Marker assisted selection of potato breeding lines with combination of PVY resistance genes from different wild species

Potato virus Y (PVY) is considered as one of the most harmful virus infections of this crop. Thus, it is a topical problem to breed potato varieties resistant against a wide range of PVY strains and to create initial breeding material that will have a combination of resistance genes from different species. The aim of the study was: (1) to genotype a collection of 376 breeding lines (BL), developed from complex interspecific hybrids, using DNA markers of PVY resistance genes, (2) to identify accessions with markers of resistance genes from different species for subsequent use in marker assisted selection (MAS), (3) to evaluate the suitability of DNA markers of PVY resistance genes for genotyping BL developed through interspecific hybridization. It was ascertained that the markers most widely represented in the collection were RYSC3 of the Ryadg gene (49.7%), Ry364 and RAPD38-530 of the Rychc gene (50.5% and 45.2%, respectively), and Yes3-3A of the Rysto gene (29.8%). The markers Ry186 of Rychc and GP122/EcoRV780 of Ryf-sto were found only in some accessions. The frequency of occurrence of BL that had markers of PVY resistance genes from two different species varied between 2.7% (Yes3-3a marker of Rysto and both two markers of Rychc) and 8.5-9.0% (RYSC3 marker of Ryadg and both two markers of Rychc, or only Ry364 marker of this gene). In total, the collection was found to contain 134 BL (47.6%) with markers of resistance genes from two different species. A combination of four markers for three genes of different origin (Ryadg, Rysto and Rychc) was found in 27 BL (7.2%). Extreme resistance to PVY of most BL (302 out of 357) was obviously determined by the presence in them of the currently used resistance genes detected by DNA markers applied in the study. Nevertheless, a significant part of accessions (55 of 61) that did not have any markers was resistant to PVY. At the same time, 13 BL (3.5%) with the markers were susceptible to the virus. Such a level of discrepancies is considered as acceptable for the initial MAS of breeding material. The obtained data on the presence of the markers of PVY resistance genes of different origin and their combination in BL ensures a more effective use of such BL in breeding in comparison with the BL resistant to the virus, though lacking corresponding markers.

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Characterisation of resistance genes resources against late blight available for Czech potato breeding by means of selected DNA markers

Plant Soil and Environment ◽

10.17221/3559-pse ◽

2011 ◽

Vol 51 (No. 2) ◽

pp. 82-86 ◽

Cited By ~ 1

Author(s):

P. Sedlák ◽

P. Vejl ◽

M. Melounová ◽

P. Křenek ◽

J. Domkářová ◽

...

Keyword(s):

Resistance Genes ◽

Dna Markers ◽

Marker Assisted Selection ◽

Potato Breeding ◽

Potato Research ◽

Plant Production ◽

Potato Chromosome ◽

Research Institutes ◽

New Varieties ◽

Developing Area

Marker assisted selection (MAS) in potato breeding is the most developing area at present time. Methods of DNA markers are developed in all top world potato research institutes and universities oriented on plant production. This paper presents results obtained from the testing of gene resources encompassing different resistance genes against Phytophthora infestans potentially exploitable for Czech potato breeding. Three different DNA markers were studied that are linked to R1 locus in the potato chromosome V operating as a resistance against some races of P. infestans. Markering capability and frequencies of these markers was evaluated with respect to their usage in practical Czech plant breeding that has vital importance in finding the tools as a prerequisite for creating new varieties efficiently.

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Combination Breeding and Marker-Assisted Selection to Develop Late Blight Resistant Potato Cultivars

10.20944/preprints202110.0209.v1 ◽

2021 ◽

Author(s):

Mariya P. Beketova ◽

Nadezhda A. Chalaya ◽

Nadezhda M. Zoteyeva ◽

Alena A. Gurina ◽

Mariya A. Kuznetsova ◽

...

Keyword(s):

Dna Markers ◽

Marker Assisted Selection ◽

Potato Cultivars ◽

Scar Markers ◽

Artificial Infection ◽

Breeding Lines ◽

Sequence Characterized Amplified Region ◽

Early Stages ◽

Gene Enrichment ◽

Flower Pigmentation

(1) Background: Although resistance to pathogens and pests has been researched in many potato cultivars and breeding lines with DNA markers, there is scarce evidence as to the efficiency of the marker-assisted selection (MAS) for these traits when applied at the early stages of breeding. A goal of this study was to estimate the potential of affordable DNA markers to track Rpi disease resistance genes, that are effective against the pathogen Phytophthora infestans, as a practical breeding tool on a progeny of 68 clones derived from a cross between the cultivar Sudarynya and 13/11-09. (2) Methods: this population was studied for four years to elucidate the distribution of LB resistance and other agronomical desirable or simple to phenotype traits such as tuber and flower pigmentation, capacity and structure of yield. LB resistance was phenotypically determined through natural and artificial infection and the presence/absence of nine Rpi genes was assessed via 11 sequence-characterized amplified region (SCAR) markers. To aid this analysis, the profile of Rpi genes in the 13/11-09 parent was established using diagnostic resistance gene enrichment sequencing (dRenSeq) as a gold standard. (3) Results: at the early stages of a breeding program, MAS can halve the workload when screening the segregation of F1 offspring and selected SCAR markers for Rpi-genes provide useful tools.

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Marker assisted selection in BMQ related breeding programs

Genetika ◽

10.2298/gensr0801039o ◽

2008 ◽

Vol 40 (1) ◽

pp. 39-49 ◽

Cited By ~ 1

Author(s):

Dragana Obreht ◽

Borislav Kobiljski ◽

Mihajla Djan ◽

Ljiljana Vapa

Keyword(s):

Dna Sequences ◽

Dna Markers ◽

Marker Assisted Selection ◽

Wheat Breeding ◽

Quality Traits ◽

Vegetable Crops ◽

Bread Making ◽

Technological Parameters ◽

Breeding Programs ◽

Wide Range

Implementation of marker assisted selection (MAS) in bread making quality (BMQ) oriented breeding programs could allow genetic potential assessment of genotypes prior to their phenotypic evaluation. The mechanisms underlying some quality traits in wheat are now understood. This knowledge, coupled with the availability of the DNA sequences of the genes encoding gluten proteins and the wide application of the PCR, has enabled the design of diagnostic DNA markers for these quality traits. Bread wheat breeding programs developed in Institute of Field and Vegetable Crops, Novi Sad have originated a wide range of quality cultivars with strong flours and hard grain texture. During twenty years, in the process of bread-making quality prediction, composition of HMW glutenin subunits were analyzed beside standard technological parameters. However, in order to improve our breeding strategies new generations of PCR-based BMQ related markers were included in selection programs. This paper provides an overview of diagnostic DNA markers that are currently in use in foreign and domestic wheat selection programs. .

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Combination Breeding and Marker-Assisted Selection to Develop Late Blight Resistant Potato Cultivars

Agronomy ◽

10.3390/agronomy11112192 ◽

2021 ◽

Vol 11 (11) ◽

pp. 2192

Author(s):

Mariya P. Beketova Beketova ◽

Nadezhda A. Chalaya ◽

Nadezhda M. Zoteyeva ◽

Alena A. Gurina ◽

Mariya A. Kuznetsova ◽

...

Keyword(s):

Late Blight ◽

Dna Markers ◽

Marker Assisted Selection ◽

Potato Cultivars ◽

Scar Markers ◽

Breeding Lines ◽

Sequence Characterized Amplified Region ◽

Early Stages ◽

Gene Enrichment ◽

Flower Pigmentation

(1) Background: Although resistance to pathogens and pests has been researched in many potato cultivars and breeding lines with DNA markers, there is scarce evidence as to the efficiency of the marker-assisted selection (MAS) for these traits when applied at the early stages of breeding. A goal of this study was to estimate the potential of affordable DNA markers to track resistance genes that are effective against the pathogen Phytophthora infestans (Rpi genes), as a practical breeding tool on a progeny of 68 clones derived from a cross between the cultivar Sudarynya and the hybrid 13/11-09. (2) Methods: this population was studied for four years to elucidate the distribution of late blight (LB) resistance and other agronomical desirable or simple to phenotype traits such as tuber and flower pigmentation, yield capacity and structure. LB resistance was phenotypically evaluated following natural and artificial infection and the presence/absence of nine Rpi genes was assessed with 11 sequence-characterized amplified region (SCAR) markers. To validate this analysis, the profile of Rpi genes in the 13/11-09 parent was established using diagnostic resistance gene enrichment sequencing (dRenSeq) as a gold standard. (3) Results: at the early stages of a breeding program, when screening the segregation of F1 offspring, MAS can halve the workload and selected SCAR markers for Rpi-genes provide useful tools.

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Pyramiding of Three Bacterial Blight Resistance Genes in Rice Cultivar Using Marker Assisted Selection

International Journal of Bio-resource and Stress Management ◽

10.23910/ijbsm/2018.9.2.3c0580 ◽

2018 ◽

Vol 9 (2) ◽

pp. 243-248 ◽

Cited By ~ 1

Author(s):

Kadu Tanvi P. ◽

◽

Kale Sonam S. ◽

Chavan Narendra R. ◽

Toshy Agrawal ◽

...

Keyword(s):

Resistance Genes ◽

Marker Assisted Selection ◽

Bacterial Blight ◽

Rice Cultivar ◽

Blight Resistance ◽

Bacterial Blight Resistance

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The aspects of microbial biomass use in the utilization of selected waste from the agro-food industry

Open Life Sciences ◽

10.1515/biol-2020-0099 ◽

2020 ◽

Vol 15 (1) ◽

pp. 787-796 ◽

Cited By ~ 1

Author(s):

Marek Kieliszek ◽

Kamil Piwowarek ◽

Anna M. Kot ◽

Katarzyna Pobiega

Keyword(s):

Food Industry ◽

Industrial Applications ◽

Waste Products ◽

Yeast Biomass ◽

Wide Range ◽

Innovative Solutions ◽

Biomass Management ◽

Effective Use ◽

Modern Technologies ◽

Biomass Of Microorganisms

AbstractCellular biomass of microorganisms can be effectively used in the treatment of waste from various branches of the agro-food industry. Urbanization processes and economic development, which have been intensifying in recent decades, lead to the degradation of the natural environment. In the first half of the 20th century, problems related to waste management were not as serious and challenging as they are today. The present situation forces the use of modern technologies and the creation of innovative solutions for environmental protection. Waste of industrial origin are difficult to recycle and require a high financial outlay, while the organic waste of animal and plant origins, such as potato wastewater, whey, lignin, and cellulose, is dominant. In this article, we describe the possibilities of using microorganisms for the utilization of various waste products. A solution to reduce the costs of waste disposal is the use of yeast biomass. Management of waste products using yeast biomass has made it possible to generate new metabolites, such as β-glucans, vitamins, carotenoids, and enzymes, which have a wide range of industrial applications. Exploration and discovery of new areas of applications of yeast, fungal, and bacteria cells can lead to an increase in their effective use in many fields of biotechnology.

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Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

Scientific Reports ◽

10.1038/s41598-021-88318-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Medelin Ocejo ◽

Beatriz Oporto ◽

José Luis Lavín ◽

Ana Hurtado

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Campylobacter Coli ◽

Whole Genome ◽

Northern Spain ◽

Sequence Alignments ◽

Phenotypic Data ◽

Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

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322. Evaluation of the BioFire® Bone and Joint Infection (BJI) Panel for the Detection of Microorganisms and Antimicrobial Resistance Genes in Synovial Fluid Specimens

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.518 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S233-S234

Author(s):

Corrin Graue ◽

Bryan H Schmitt ◽

Amy Waggoner ◽

Frederic Laurent ◽

Lelia Abad ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Synovial Fluid ◽

Resistance Genes ◽

Clinical Care ◽

Joint Infection ◽

High Morbidity ◽

Bone And Joint Infection ◽

Microbiological Methods ◽

Antimicrobial Resistance Genes ◽

Wide Range

Abstract Background Bone and Joint Infections (BJIs) present with non-specific symptoms that may include pain, swelling, and fever and are associated with high morbidity and significant risk of mortality. BJIs can be caused by a variety of bacteria and fungi, including anaerobes and microorganisms that can be challenging to culture or identify by traditional microbiological methods. Clinicians primarily rely on culture to identify the pathogen(s) responsible for infection. The BioFire® Bone and Joint Infection (BJI) Panel (BioFire Diagnostics, Salt Lake City, UT) is designed to detect 15 gram-positive bacteria (including seven anaerobes), 14 gram-negative bacteria (including one anaerobe), two yeast, and eight antimicrobial resistance (AMR) genes from synovial fluid specimens in about an hour. The objective of this study was to evaluate the performance of an Investigational Use Only (IUO) version of the BioFire BJI Panel compared to various reference methods. Methods Remnant synovial fluid specimens, which were collected for routine clinical care at 13 study sites in the US and Europe, underwent testing using an IUO version of the BioFire BJI Panel. Performance of this test was determined by comparison to Standard of Care (SoC) consisting of bacterial culture performed at each study site according to their routine procedures. Results A total of 1544 synovial fluid specimens were collected and tested with the BioFire BJI Panel. The majority of specimens were from knee joints (77.9%) and arthrocentesis (79.4%) was the most common collection method. Compared to SoC culture, overall sensitivity was 90.2% and specificity was 99.8%. The BioFire BJI Panel yielded a total of 268 Detected results, whereas SoC yielded a total of 215 positive results for on-panel analytes. Conclusion The BioFire BJI Panel is a sensitive, specific, and robust test for rapid detection of a wide range of analytes in synovial fluid specimens. The number of microorganisms and resistance genes included in the BioFire BJI Panel, together with a reduced time-to-result and increased diagnostic yield compared to culture, is expected to aid in the timely diagnosis and appropriate management of BJIs. Disclosures Benjamin von Bredow, PhD, BioFire (Grant/Research Support) Jennifer Dien Bard, PhD, BioFire Diagnostic (Consultant, Scientific Research Study Investigator) Bart Kensinger, PhD, BioFire Diagnostics (Employee) Benedicte Pons, PhD, bioMerieux SA (Employee) Corinne Jay, PhD, bioMerieux SA (Employee)

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