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Rye Genetics, Genomics and Breeding
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Rye Genetics, Genomics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 16542

Special Issue Editors

Dr. Rolf Schlegel

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Guest Editor
Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
Interests: cereal genetics
Prof. Dr. Thomas Miedaner

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Guest Editor
State Plant Breeding Institute (720), University of Hohenheim, Stuttgart, Germany
Interests: rye breeding; resistance genetics; genomics
Dr. Viktor Korzun

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Guest Editor
KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
Interests: cereals genomics; genetics and molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rye was domesticated first in Anatolia from wild grass of Secale strictum. In Europe, and later in some other regions of the world, it became to flourish in unforgiving environments and poor soils. For long, it served as a main cereal crop of Northern Europe. Despite formidable achievements during the last few decades, particularly by utilization of hybrid varieties, major challenges in rye production remain. Breeding of cultivars with high yield potential, strong fungi defense, and targeted grain qualities is inevitable to further advance rye to a high-performance crop with different types of end-use. Progress in rye phenomics and functional genomics research is focused on improved growth and development.

Dr. Rolf Schlegel
Prof. Dr. Thomas Miedaner
Dr. Viktor Korzun
Guest Editors

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Keywords

  • taxonomy and cytotaxonomy
  • cytology
  • genebank collections
  • cold tolerance
  • aneuploids
  • abiotic stress tolerance
  • biotic stress tolerance
  • micronutritional efficiency
  • genetics
  • comparative mapping
  • gene transfer
  • cytoplasmic male sterility
  • restorer
  • hybrid breeding
  • molecular breeding
  • allelopathic effects
  • utilization
  • biomass and biogas production
  • nutritional properties

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Published Papers (7 papers)

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Research

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18 pages, 1983 KiB  
Article
Resistance to Snow Mold as a Target Trait for Rye Breeding
by Mira Ponomareva, Vladimir Gorshkov, Sergey Ponomarev, Gulnaz Mannapova, Danil Askhadullin, Damir Askhadullin, Olga Gogoleva, Azat Meshcherov and Viktor Korzun
Plants 2022, 11(19), 2516; https://doi.org/10.3390/plants11192516 - 26 Sep 2022
Viewed by 1858
Abstract
Winter rye is a versatile crop widely used for food and industry. Although rye is resistant to abiotic stressors and many phytopathogens, it is severely damaged by pink snow mold (SM)—a progressive disease caused by the psychrotolerant fungus Microdochium nivale under the snow [...] Read more.
Winter rye is a versatile crop widely used for food and industry. Although rye is resistant to abiotic stressors and many phytopathogens, it is severely damaged by pink snow mold (SM)—a progressive disease caused by the psychrotolerant fungus Microdochium nivale under the snow cover or during prolonged periods of wet and cool conditions. Due to little use of the SM resistance sources in contemporary breeding, varieties with at least moderate resistance to SM are limited. Our study aimed to integrate field assessment under natural conditions and an artificially enriched infection background with laboratory techniques for testing rye accessions and selecting SM resistant sources for applied breeding programs and genetic research. We revealed valuable sources of SM resistance and split rye accessions, according to the level of the genetic divergence of the SM resistance phenotype. This allowed us to select the most distinct donors of the SM resistance, for their use as parental forms, to include novel variability sources in the breeding program for achieving high genetic variability, as well as enhanced and durable SM resistance, in progeny. The rye accessions analyzed here, and the suggested options for their use in breeding, are valuable tools for rye breeding. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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20 pages, 3074 KiB  
Article
High Dietary Intake of Rye Affects Porcine Gut Microbiota in a Salmonella Typhimurium Infection Study
by Julia Hankel, Bussarakam Chuppava, Volker Wilke, Clara Berenike Hartung, Uthayakumar Muthukumarasamy, Till Strowig, Knud Erik Bach Knudsen, Josef Kamphues and Christian Visscher
Plants 2022, 11(17), 2232; https://doi.org/10.3390/plants11172232 - 28 Aug 2022
Cited by 8 | Viewed by 2449
Abstract
Bacterial fermentation of undigested carbohydrates in the hindgut has considerable potential for the stimulation or inhibition of the growth of distinct bacteria within microbiota. The aim of the present study was to evaluate whether high levels of rye affect porcine gut microbiota composition [...] Read more.
Bacterial fermentation of undigested carbohydrates in the hindgut has considerable potential for the stimulation or inhibition of the growth of distinct bacteria within microbiota. The aim of the present study was to evaluate whether high levels of rye affect porcine gut microbiota composition with subsequent effects on the load of Salmonella Typhimurium, an intestinal pathogen with zoonotic relevance. Therefore, forty-two 25-day-old piglets were allocated to two groups and fed a diet containing either 69% wheat or 69% rye for 35 days. One week after introducing the two different diets, the piglets were experimentally infected with Salmonella Typhimurium. The microbiota composition of cecal and fecal samples of the piglets were evaluated 28 days after infection. In the cecum, promoted growth of Bifidobacterium, several lactic acid bacteria and Faecalibacterium prausnitzii were seen in pigs fed the diet containing 69% rye. Bacterial species belonging to the genera Bifidobacterium and Catenisphaera were associated with differing bacterial counts of Salmonella Typhimurium detected in the cecal contents of all piglets in both feeding groups via cultural cultivation. The high intake of rye instead of wheat seems to promote the growth of beneficial intestinal bacteria accompanied by impaired growth conditions for the foodborne pathogen Salmonella Typhimurium. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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Review

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14 pages, 706 KiB  
Review
Exploiting Rye in Wheat Quality Breeding: The Case of Arabinoxylan Content
by Maria Chiara Piro, Hilde Muylle and Geert Haesaert
Plants 2023, 12(4), 737; https://doi.org/10.3390/plants12040737 - 7 Feb 2023
Cited by 2 | Viewed by 2327
Abstract
Rye (Secale cereale subsp. cereale L.) has long been exploited as a valuable alternative genetic resource in wheat (Triticum aestivum L.) breeding. Indeed, the introgression of rye genetic material led to significant breakthroughs in the improvement of disease and pest resistance [...] Read more.
Rye (Secale cereale subsp. cereale L.) has long been exploited as a valuable alternative genetic resource in wheat (Triticum aestivum L.) breeding. Indeed, the introgression of rye genetic material led to significant breakthroughs in the improvement of disease and pest resistance of wheat, as well as a few agronomic traits. While such traits remain a high priority in cereal breeding, nutritional aspects of grain crops are coming under the spotlight as consumers become more conscious about their dietary choices and the food industry strives to offer food options that meet their demands. To address this new challenge, wheat breeding can once again turn to rye to look for additional genetic variation. A nutritional aspect that can potentially greatly benefit from the introgression of rye genetic material is the dietary fibre content of flour. In fact, rye is richer in dietary fibre than wheat, especially in terms of arabinoxylan content. Arabinoxylan is a major dietary fibre component in wheat and rye endosperm flours, and it is associated with a variety of health benefits, including normalisation of glycaemic levels and promotion of the gut microbiota. Thus, it is a valuable addition to the human diet, and it can represent a novel target for wheat–rye introgression breeding. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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14 pages, 1560 KiB  
Review
Genetic Redundancy in Rye Shows in a Variety of Ways
by Alexander V. Vershinin, Evgeny A. Elisafenko and Elena V. Evtushenko
Plants 2023, 12(2), 282; https://doi.org/10.3390/plants12020282 - 7 Jan 2023
Cited by 2 | Viewed by 1750
Abstract
Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy. DNA [...] Read more.
Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy. DNA that does not have a positive effect on the fitness of organisms has been characterized as “junk or selfish DNA”. The controversial concept of junk DNA remains viable. Rye is a convenient subject for yet another test of the correctness and scientific significance of this concept. The genome of cultivated rye, Secale cereale L., is considered one of the largest among species of the tribe Triticeae and thus it tops the average angiosperm genome and the genomes of its closest evolutionary neighbors, such as species of barley, Hordeum (by approximately 30–35%), and diploid wheat species, Triticum (approximately 25%). The review provides an analysis of the structural organization of various regions of rye chromosomes with a description of the molecular mechanisms contributing to their size increase during evolution and the classes of DNA sequences involved in these processes. The history of the development of the concept of eukaryotic genome redundancy is traced and the current state of this problem is discussed. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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23 pages, 8504 KiB  
Review
100 Years of Chromosome Research in Rye, Secale L.
by Rolf Schlegel
Plants 2022, 11(13), 1753; https://doi.org/10.3390/plants11131753 - 30 Jun 2022
Cited by 2 | Viewed by 2975
Abstract
Although microscopy and genetics were still in their infancy, there are cytological results produced a hundred years ago that are still relevant today. Since the 1920s, rye has been a subject of chromosome research. It started by plotting its mitotic and meiotic chromosomes [...] Read more.
Although microscopy and genetics were still in their infancy, there are cytological results produced a hundred years ago that are still relevant today. Since the 1920s, rye has been a subject of chromosome research. It started by plotting its mitotic and meiotic chromosomes to determine genome size. After controversial evidence, it became clear that the base number is n = 7. However, structural differences exist between species within the genus Secale. Some rye populations even carry accessory chromosomes evolutionary derived from the A genome. The development of tetraploid strains significantly promoted chromosome analysis. Various techniques have tried to stabilize the disturbed chromosome pairing of the induced tetraploids. Although slight improvements could be achieved, they did not lead to a breakthrough. However, the various aneuploid derivatives of the polyploids found major advances in the genetic analysis of rye. Trisomics, telo-trisomics, and reciprocal translocation have served as important tools for gene mapping. Since the 1970s, various chromosome banding techniques have stimulated scientific progress. The seven haploid chromosomes could be diagnosed unequivocally, not only in S. cereale but also in related species. These findings led to a clear homoeologous assignment to the genomes of related grass species such as wheat, barley, rice, etc. Current applications of in situ fluorescence staining methods, such as GISH and FISH, allow even more precise results, depending on the specificity of the DNA samples. Advanced preparation techniques are supplemented by the variety of innovations in the field of molecular genome analysis. They replace complex cytological examinations. In this way, introgressions can be safely detected by DNA markers and be much more detailed. In addition, CRISPR/CAS-mediated chromosome engineering will become an important method of the future. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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17 pages, 3374 KiB  
Review
Effective Pollen-Fertility Restoration Is the Basis of Hybrid Rye Production and Ergot Mitigation
by Thomas Miedaner, Viktor Korzun and Peer Wilde
Plants 2022, 11(9), 1115; https://doi.org/10.3390/plants11091115 - 20 Apr 2022
Cited by 10 | Viewed by 2758 | Correction
Abstract
Hybrid rye breeding leads to considerably higher grain yield and a higher revenue to the farmer. The basis of hybrid seed production is the CMS-inducing Pampa (P) cytoplasm derived from an Argentinean landrace and restorer-to-fertility (Rf) genes. European sources show an [...] Read more.
Hybrid rye breeding leads to considerably higher grain yield and a higher revenue to the farmer. The basis of hybrid seed production is the CMS-inducing Pampa (P) cytoplasm derived from an Argentinean landrace and restorer-to-fertility (Rf) genes. European sources show an oligogenic inheritance, with major and minor Rf genes, and mostly result in low-to-moderate pollen-fertility levels. This results in higher susceptibility to ergot (Claviceps purpurea) because rye pollen and ergot spores are in strong competition for the unfertilized stigma. Rf genes from non-adapted Iranian primitive rye and old Argentinean cultivars proved to be most effective. The major Rf gene in these sources was localized on chromosome 4RL, which is also a hotspot of restoration in other Triticeae. Marker-based introgression into elite rye materials led to a yield penalty and taller progenies. The Rfp1 gene of IRAN IX was fine-mapped, and two linked genes of equal effects were detected. Commercial hybrids with this gene showed a similar low ergot infection when compared with population cultivars. The task of the future is to co-adapt these exotic Rfp genes to European elite gene pools by genomic-assisted breeding. Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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Other

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2 pages, 179 KiB  
Correction
Correction: Miedaner et al. Effective Pollen-Fertility Restoration Is the Basis of Hybrid Rye Production and Ergot Mitigation. Plants 2022, 11, 1115
by Thomas Miedaner, Viktor Korzun and Peer Wilde
Plants 2023, 12(12), 2261; https://doi.org/10.3390/plants12122261 - 9 Jun 2023
Viewed by 773
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Rye Genetics, Genomics and Breeding)
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