Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa

<p>Abstract</p> <p>Background</p> <p>Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (<it>Lolium perenne</it>). We report on the exploitation of a comprehensive EST collection in <it>L. perenne </it>for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of <it>L. perenne</it>, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of <it>L. perenne</it>, <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>O. sativa</it>, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding.</p> <p>Results</p> <p>From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of <it>L. perenne</it>, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the <it>L. perenne </it>EST-SSRs with sequences of <it>Festuca arundinacea</it>, <it>Brachypodium distachyon</it>, and <it>Oryza sativa </it>identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species <it>F. arundinacea</it>, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species <it>B. distachyon </it>and <it>O. sativa</it>.</p> <p>Conclusion</p> <p>The results indicate that the <it>L. perenne </it>EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.</p

Development of doubled haploid inducer lines facilitates selection of superior haploid inducers in maize

Haploid inducers are key components of doubled haploid (DH) technology in maize. Robust agronomic performance and better haploid induction ability of inducers are persistently sought through genetic improvement. We herein developed C1-I inducers enabling large-scale in vivo haploid induction of inducers and discovered superior inducers from the DH progenies. The haploid induction rate (HIR) of C1-I inducers ranged between 5.8% and 12.0%. Overall, the success rate of DH production was 13% on average across the 23 different inducer crosses. The anthesis–silking interval and days to flowering of inducer F1s are significantly correlated with the success rate of DH production (r = −0.48 and 0.47, respectively). Transgressive segregants in DH inducers (DHIs) were found for the traits (days to flowering, HIR, plant height, and total primary branch length). Moreover, the best HIR in DHIs exceeded 23%. Parental genome contributions to DHI progenies ranged between 0.40 and 0.55, respectively, in 25 and 75 percentage quantiles, and the mean and median were 0.48. The allele frequency of the four traits from inducer parents to DHI progenies did not correspond with the phenotypic difference between superior and inferior individuals in the DH populations by genome-wide Fst analysis. This study demonstrated that the recombinant DHIs can be accessed on a large scale and used as materials to facilitate the genetic improvement of maternal haploid inducers by in vivo DH technology.This article is published as Chen Y-R, Lübberstedt T and Frei UK (2024) Development of doubled haploid inducer lines facilitates selection of superior haploid inducers in maize. Front. Plant Sci. 14:1320660. doi: 10.3389/fpls.2023.1320660.© 2024 Chen, Lübberstedt and Frei. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms

Distribution of different repeat type classes for EST-SSRs of the genotypes NV20F1-30, NV20F1-39, and F6

<p><b>Copyright information:</b></p><p>Taken from "Frequency, type, and distribution of EST-SSRs from three genotypes of , and their conservation across orthologous sequences of , and "</p><p>http://www.biomedcentral.com/1471-2229/7/36</p><p>BMC Plant Biology 2007;7():36-36.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1950305.</p><p></p

Protocols for In Vivo Doubled Haploid (DH) Technology in Maize Breeding: From Haploid Inducer Development to Haploid Genome Doubling

Doubled haploid (DH) technology reduces the time required to obtain homozygous genotypes and accelerates plant breeding among other advantages. It is established in major crop species such as wheat, barley, maize, and canola. DH lines can be produced by both in vitro and in vivo methods and the latter is focused here. The major steps involved in in vivo DH technology are haploid induction, haploid selection/identification, and haploid genome doubling. Herein, we elaborate on the various steps of DH technology in maize breeding from haploid induction to haploid genome doubling to produce DH lines. Detailed protocols on the following topics are discussed: in vivo haploid inducer line development, haploid selection using seed and root color markers and automated seed sorting based on embryo oil content using QSorter, artificial genome doubling, and the identification of genotypes with spontaneous haploid genome doubling (SHGD) ability.This is a manuscript of a chapter published as Aboobucker S.I. et al. (2022) Protocols for In Vivo Doubled Haploid (DH) Technology in Maize Breeding: From Haploid Inducer Development to Haploid Genome Doubling. In: Lambing C. (eds) Plant Gametogenesis. Methods in Molecular Biology, vol 2484. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2253-7_16. Posted with permission

Hypervariability of Biofilm Formation and Oxacillin Resistance in a Staphylococcus epidermidis Strain Causing Persistent Severe Infection in an Immunocompromised Patient▿

We report on a leukemic patient who suffered from a persistent, generalized, and eventually fatal Staphylococcus epidermidis infection during prolonged aplasia. Over a 6-week period, we isolated a genetically and phenotypically unstable S. epidermidis strain related to an epidemic clone associated with hospital infections worldwide. Strikingly, the strain showed a remarkable degree of variability, with evidence of selection and increasing predominance of biofilm-producing and oxacillin-resistant variants over time. Thus, in the early stages of the infection, the strain was found to generate subpopulations which had spontaneously lost the biofilm-mediating ica locus along with the oxacillin resistance-conferring mecA gene. These deletion mutants were obviously outcompeted by the ica- and mecA-positive wild-type genotype, with the selection and predominance of strongly biofilm-forming and oxacillin-resistant variants in the later stages of the infection. Also, a switch from protein- to polysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG)-mediated-biofilm production was detected among ica-positive variants in the course of the infection. The data highlight the impact of distinct S. epidermidis clonal lineages as serious nosocomial pathogens that, through the generation and selection of highly pathogenic variants, may critically determine disease progression and outcome

Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

Adapted exotic maize (Zea mays L.) germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of U.S. Corn Belt germplasm. In vivo doubled haploid (DH) technology has been used to efficiently exploit exotic germplasm. It can help to purge deleterious recessive alleles. The objectives of this study were to determine the usefulness of BS39-derived inbred lines using both SSD and DH methods, to determine the impact of spontaneous as compared to artificial haploid genome doubling on genetic variance among BS39-derived DH lines, and to identify SNP markers associated with agronomic traits among BS39 inbreds monitored at testcross level. We developed two sets of inbred lines directly from BS39 by DH and SSD methods, named BS39_DH and BS39_SSD. Additionally, two sets were derived from a cross between BS39 and A427 (SHGD donor) by DH and SSD methods, named BS39×A427_DH and BS39×A427_SSD, respectively. Grain yield, moisture, plant height, ear height, stalk lodging, and root lodging were measured to estimate genetic parameters. For genome-wide association (GWAS) analysis, inbred lines were genotyped using Genotype-by-Sequencing (GBS) and Diversity Array Technology Sequencing (DArTSeq). Some BS39-derived inbred lines performed better than elite germplasm inbreds and all sets showed significant genetic variance. The presence of spontaneous haploid genome doubling genes did not affect performance of inbred lines. Five SNPs were significant and three of them located within genes related to plant development or abiotic stresses. These results demonstrate the potential of BS39 to add novel alleles to temperate elite germplasm.This is a preprint made available through Research Square at doi:10.21203/rs.3.rs-799789/v1. This work is licensed under a CC BY 4.0 License