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Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species.

ABSTRACT: We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with the addition of some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F₂ and F₃) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F₂. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: self-compatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F₂ seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F₁ hybrids, is discussed.

SUBMITTER: Eduardo I

PROVIDER: S-EPMC7427350 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Harnessing plant-microbe interactions to advance crop resistance to pathogens could be a keystone in sustainable agriculture. The breeding of crops to maximize yield in intensive agriculture might have led to the loss of traits that are necessary for beneficial plant-soil feedback. In this study, we tested whether the soil microbiome can induce a stronger plant defense against root-lesion nematodes in ancestral genotypes of barley than in elite cultivars. Plants were grown in a sterile substrate with or without the inoculation of rhizosphere microbiomes, and Pratylenchus neglectus was inoculated to the roots. Unexpectedly, elite cultivars profited significantly more from the microbiome than ancestral genotypes, by the reduction of nematodes in roots and the increased shoot weight relative to control plants. The elite cultivars had higher microbial densities in the rhizosphere, which were correlated with root weight. The structure of the bacterial and fungal community of elite and ancestral genotypes differed, as compared by 16S rDNA or internal transcribed spacer amplicon profiles in denaturing gradient gel electrophoresis. The elite cultivars differed in responsiveness to the microbiome. For the most responsive cultivars Beysehir and Jolgeh, the strong microbe-induced suppression of nematodes coincided with the strongest microbe-dependent increase in transcripts of salicylic acid-regulated defense genes after nematode invasion, while the jasmonate-regulated genes LOX2 and AOS were downregulated in roots with the inoculated microbiome. The microbe-triggered modulation of defense gene expression differed significantly between elite and ancestral genotypes of barley. Soil microbiomes conditioned by maize roots suppressed the nematodes in elite cultivars, while the corresponding bulk soil microbiome did not. In conclusion, cultivars Beysehir and Jolgeh harbor the genetic background for a positive plant-microbiome feedback. Exploiting these traits in breeding for responsiveness to beneficial soil microbiomes, accompanied by soil biome management for compatible plant-microbe interactions, will support low-input agriculture and sustainability.

Project description:BackgroundPancreatic cancer remains one of the five leading causes of cancer deaths in industrialized nations. For adenocarcinomas in the head of the gland and premalignant lesions, partial pancreaticoduodenectomy represents the standard treatment for resectable tumours. The gastro- or duodenojejunostomy after partial pancreaticoduodenectomy can be reestablished via either an antecolic or a retrocolic route. The debate about the more favourable technique for bowel reconstruction is ongoing.ObjectivesTo compare the effectiveness and safety of antecolic and retrocolic gastro- or duodenojejunostomy after partial pancreaticoduodenectomy.Search methodsWe conducted a systematic literature search on 29 September 2015 to identify all randomised controlled trials in the Cochrane Central Register of Controlled Trials (CENTRAL), The Cochrane Library 2015, issue 9, MEDLINE (1946 to September 2015), and EMBASE (1974 to September 2015). We applied no language restrictions. We handsearched reference lists of identified trials to identify further relevant trials, and searched the trial registry clinicaltrials.gov for ongoing trials.Selection criteriaWe considered all randomised controlled trials that compared antecolic versus retrocolic reconstruction of bowel continuity after partial pancreaticoduodenectomy for any given indication to be eligible.Data collection and analysisTwo review authors independently screened the identified references and extracted data from the included trials. The same two review authors independently assessed risk of bias of included trials, according to standard Cochrane methodology. We used a random-effects model to pool the results of the individual trials in a meta-analysis. We used odds ratios to compare binary outcomes and mean differences for continuous outcomes.Main resultsOf a total of 216 citations identified by the systematic literature search, we included six randomised controlled trials (reported in nine publications), with a total of 576 participants. We identified a moderate heterogeneity of methodological quality and risk of bias of the included trials. None of the pooled results for our main outcomes of interest showed significant differences: delayed gastric emptying (OR 0.60; 95% CI 0.31 to 1.18; P = 0.14), mortality (RD -0.01; 95% CI -0.03 to 0.02; P = 0.72), postoperative pancreatic fistula (OR 0.98; 95% CI 0.65 to 1.47; P = 0.92), postoperative haemorrhage (OR 0.79; 95% CI 0.38 to 1.65; P = 0.53), intra-abdominal abscess (OR 0.93; 95% CI 0.52 to 1.67; P = 0.82), bile leakage (OR 0.89; 95% CI 0.36 to 2.15; P = 0.79), reoperation rate (OR 0.59; 95% CI 0.27 to 1.31; P = 0.20), and length of hospital stay (MD -0.67; 95%CI -2.85 to 1.51; P = 0.55). Furthermore, the perioperative outcomes duration of operation, intraoperative blood loss and time to NGT removal showed no relevant differences. Only one trial reported quality of life, on a subgroup of participants, also without a significant difference between the two groups at any time point. The overall quality of the evidence was only low to moderate, due to heterogeneity, some inconsistency and risk of bias in the included trials.Authors' conclusionsThere was low to moderate quality evidence suggesting no significant differences in morbidity, mortality, length of hospital stay, or quality of life between antecolic and retrocolic reconstruction routes for gastro- or duodenojejunostomy. Due to heterogeneity in definitions of the endpoints between trials, and differences in postoperative management, future research should be based on clearly defined endpoints and standardised perioperative management, to potentially elucidate differences between these two procedures. Novel strategies should be evaluated for prophylaxis and treatment of common complications, such as delayed gastric emptying.

Project description:BackgroundThe renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are mediated by DNA methylation, stable chromatin modifications and non-coding RNA-associated gene silencing involving specific proteins called epigenetic factors. Multiple organisms, ranging from plants to yeast and mammals, have been used as model systems to study epigenetics. The interactions between parasites and their hosts are models of choice to study these mechanisms because the selective pressures are strong and the evolution is fast. The asexually reproducing root-knot nematodes (RKN) offer different advantages to study the processes and mechanisms involved in epigenetic regulation. RKN genomes sequencing and annotation have identified numerous genes, however, which of those are involved in the adaption to an environment and potentially relevant to the evolution of plant-parasitism is yet to be discovered.ResultsHere, we used a functional comparative annotation strategy combining orthology data, mining of curated genomics as well as protein domain databases and phylogenetic reconstructions. Overall, we show that (i) neither RKN, nor the model nematode Caenorhabditis elegans possess any DNA methyltransferases (DNMT) (ii) RKN do not possess the complete machinery for DNA methylation on the 6th position of adenine (6mA) (iii) histone (de)acetylation and (de)methylation pathways are conserved between C. elegans and RKN, and the corresponding genes are amplified in asexually reproducing RKN (iv) some specific non-coding RNA families found in plant-parasitic nematodes are dissimilar from those in C. elegans. In the asexually reproducing RKN Meloidogyne incognita, expression data from various developmental stages supported the putative role of these proteins in epigenetic regulations.ConclusionsOur results refine previous predictions on the epigenetic machinery of model species and constitute the most comprehensive description of epigenetic factors relevant to the plant-parasitic lifestyle and/or asexual mode of reproduction of RKN. Providing an atlas of epigenetic factors in RKN is an informative resource that will enable researchers to explore their potential role in adaptation of these parasites to their environment.

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Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species.

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