene have been suggested to cause ALPS-IV.ResultsThis work reports two patients that are combined heterozygous for single nucleotide substitutions in the Fas and caspase-10 genes. The first patient carried a splice site defect suppressing allele expression in the Fas gene and the P501L substitution in caspase-10. The second had a mutation causing a premature stop codon (Q47X) in the Fas gene and the Y446C substitution in caspase-10. Fas expression was reduced and caspase-10 activity was decreased in both patients. In both patients, the mutations were inherited from distinct healthy parents.ConclusionThese data strongly suggest that co-transmission of these mutation was responsible for ALPS.

Quantitative trait loci mapped to single-nucleotide resolution in yeast

Identifying the genetic variation underlying quantitative trait loci remains problematic. Consequently, our molecular understanding of genetically complex, quantitative traits is limited. To address this issue directly, we mapped three quantitative trait loci that control yeast sporulation efficiency to single-nucleotide resolution in a noncoding regulatory region (RME1) and to two missense mutations (TAO3 and MKT1). For each quantitative trait locus, the responsible polymorphism is rare among a diverse set of 13 yeast strains, suggestive of genetic heterogeneity in the control of yeast sporulation. Additionally, under optimal conditions, we reconstituted approximately 92% of the sporulation efficiency difference between the two genetically distinct parents by engineering three nucleotide changes in the appropriate yeast genome. Our results provide the highest resolution to date of the molecular basis of a quantitative trait, showing that the interaction of a few genetic variants can have a profound phenotypic effect.

Labile trace elements in carbonaceous chondrites: A survey

We report radiochemical neutron activation analysis data for Co, Au, Ga, Rb, Sb, Ag, Se, Cs, Te, Zn, Cd, Bi, Tl, and In (ordered by increasing putative volatility in primary nebular processes) in 42 C2–C6 chondrites, all but three from Antarctica. From these and literature data for 19 additional chondrites, Cl‐normalized concentrations of the nine most volatile elements (Ag → In) are quite constant in most meteorites. Trace element trends in 39 Antarctic and 22 non‐Antarctic carbonaceous chondrites are similar: no evidence exists for substantial alteration by weathering of samples in Antarctica, nor do the data reflect modification by open‐system, parent body metamorphism at ≥ 500°C. Volatile element concentrations and siderophile ratios (Au/Co and Ga/Co) define continua which correlate at statistically significant levels. Carbonaceous chondrites sample not a few, compositionally distinct parents but rather a compositional continuum in which parent materials forming under more oxidizing conditions incorporated lesser complements of volatiles, essentially unfractionated from cosmic composition. This may well reflect the range of formation conditions (temperature, duration, and water/rock ratios) represented by oxygen isotope variations during preterrestrial aqueous alteration of parent materials.

Geochemical and structural studies of the Lamont seamounts: seamounts as indicators of mantle processes

A chain of seamounts located just west of the East Pacific Rise (EPR) axis at 09°55′N (herein called the Lamont seamounts) have been investigated using Sea MARC I and Sea Beam sonar surveys, “Alvin” submersible dives, deep-sea camera tows and dredging. The most recently active volcanic vents on the summits of these volcanoes are located at the periphery of each caldera or crater rim or at the margins of caldera floors. The distribution of recent volcanic vents and the morphology of the summit plateaus suggest the possible existence of ring fractures on these seamounts. Ring fractures could be important in focusing post-caldera collapse eruptions around summit craters and building summit plateaus. Structural and morphological data and the petrology of recovered lavas suggest that calderas in the Lamont seamounts probably formed by collapse associated with magma withdrawal into large, primary vertical magma conduit systems, rather than by repeated inflation/deflation cycles associated with steady-state shallow-level magma chambers. Calderas in the Lamont seamounts have evolved through coalescence of adjoining craters and the plan-view shape and morphology of each caldera suggest that primary magma conduits have migrated beneath the summit of each seamount through time. Compared to lavas from the adjacent EPR, the majority of Lamont seamount and cone lavas are more primitive, depleted in incompatible elements and compositionally heterogeneous. Variations in light rare earth elements relative to major elements (e.g. TiO 2, Na 2O/(Na 2O + CaO) ) and radiogenic isotopes cannot be ascribed to differences in the amount of partial melting of a single N-type MORB source. Rather it appears that Lamont seamount lavas were derived from heterogeneous mantle sources variably depleted in highly incompatible elements. Comparison with lavas from the adjacent ridge crest suggests that magma plumbing and ascent mechanisms beneath the Lamont seamounts are separate from those along the EPR. In particular seamount magmas appear to reflect near-primary melting events in the mantle whereas EPR lavas are the products of shallow-level crystallization and mixing in crustal magma chambers. Absence of long-lived magma chambers within the Lamont seamounts may account for the low level of hydrothermal activity observed throughout the chain. Furthermore, because of the tight control on sample location and the recovery of lavas having distinct parents from individual volcanoes as well as the Lamont chain as a whole, we propose that the scale of mantle chemical heterogeneities is less than 5 km.

Passive protection against rotavirus-induced diarrhea by monoclonal antibodies to surface proteins vp3 and vp7

Monoclonal antibodies directed against two rotavirus surface proteins (vp3 and vp7) as well as a rotavirus inner capsid protein (vp6) were tested for their ability to protect suckling mice against virulent rotavirus challenge. Monoclonal antibodies to two distinct epitopes of vp7 of simian rotavirus strain RRV neutralized RRV in vitro and passively protected suckling mice against RRV challenge. A monoclonal antibody directed against vp3 of porcine rotavirus strain OSU neutralized three distinct serotypes in vitro (OSU, RRV, and UK) and passively protected suckling mice against OSU, RRV, and UK virus-induced diarrhea. The role of vp3 in eliciting protection against heterotypic rotavirus challenge should be considered when developing a vaccine with cloned rotavirus genes. Alternatively, immunization with a reassortant rotavirus containing vp3 and vp7 from two antigenically distinct rotavirus parents might protect against diarrhea induced by two or more rotavirus serotypes.

The Germplasm and its Architecture.1

THE individuals of a generation die but life is transmitted to its suceessor through the exercise of the function of roduction. This handing on of the torch of life, in the more highly organised forms, consists in theunion of the gametes, egg and sperm, to form the zygote, the new in- dividual and the next generation, specific to the highest degree and embodying all the possibilities of individual development and of racial perpetuation. Each of the sexually distinct parents con- tributes but a single cell, so minute as to be far beyond the limits of the unaided eye, yet these gametes are the only material link between the generations, and across this, the narrowest of bridges, everything organic that one generation can receive from its predecessor must pass. The zygote exhibits none of these details of structure and of function which, when the individual has assumed its definitive form, will enable the observer to describe and to classify it, yet in this fertilised egg there must surely be something that predetermines much of the individual's future morphological, physiological, and psychological limitations.