Structural variation and the plant pan genomes

The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, consisting of both smaller insertion/deletions, mostly due to recent insertions of transposable elements, and of larger insertion/deletion similar to those termed in humans Copy Number Variants (CNVs). These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome

Effect of the dam’s feeding regimen on the meat quality of light suckling lambs

In order to verify the effect of the introduction of concentrates without GMO risk and at low aflatoxin risk in the diet of grazing milk ewes on the quanti-qualitative production of meat of their milk-fed light lambs, two trials were carried out - in Sicily, on 32 Comisana lambs, slaughtered at 49±4 days (trial 1); and in Sardinia, on 28 Sarda lambs, slaughtered at 31±4 days(trial 2) - comparing the following grazing dams’ feeding regimes: High stocking rate + Organic (barley – tickbean or pea) Concentrate (HO); High stocking rate + Conventional (maize-soybean) Concentrate (HC); Low stocking rate + Organic Concentrate (LO); Low stocking rate + Conventional Concentrate (LC). Lamb performances, carcass quality, meat colour and lipid content were not modified by dam’s feeding regimen. However, significant differences were observed in the fatty acid (FA) composition of the intramuscular fat of the older suckling lambs of trial 1. The main variation concerned n-3 polyunsaturated FAs and conjugated linoleic acids

Automated FingerPrint Background removal: FPB

<p>Abstract</p> <p>Background</p> <p>The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions. Fingerprinting is usually the method of choice for construction of physical maps. A clone fingerprint is composed of true peaks representing real fragments and background peaks, mainly composed of <it>E. coli </it>genomic DNA, partial digestions, star activity by-products, and machine background. High-throughput fingerprinting leads to the production of thousands of BAC clone fingerprints per day. That is why background peaks removal has become an important issue and needs to be automatized, especially in capillary electrophoresis based fingerprints.</p> <p>Results</p> <p>At the moment, the only tools available for such a task are <it>GenoProfiler </it>and its descendant <it>FPMiner</it>. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, <it>FPB </it>(FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones.</p> <p>Conclusion</p> <p><it>FPB </it>is freely available at <url>http://www.appliedgenomics.org/tools.php</url>. <it>FPB </it>was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.</p

Effect of the dam's feeding regimen on the meat quality of light suckling lambs

In order to verify the effect of the introduction of concentrates without GMO risk and at low aflatoxin risk in the diet of grazing milk ewes on the quanti-qualitative production of meat of their milk-fed light lambs, two trials were carried out - in Sicily, on 32 Comisana lambs, slaughtered at 49±4 days (trial 1); and in Sardinia, on 28 Sarda lambs, slaughtered at 31±4 days(trial 2) - comparing the following grazing dams' feeding regimes: High stocking rate + Organic (barley – tickbean or pea) Concentrate (HO); High stocking rate + Conventional (maize-soybean) Concentrate (HC); Low stocking rate + Organic Concentrate (LO); Low stocking rate + Conventional Concentrate (LC). Lamb performances, carcass quality, meat colour and lipid content were not modified by dam's feeding regimen. However, significant differences were observed in the fatty acid (FA) composition of the intramuscular fat of the older suckling lambs of trial 1. The main variation concerned n-3 polyunsaturated FAs and conjugated linoleic acids

Transgenerational Response to Nitrogen Deprivation in Arabidopsis thaliana

Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive generations of N-sufficient and N-limited Arabidopsis was used to evaluate the existence of a transgenerational memory. The results demonstrated that the ability to take up high amounts of nitrate is induced more quickly as a result of multigenerational stress exposure. This behavior was paralleled by changes in the expression of nitrate responsive genes. RNAseq analyses revealed the enduring modulation of genes in downstream generations, despite the lack of stress stimulus in these plants. The modulation of signaling and transcription factors, such as NIGTs, NFYA and CIPK23 might indicate that there is a complex network operating to maintain the expression of N-responsive genes, such as NRT2.1, NIA1 and NIR. This behavior indicates a rapid acclimation of plants to changes in N availability. Indeed, when fourth generation plants were exposed to N limitation, they showed a rapid induction of N-deficiency responses. This suggests the possible involvement of a transgenerational memory in Arabidopsis that allows plants to adapt efficiently to the environment and this gives an edge to the next generation that presumably will grow in similar stressful conditions

A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

BACKGROUND: Individual fingerprinting based on molecular markers has become a popular tool for studies of population genetics and analysis of genetic diversity in germplasm collections, including the solution of synonymy/homonymy and analysis of paternity and kinship. Genetic profiling of individuals is nowadays based on SSR (Simple Sequence Repeat) markers, which have a number of positive features that make them superior to any other molecular marker developed so far. In humans, SSRs with core repeats three to five nucleotides long are preferred because neighbour alleles are more easily separated and distinguished from each other; while in plants, SSRs with shorter repeats, namely two-nucleotides long, are still in use although they suffer lower separation of neighbour alleles and uncomfortable stuttering. RESULTS: New microsatellite markers, containing tri-, tetra-, and penta-nucleotide repeats, were selected from a total of 26,962 perfect microsatellites in the genome sequence of nearly homozogous grapevine PN40024, assembled from reads covering 8.4 X genome equivalents. Long nucleotide repeats were selected for fingerprinting, as previously done in many species including humans. The new grape SSR markers were tested for their reproducibility and information content in a panel of 48 grape cultivars. Allelic segregation was tested in progenies derived from two controlled crosses. CONCLUSION: A list of 38 markers with excellent quality of peaks, high power of discrimination, and uniform genome distribution (1–3 markers/chromosome), is proposed for grape genotyping. The reasons for exclusion are given for those that were discarded. The construction of marker-specific allelic ladders is also described, and their use is recommended to harmonise allelic calls and make the data obtained with different equipment and by different laboratories fully comparable

Physiological and RNA sequencing data of white lupin plants grown under Fe and P deficiency

This DIB article provides details about transcriptional and physiological response of Fe- and P-deficient white lupin roots, an extensive and complete description of plant response is shown in the research article \u201cPhysiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots\u201d Venuti et al. [1]. White lupin plants were grown under hydroponic system and three different nutritional regimes: Fe deficiency (-Fe), P deficiency (-P), or Fe and P sufficiency (+P + Fe). Depending on nutritional treatment, white lupin plants showed changes in the fresh weights, in root external acidification and FeIII-reductase activity. Moreover, the transcriptomic changes occurring in apices and clusters of Fe-deficient lupin roots were investigated and compared with differences of gene expression occurring in P-deficient plants (-P) and in Fe- and P-sufficient plants (+P + Fe). Transcriptomic data are available in the public repository Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under the series entry (GSE112220). The annotation, mapping and enrichment analyses of differentially modulated transcripts were assessed