Multiple Crosses Research Articles

Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice.

Mendelian inheritance can ensure equal segregation of alleles from parents to offspring, which provides fundamental basis for genetics and molecular biology. Segregation distortion (SD) leads to preferential transmission of certain alleles from generation to generation. Such violation of Mendelian genetic principle is often accompanied by reproductive isolation and eventually speciation. Although SD is observed in a wide range of species from plants to animals, genome-wide dissection of such biased transmission of gametes is rare. Using nine inter-subspecific rice crosses, a genome-wide screen for SD loci is performed, which reveals 61 single-locus quantitative trait loci and 194 digenic interactions showing distorted transmission ratio, among which 24 new SD loci are identified. Biased transmission of alleles is observed in all nine crosses, suggesting that SD exists extensively in rice populations. 72.13% distorted regions are repeatedly detected in multiple populations, and the most prevalent SD hotspot that observed in eight populations is mapped to chromosome 3. Xian alleles are transmitted at higher frequencies than geng alleles in inter-subspecific crosses, which change the genetic composition of the rice populations. Epistatic interaction contributes significantly to the deviation of Mendelian segregation at the whole-genome level in rice, which is distinct from that in animals. These results provide an extensive archive for investigating the genetic basis of SD in rice, which have significant implications in understanding the reproductive isolation and formation of inter-subspecific barriers during the evolution.

Power and precision of QTL mapping in simulated multiple porcine F2 crosses using whole-genome sequence information

BackgroundDuring the last two decades, many QTL (quantitative trait locus) mapping experiments in pigs have been conducted using F2 crosses established from two outbred founder breeds. The founder breeds were frequently chosen from the Asian and European type breeds. A combination of next-generation sequencing, SNP (single nucleotide polymorphism) genotyping technology using SNP-chips, and genotype imputation techniques, can be used to infer the sequence information of all F2 individuals in a cost-effective way. The aim of the present simulation study was to analyze the power and precision of genome-wide association studies (GWASs) with whole-genome sequence data in several types of F2 crosses, including pooled crosses.MethodsBased on a common historical population, three breeds representing two European type breeds (EU1 and EU2) and one Asian type breed (AS) were simulated. Two F2 designs of 500 individuals each were simulated. The cross EU1xEU2 (ASxEU2) was simulated using the phylogenetically closely related breeds EU1 and EU2 (or distantly related breeds AS and EU2) as the founder breeds. The simulated genomes comprised ten chromosomes, each with a length of 1 Morgan and whole-genome sequence information. A polygenic trait with a heritability of 0.5, which was affected by approximately 20 QTL per Morgan, was simulated. GWASs were conducted using single marker mixed linear models, either within the crosses or in their pooled datasets. Additionally, the studies were conducted in the breed EU2, which was a founder breed in both simulated crosses.ResultsThe power to map QTL was high (low) in the ASxEU2 (EU1xEU2) cross and was highest when the data of both crosses were analyzed jointly. By contrast, the mapping precision was the highest in the EU1xEU2 cross. Pooling data led to a precision that was in between the precision of the EU1xEU2 cross and the ASxEU2 cross. A higher mapping precision was observed for QTL segregating within a founder breed.ConclusionsThese results suggest that the existing F2 crosses are promising databases for QTL mapping when the founder breeds are closely related or several crosses can be pooled. This conclusion is particularly applicable for QTL that segregate in a founder breed.

Registration of Sugar Beet Germplasm Lines CN921‐515 and CN921‐516 with Sugar Beet Cyst Nematode Resistance from Beta vulgaris subsp. maritima

CN921‐515 (Reg. No. GP‐295, PI 669447) and CN921‐516 (Reg. No. GP‐296, PI 669448) sugar beet (Beta vulgaris L.) germplasm lines, with sugar beet cyst nematode (SBCN) resistance derived from Beta vulgaris subsp. maritima L. (Bvm), were developed and released by the USDA‐ARS at Salinas, CA, in cooperation with the Beet Sugar Development Foundation in Denver, CO. CN921‐515 and CN921‐516 are multigerm, green hypocotyl, self‐fertile, partially inbred lines extracted from genetic‐male‐sterile facilitated, random‐mated lines. Greenhouse SBCN screening of individual plants and progeny tests indicate each is likely homozygous resistant. CN921‐306 is the progenitor population and was developed from multiple composite crosses involving >40 Bvm accessions. Therefore, the original wild beet accession that contributed sugar beet cyst nematode resistance to these lines is not known, nor are the allelic relationships with recently released CN12‐446, CN12‐770, and CN72‐652. CN921‐515 and CN921‐516 have a higher frequency of SBCN resistance (higher number of resistant individuals per line) than CN921‐306. CN921‐515 and CN921‐516 also have an increased number of rhizomania‐resistant individuals compared with CN921‐306.

Spectral Control of Near-Field Thermal Radiation With Periodic Cross Resonance Metasurfaces

Near-field thermal spectra can be engineered using periodic cross resonance metasurfaces. Structures consisting of single crosses, double crosses, and multiple crosses are proposed to control the spectral heat flux from narrow band to broadband with the Fabry-Perot-cavity-like effect and the interaction between the emitter and receiver. Radiation peaks originating from the cross structures split into two adjacent peaks in the near-field, due to the separate contributions of s- and p-polariton modes. Their frequency can be manipulated by adjusting the length of the crosses. Multiple radiation peaks can be generated by double crosses, and due to the strong coupling of resonance modes, multiple crosses can yield a broadband thermal spectrum ranging from 100-180 THz, with the total heat flux two orders of magnitude above the blackbody limit. The inherent physical mechanisms are illustrated by analyzing the energy transmission coefficients of the cross structures. The features of the radiation peaks and spectra are robust to the change of the gap distance or the temperature, which is advantageous for both the experimental design and fabrication of thermal radiation devices.

Combining ability analysis for yield and yield attributing traits in interspecific (G. hirsutum L. X G. barabdense L.) hybrids of cotton

Combining ability studies were carried out in interspecific (G. hirsutum L. X G. barabdense L.) hybrids of cotton for plant height, number of monopodia, number of sympodia, number of bolls per plant, boll weight, lint index, seed index, ginning out turn and seed cotton yield by following the line x tester analysis, involving 17 hirsutum lines and three barbadense testers with their 51 hybrids. The analysis revealed predominance of non-additive gene action for most of the characters except for number of monopodia and number of sympodia. This suggests the possibility of exploiting heterosis in the present material. Superior parents HBS-1, FQT-37 and HBS-146 in lines while BCS-23 in testers are having high gca effects for yield and its components and can be used to develop multiple crosses leading to further selection. Top five cross combinations viz., FQT-37 X SB-YF-425, 543403A03N106 X BCS-23, CSHH-243M X BCS-23, HBS-1 X Suvin and HAG-1055 X SB-YF-425 exhibited high mean value with high sca effects for seed cotton yield. These crosses were found to involve at least one parent with high gca effect and the other parent having either high or low gca effect indicating the involvement of additive as well as non-additive gene action operating in these crosses except one cross where both the parents having high sca effects indicating the involvement of additive gene action.

Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient

The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barriers. Spatial expansion of the currently most widespread “albipes” mtDNA clade was followed by population fragmentation, lineage sorting and again by hybridization and mtDNA introgression. Comparison of this genetic structure to other Ethiopian endemic taxa highlight the geographical areas of special conservation concern, where more detailed biodiversity studies should be carried out to prevent many endemic taxa from going extinct even before they are recognized.

High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population.

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0–34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

Genetic and nongenetic factors associated with milk color in dairy cows

Milk color is one of the sensory properties that can influence consumer choice of one product over another and it influences the quality of processed dairy products. This study aims to quantify the cow-level genetic and nongenetic factors associated with bovine milk color traits. A total of 136,807 spectra from Irish commercial and research herds (with multiple breeds and crosses) were used. Milk lightness (Lˆ*), red-green index (aˆ*) and yellow-blue index (bˆ*) were predicted for individual milk samples using only the mid-infrared spectrum of the milk sample. Factors associated with milk color were breed, stage of lactation, parity, milking-time, udder health status, pasture grazing, and seasonal calving. (Co)variance components for Lˆ*,aˆ*, and bˆ* were estimated using random regressions on the additive genetic and within-lactation permanent environmental effects. Greater bˆ* value (i.e., more yellow color) was evident in milk from Jersey cows. Milk Lˆ* increased consistently with stage of lactation, whereas aˆ* increased until mid lactation to subsequently plateau. Milk bˆ* deteriorated until 31 to 60 DIM, but then improved thereafter until the end of lactation. Relative to multiparous cows, milk yielded by primiparae was, on average, lighter (i.e., greater Lˆ*), more red (i.e., greater aˆ*), and less yellow (i.e., lower bˆ*). Milk from the morning milk session had lower Lˆ*,aˆ*, and bˆ* Heritability estimates (±SE) for milk color varied between 0.15 ± 0.02 (30 DIM) and 0.46 ± 0.02 (210 DIM) for Lˆ*, between 0.09 ± 0.01 (30 DIM) and 0.15 ± 0.02 (305 DIM) for aˆ*, and between 0.18 ± 0.02 (21 DIM) and 0.56 ± 0.03 (305 DIM) for bˆ* For all the 3 milk color features, the within-trait genetic correlations approached unity as the time intervals compared shortened and were generally <0.40 between the peripheries of the lactation. Strong positive genetic correlations existed between bˆ* value and milk fat concentration, ranging from 0.82 ± 0.19 at 5 DIM to 0.96 ± 0.01 at 305 DIM and confirming the observed phenotypic correlation (0.64, SE = 0.01). Results of the present study suggest that breeding strategies for the enhancement of milk color traits could be implemented for dairy cattle populations. Such strategies, coupled with the knowledge of milk color traits variation due to nongenetic factors, may represent a tool for the dairy processors to reduce, if not eliminate, the use of artificial pigments during milk manufacturing.

High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis.

Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. In the present study, we utilize recombinant inbred lines (RILs) derived from indica-japonica hybridization to analyze the effect factors of rice quality derived from genetic factors, which contain both regulatory genes concerning rice quality and genetic backgrounds' random introduction frequency coming from indica (Di value), and the improvement strategy was further discussed. The regulatory genes involved in amylase content (Wx) and nitrogen utilization efficiency (NRT1.1B) were the major factors affecting the amylose content (AC) and protein content (PC) in RILs, respectively. Both the Di value and the major grain width gene (GS5) had regulatory effects on milled rice width (MRW) in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree (C), Di value had a further impact on head rice rate (HR), which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by backcrossing or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection.

Abstract 204: Prioritizing Genome-Wide Association Study Lipid Loci With Global Gene Networks

Large genome-wide association studies (GWAS) conducted in humans by the Global Lipids Genetics Consortium (GLGC) have identified more than 150 genome-wide significant loci that are associated with variation in plasma lipid levels (cholesterol, LDL/HDL-cholesterol, and triglycerides). Some loci contain genes with well-described roles in lipid metabolism, such as CETP , LDLR , and APOB ; however, for many genome-wide significant loci, there is no clear causal gene. To test the hypothesis that lipid genes in the liver are co-regulated, we constructed global co-expression gene networks from genome-wide gene expression data obtained from the livers of multiple independent mouse genetic crosses. All together, we constructed global gene networks from eight distinct studies, representing more than 800 unique mice of diverse genetic backgrounds. For all studies analyzed, we identified a module (or sub-network) of genes that is significantly enriched (p&lt;1x10 -15 ) functionally for cholesterol biosynthesis and metabolism genes. This module ranges in size from 70 to 824 genes across the eight studies and contains all genes involved in the cholesterol biosynthesis pathway ( Acat2, Hmgcs2, Hmgcr, Lss, Sc5d, etc. ). This module also contains many genes involved in the regulation of cholesterol metabolism, such as Ldlr , Pcsk9 , and Insig1 . Because of the significant enrichment of cholesterol genes in this module, we have begun to cross-reference all genes in the module against the GLGC lipid GWAS data. Through this analysis, we have identified genes of unknown function that are clearly located within genome-wide significant lipid loci as well as sub-threshold (suggestive significant) lipid loci. Among the genes we identified was Sestrin1 , which was located within a clear sub-threshold locus associated with plasma cholesterol (rs12206606; p=1.4 x 10 -5 ). In conclusion, our studies provide a framework to identify causal genes within reported lipid GWAS loci as well as to identify novel sub-threshold loci associated with variations in lipids among humans. We illustrate the approach by identifying Sestrin1 within a sub-threshold locus associated with plasma cholesterol levels and show that Sestrin1 is transcriptionally regulated in the liver by dietary cholesterol.

Genetic analysis of yield and its biometric traits in castor (Ricinus communis L.)

The genetics of seed yield and its components was studied in castor (Ricinus communis L.) utilizing three crosses viz., AKC-1 x RG1636 (Cross - I); Aruna x RG1636 (Cross-II) and AKD-1 x RG1636 (Cross-III) through generation mean analysis. The additive-dominance model was found to be adequate for days to maturity of primary spikes in cross II (Aruna x RG1636) indicating the absence on non- allelic interactions. Additive (d) gene actions along with epistatic gene interactions were found to be significant for effective length of secondary spikes, oil content in the cross I (AKC-1 x RG1636); total number of capsules, 100 seed weight in the cross III (AKD-1 x RG1636), while rest of the characters were found to be governed by non additive gene actions. The classification of gene actions showed the importance of duplicate type of gene action for most of the characters in all the three crosses. Breeding procedures involving either multiple crosses or biparental crosses may be resorted to get transgressive segregants.

Genetic Mapping by Bulk Segregant Analysis in Drosophila: Experimental Design and Simulation-Based Inference.

Identifying the genomic regions that underlie complex phenotypic variation is a key challenge in modern biology. Many approaches to quantitative trait locus mapping in animal and plant species suffer from limited power and genomic resolution. Here, I investigate whether bulk segregant analysis (BSA), which has been successfully applied for yeast, may have utility in the genomic era for trait mapping in Drosophila (and other organisms that can be experimentally bred in similar numbers). I perform simulations to investigate the statistical signal of a quantitative trait locus (QTL) in a wide range of BSA and introgression mapping (IM) experiments. BSA consistently provides more accurate mapping signals than IM (in addition to allowing the mapping of multiple traits from the same experimental population). The performance of BSA and IM is maximized by having multiple independent crosses, more generations of interbreeding, larger numbers of breeding individuals, and greater genotyping effort, but is less affected by the proportion of individuals selected for phenotypic extreme pools. I also introduce a prototype analysis method for simulation-based inference for BSA mapping (SIBSAM). This method identifies significant QTL and estimates their genomic confidence intervals and relative effect sizes. Importantly, it also tests whether overlapping peaks should be considered as two distinct QTL. This approach will facilitate improved trait mapping in Drosophila and other species for which hundreds or thousands of offspring (but not millions) can be studied.

Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an “island model” inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic selection in autogamous crops, especially bringing long-term improvement.

Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm.

BackgroundThe commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil.ResultsIn this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 – 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses.ConclusionsThe candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2607-4) contains supplementary material, which is available to authorized users.

Identification and Quantification of a Toxigenic and Non-Toxigenic Aspergillus flavus Strain in Contaminated Maize Using Quantitative Real-Time PCR.

Aflatoxins, which are produced by Aspergillus flavus, are toxic to humans, livestock, and pets. The value of maize (Zea mays) grain is markedly reduced when contaminated with aflatoxin. Plant resistance and biological control using non-toxin producing strains are considered effective strategies for reducing aflatoxin accumulation in maize grain. Distinguishing between the toxin and non-toxin producing strains is important in determining the effectiveness of bio-control strategies and understanding inter-strain interactions. Using polymorphisms found in the fungal rRNA intergenic spacer region (IGS) between a toxigenic strain of A. flavus (NRRL 3357) and the non-toxigenic strain used in the biological control agent Afla-Guard® (NRRL 21882), we developed a set of primers that allows for the identification and quantification of the two strains using quantitative PCR. This primer set has been used to screen maize grain that was inoculated with the two strains individually and co-inoculated with both strains, and it has been shown to be effective in both the identification and quantification of both strains. Screening of co-inoculated ears from multiple resistant and susceptible genotypic crosses revealed no significant differences in fungal biomass accumulation of either strain in the field tests from 2010 and 2011 when compared across the means of all genotypes. Only one genotype/year combination showed significant differences in strain accumulation. Aflatoxin accumulation analysis showed that, as expected, genotypes inoculated with the toxigenic strain accumulated more aflatoxin than when co-inoculated with both strains or inoculated with only the non-toxigenic strain. Furthermore, accumulation of toxigenic fungal mass was significantly correlated with aflatoxin accumulation while non-toxigenic fungal accumulation was not. This primer set will allow researchers to better determine how the two fungal strains compete on the maize ear and investigate the interaction between different maize lines and these A. flavus strains.

Combining ability studies for yield and yield contributing traits in rice (Oryza sativaL.)

The present study was conducted to estimate combining ability, gene action and proportional contribution of cross components in rice genotypes. Combining ability estimates were worked out through Line × Tester analysis of 25 hybrids developed by crossing five lines with five testers to know the genetic architecture of 10 physio-morphological traits. The analysis of variance of combining ability displayed variances of specific combining ability (SCA) and were higher in magnitude than the corresponding general combining ability (GCA) variances for all the traits under study which indicated preponderance of non-additive gene action governing these traits. Results of per se and gca effects of parents revealed that multiple crosses involving ADT 37, ADT (R) 47, TNAU Rice ADT49, FL478, Pokkali would be considered as invaluable sources of genetic materials. An outset on perusal of data for hybrids based on per se performance and high sca effects the hybrids viz., ADT 37 x Nonabokra, ADT37 x Pokkali, TNAU Rice ADT 49 x Nonabokra, ADT47x FL478, ADT 43 x Nonabokra and ADT 47 x CSR36 were good specific combiners for grain yield per plant and their components which could be used for exploitation of heterosis for yield.

Antiviral Protection via RdRP-Mediated Stable Activation of Innate Immunity.

For many emerging and re-emerging infectious diseases, definitive solutions via sterilizing adaptive immunity may require years or decades to develop, if they are even possible. The innate immune system offers alternative mechanisms that do not require antigen-specific recognition or a priori knowledge of the causative agent. However, it is unclear whether effective stable innate immune system activation can be achieved without triggering harmful autoimmunity or other chronic inflammatory sequelae. Here, we show that transgenic expression of a picornavirus RNA-dependent RNA polymerase (RdRP), in the absence of other viral proteins, can profoundly reconfigure mammalian innate antiviral immunity by exposing the normally membrane-sequestered RdRP activity to sustained innate immune detection. RdRP-transgenic mice have life-long, quantitatively dramatic upregulation of 80 interferon-stimulated genes (ISGs) and show profound resistance to normally lethal viral challenge. Multiple crosses with defined knockout mice (Rag1, Mda5, Mavs, Ifnar1, Ifngr1, and Tlr3) established that the mechanism operates via MDA5 and MAVS and is fully independent of the adaptive immune system. Human cell models recapitulated the key features with striking fidelity, with the RdRP inducing an analogous ISG network and a strict block to HIV-1 infection. This RdRP-mediated antiviral mechanism does not depend on secondary structure within the RdRP mRNA but operates at the protein level and requires RdRP catalysis. Importantly, despite lifelong massive ISG elevations, RdRP mice are entirely healthy, with normal longevity. Our data reveal that a powerfully augmented MDA5-mediated activation state can be a well-tolerated mammalian innate immune system configuration. These results provide a foundation for augmenting innate immunity to achieve broad-spectrum antiviral protection.

Diploid hybrid origin ofHippophaë gyantsensis(Elaeagnaceae) in the western Qinghai-Tibet Plateau

Homoploid hybrid speciation, the origin of a hybrid species without change in chromosome number, is currently considered to be a rare form of speciation. In the present study, we examined the phylogenetic origin of Hippophaë gyantsensis, a diploid species occurring in the western Qinghai–Tibet Plateau. Some of its morphological and molecular traits suggest a close relationship to H. rhamnoides ssp. yunnanensis while others indicate H. neurocarpa. We conducted phylogenetic analyses of sequence data of two maternally inherited chloroplast (cp) DNA fragments and the bi-parentally inherited nuclear ribosomal internal transcribed spacer (ITS) from 17 populations of H. gyantsensis, 15 populations of H. rhamnoides ssp. yunnanensis and 27 populations of H. neurocarpa across their distributional ranges, and modelled the niche differentiation of the three taxa. Multiple lines of evidence suggested that H. gyantsensis is a morphologically stable, genetically independent and ecologically distinct species. The inconsistent phylogenetic placements of the H. gyantsensis clade that comprised the dominant cpDNA haplotypes and ITS ribotypes suggested a probable diploid hybrid origin from multiple crosses between H. rhamnoides ssp. yunnanensis and H. neurocarpa. This tentative hypothesis is more parsimonious than alternative explanations according to the data available, although more evidence based on further testing is needed.

Comparative study on morphological and morphometric features of village chicken in Sri Lanka

A study was conducted in two selected sites (Anuradhapura and Puttlam districts) to phenotypic ally characterize various types of village chicken present in Sri Lanka. Qualitative traits such as characteristics of plumage, comb, shank, eye and earlobe, and body condition score were recorded with a full inventory of management conditions. Quantitative traits included body weight and linear morphometric measurements such as chest circumference, wing length, back length, breast width, keel length, pelvis width, shanklength and shank circumference. Seven distinct phenotypic groups could be identified as naked neck (NNC), long legged (LLC), crest/crown (CC), Giri raj (GRC), commercial crosses (ComC), frizzle feathered (FFC) and non-descript (NVC). NVC group included multiple crosses of other groups. Occurrence of different morphological features varied significantly (p Tropical Agricultural Research Vol. 26 (2): 261 – 273 (2015)