Herbaceous Legume Encroachment Reduces Grass Productivity and Density in Arid Rangelands

Worldwide savannas and arid grasslands are mainly used for livestock grazing, providing livelihood to over a billion people. While normally dominated by perennial C-4 grasses, these rangelands are increasingly affected by the massive spread of native, mainly woody legumes. The consequences are often a repression of grass cover and productivity, leading to a reduced carrying capacity. While such encroachment by woody plants has been extensively researched, studies on similar processes involving herbaceous species are rare. We studied the impact of a sustained and massive spread of the native herbaceous legume Crotalaria podocarpa in Namibia's escarpment region on the locally dominant fodder grasses Stipagrostis ciliata and Stipagrostis uniplumis. We measured tussock densities, biomass production of individual tussocks and tussock dormancy state of Stipagrostis on ten 10 m x 10 m plots affected and ten similarly-sized plots unaffected by C. podocarpa over eight consecutive years and under different seasonal rainfalls and estimated the potential relative productivity of the land. We found the percentage of active Stipagrostis tussocks and the biomass production of individual tussocks to increase asymptotically with higher seasonal rainfall reaching a maximum around 300 mm while the land's relative productivity under average local rainfall conditions reached only 40% of its potential. Crotalaria podocarpa encroachment had no effect on the proportion of productive grass tussocks, but reduced he productivity of individual Stipagrostis tussocks by a third. This effect of C. podocarpa on grass productivity was immediate and direct and was not compensated for by above-average rainfall. Besides this immediate effect, over time, the density of grass tussocks declined by more than 50% in areas encroached by C. podocarpa further and lastingly reducing the lands carrying capacity. The effects of C. podocarpa on grass productivity hereby resemble those of woody encroachers. Therefore, against the background of global change, the spread of herbaceous legumes and the underlying patterns needs to be further investigated to develop adequate counter measures for a sustainable land use.DF

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

Abstract Background Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. Results A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. Conclusion BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.</p

Various types of primer design can be selected from the primer type pull-up combo-box, and corresponding parameter setting panels are placed below the sequence input box

Pre-analysis of input sequences can be performed before batch primer design.<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p

The picture shows the primer design results of sequence ID (rs16791736) for tetra-primer ARMS PCR

<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p

Any unwanted regions for primer design in sequences can be masked using a pair of "" to keep the sequence unchanged

Alternatively, the unwanted regions can be replaced with "Ns" (). The included region can be specified by one pair "{}" and only one included region can be masked.<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.

GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops

De Novo Pathogenic Variants in N-cadherin Cause a Syndromic Neurodevelopmental Disorder with Corpus Callosum, Axon, Cardiac, Ocular, and Genital Defects

International audienceCadherins constitute a family of transmembrane proteins that mediate calcium-dependent cell-cell adhesion. The extracellular domain of cadherins consists of extracellular cadherin (EC) domains, separated by calcium binding sites. The EC interacts with other cadherin molecules in cis and in trans to mechanically hold apposing cell surfaces together. CDH2 encodes N-cadherin, whose essential roles in neural development include neuronal migration and axon pathfinding. However, CDH2 has not yet been linked to a Mendelian neurodevelopmental disorder. Here, we report de novo heterozygous pathogenic variants (seven missense, two frameshift) in CDH2 in nine individuals with a syndromic neurodevelopmental disorder characterized by global developmental delay and/or intellectual disability, variable axon pathfinding defects (corpus callosum agenesis or hypoplasia, mirror movements, Duane anomaly), and ocular, cardiac, and genital anomalies. All seven missense variants (c.1057G>A [p.Asp353Asn]; c.1789G>A [p.Asp597Asn]; c.1789G>T [p.Asp597Tyr]; c.1802A>C [p.Asn601Thr]; c.1839C>G [p.Cys613Trp]; c.1880A>G [p.Asp627Gly]; c.2027A>G [p.Tyr676Cys]) result in substitution of highly conserved residues, and six of seven cluster within EC domains 4 and 5. Four of the substitutions affect the calcium-binding site in the EC4-EC5 interdomain. We show that cells expressing these variants in the EC4-EC5 domains have a defect in cell-cell adhesion; this defect includes impaired binding in trans with N-cadherin-WT expressed on apposing cells. The two frameshift variants (c.2563_2564delCT [p.Leu855Valfs∗4]; c.2564_2567dupTGTT [p.Leu856Phefs∗5]) are predicted to lead to a truncated cytoplasmic domain. Our study demonstrates that de novo heterozygous variants in CDH2 impair the adhesive activity of N-cadherin, resulting in a multisystemic developmental disorder, that could be named ACOG syndrome (agenesis of corpus callosum, axon pathfinding, cardiac, ocular, and genital defects)