A relatively light, highly bino-like dark matter in the Z3Z_3-symmetric NMSSM and recent LHC searches

A highly bino-like Dark Matter (DM), which is the Lightest Supersymmetric Particle (LSP), could be motivated by the stringent upper bounds on the DM direct detection rates. This is especially so when its mass is around or below 100 GeV for which such a bound tends to get most severe. Requiring not so large a higgsino mass parameter, that would render the scenario reasonably natural, prompts such a bino-like state to be relatively light. In the Minimal Supersymmetric Standard Model (MSSM), in the absence of comparably light scalars, such an excitation, if it has to be a thermal relic, is unable to meet the stringent experimental upper bound on its abundance unless its self-annihilation hits a funnel involving either the $Z$-boson or the Standard Model (SM)-like Higgs boson. We demonstrate that, in such a realistic situation, a highly bino-like DM of the popular $Z_3$-symmetric Next-to-Minimal Supersymmetric Standard Model (NMSSM) is viable over an extended range of its mass, from our targeted maximum in the vicinity of the mass of the top quark down to about 30 GeV. This is facilitated by the presence of comparably light singlet-like states that could serve as funnel (scalars) and/or coannihilating (singlino) states even as the bino-like LSP receives a minimal (but optimal) tempering triggered by suitably light higgsino states that, in the first place, evade stringent lower bounds on their masses that can be derived from the Large Hadron Collider (LHC) experiments only in the presence of a lighter singlino-like state. An involved set of blind spot conditions is derived for the DM direct detection rates by considering for the very first time the augmented system of neutralinos comprising of the bino, the higgsinos and the singlino which highlights the important roles played by the NMSSM parameters $\lambda$ and $\tan\beta$ in delivering a richer phenomenology.Comment: 70 pages, 16 figures and 3 table

A systematic review: efficacy of botulinum toxin in walking and quality of life in post-stroke lower limb spasticity.

BACKGROUND: Improved walking is one of the highest priorities in people living with stroke. Post-stroke lower limb spasticity (PSLLS) impedes walking and quality of life (QOL). The understanding of the evidence of improved walking and QOL following botulinum toxin (BoNTA) injection is not clear. We performed a systematic review of the randomized control trials (RCT) to evaluate the effectiveness of BoNTA injection on walking and QOL in PSLLS. METHODS: We searched PubMed, Web of Science, Embase, CINAHL, ProQuest Thesis and Dissertation checks, Google Scholar, WHO International Clinical Trial Registry Platform, ClinicalTrials.gov , Cochrane, and ANZ and EU Clinical Trials Register for RCTs looking at improvement in walking and QOL following injection of BoNTA in PSLLS. The original search was carried out prior to 16 September 2015. We conducted an additional verifying search on CINHAL, EMBASE, and MEDLINE (via PubMed) from 16 September 2015 to 6 June 2017 using the same clauses as the previous search. Methodological quality of the individual studies was critically appraised using Joanna Briggs Institute's instrument. Only placebo-controlled RCTs looking at improvement in walking and QOL were included in the review. RESULTS: Of 2026 records, we found 107 full-text records. Amongst them, we found five RCTs qualifying our criteria. No new trials were found from the verifying search. Two independent reviewers assessed methodological validity prior to inclusion in the review using Joanna Briggs Institute's appraisal instrument. Two studies reported significant improvement in gait velocity (p = 0.020) and < 0.05, respectively. One study showed significant improvement in 2-min-walking distance (p < 0.05). QOL was recorded in one study without any significant improvement. Meta-analysis of reviewed studies could not be performed because of different methods of assessing walking ability, small sample size with large confidence interval and issues such as lack of power calculations in some studies. Findings from our systematic and detailed study identify the need for a well-designed RCT to adequately investigate the issues highlighted. CONCLUSIONS: This review could not conclude there was sufficient evidence to support or refute improvement on walking or QOL following BoNTA injection. Reasons for this are discussed, and methods for future RCTs are developed

Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe ‘‘domestication bottleneck’’ during pigeonpea domestication

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago

Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor

Chickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea\u27s B locus that conditions flower and seed colors, orthologous to Mendel\u27s A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

<p>Abstract</p> <p>Background</p> <p>Pigeonpea [<it>Cajanus cajan </it>(L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.</p> <p>Results</p> <p>In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped <it>in silico </it>identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.</p> <p>Conclusion</p> <p>We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus <it>Cajanus</it>. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.</p

Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during pigeonpea domestication

Not Available

Not AvailablePaucity of polymorphic molecular markers in pigeonpea, Cajanus cajan (L.) Millsp., has been a major limiting factor in application of molecular tools for its genetic improvement. As the development of microsatellite markers requires considerable time, expertise and research infrastructure, transfer of markers from other related genera offers an alternative option to increase the number of available markers. Since microsatellite sequences are conserved across Fabaceae taxa, transferability of 100 chickpea (Cicer arietinum L.)-specific SSR markers was studied in two genotypes each of five wild and one cultivated species of Cajanus. The results revealed a significant transferability (46%) of chickpea microsatellites to Cajanus. In cultivated pigeonpea, chickpea-specific SSRs showed 38–39% transferability, while among wild Cajanus species, it ranged from 26% in Cajanus sericeus ICP 15760 to 40% in C. sericeus ICP 15761. The transferable primers exhibited extensive polymorphism in Cajanus with an average number of 4.11 alleles per marker. High level of polymorphism exhibited by chickpea microsatellite markers in the present study indicates their usefulness in diversity analysis, mapping agronomically important traits and marker-assisted breeding in pigeonpea.Not Availabl

Development of EST derived microsatellite markers in chickpea and their validation in diversity analysis

55-58Microsatellites are widely used as genetic markers because they are co-dominant, multi-allelic, easily scorable and highly polymorphic. In order to enhance availability of genomic resources, microsatellite loci were identified from chickpea (Cicer arietinum L.), the third most important grain legume in the world. A total of 20 SSR markers were developed from EST clones of wilt resistant cultivar (JG 315) of chickpea. Chickpea varieties (15) were analyzed for genetic diversity with these markers, which produced a total of 35 alleles with a mean of 1.5 alleles per primer. About 5 markers were polymorphic in the selected genotypes and observed heterozygosity ranged from 0.12 to 0.87 with an average of 0.32. These microsatellite markers will be useful in diversity analysis, mapping agronomically important traits and marker assisted breeding in chickpea