1
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Kristensen PS, Sarup P, Fé D, Orabi J, Snell P, Ripa L, Mohlfeld M, Chu TT, Herrström J, Jahoor A, Jensen J. Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1193433. [PMID: 38162304 PMCID: PMC10756082 DOI: 10.3389/fpls.2023.1193433] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/16/2023] [Indexed: 01/03/2024]
Abstract
Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses. Here, GCA was estimated as the sum of additive genetic effects and within-group epistasis due to high degree of inbreeding in parental lines. SCA was estimated as the sum of across-group epistasis and dominance effects. Three models were compared. In model 1, it was assumed that each hybrid was produced from two completely inbred parental lines. Model 1 was extended to include three-way hybrids from parental lines with arbitrary levels of inbreeding: In model 2, parents of the three-way hybrids could have any levels of inbreeding, while the grandparents of the maternal parent were assumed completely inbred. In model 3, all parental components could have any levels of inbreeding. Data from commercial breeding programs for hybrid rye and sugar beet was used to evaluate the models. The traits grain yield and root yield were analyzed for rye and sugar beet, respectively. Additive genetic variances were larger than epistatic and dominance variances. The models' predictive abilities for total genetic value, for GCA of each parental line and for SCA were evaluated based on different cross-validation strategies. Predictive abilities were highest for total genetic values and lowest for SCA. Predictive abilities for SCA and for GCA of maternal lines were higher for model 2 and model 3 than for model 1. The implementation of the genomic prediction models in hybrid breeding programs can potentially lead to increased genetic gain in two different ways: I) by facilitating the selection of crossing parents with high GCA within heterotic groups and II) by prediction of SCA of all realized and potential combinations of parental lines to produce hybrids with high total genetic values.
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Affiliation(s)
| | - Pernille Sarup
- Research and Development, Nordic Seed A/S, Odder, Denmark
| | - Dario Fé
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Jihad Orabi
- Research and Development, Nordic Seed A/S, Odder, Denmark
| | - Per Snell
- Research and Development, DLF Beet Seed AB, Landskrona, Sweden
| | - Linda Ripa
- Research and Development, DLF Beet Seed AB, Landskrona, Sweden
| | | | - Thinh Tuan Chu
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | | | - Ahmed Jahoor
- Research and Development, Nordic Seed A/S, Odder, Denmark
- Breeding, Nordic Seed Germany GmbH, Nienstädt, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
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Che Y, Yang Y, Yang Y, Wei L, Guo J, Yang X, Li X, Liu W, Li L. Construction of a high-density genetic map and mapping of a spike length locus for rye. PLoS One 2023; 18:e0293604. [PMID: 37903124 PMCID: PMC10615298 DOI: 10.1371/journal.pone.0293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yunjie Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Juan Guo
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Wan H, Yang M, Li J, Wang Q, Liu Z, Zheng J, Li S, Yang N, Yang W. Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:40. [PMID: 37312750 PMCID: PMC10248656 DOI: 10.1007/s11032-023-01386-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/13/2023] [Indexed: 06/15/2023]
Abstract
Rye (Secale cereale L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent Chuanmai 42 from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome centromere breakage and fusion were detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting alien germplasm to enhance wheat-breeding founder parents or to breed new varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01386-0.
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Affiliation(s)
- Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Manyu Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Shizhao Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
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Brodführer S, Mohler V, Stadlmeier M, Okoń S, Beuch S, Mascher M, Tinker NA, Bekele WA, Hackauf B, Herrmann MH. Genetic mapping of the powdery mildew resistance gene Pm7 on oat chromosome 5D. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:53. [PMID: 36913008 PMCID: PMC10011287 DOI: 10.1007/s00122-023-04288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Three independent experiments with different genetic backgrounds mapped the resistance gene Pm7 in the oat genome to the distal part of the long arm of chromosome 5D. Resistance of oat to Blumeria graminis DC. f. sp. avenae is an important breeding goal in Central and Western Europe. In this study, the position of the effective and widely used resistance gene Pm7 in the oat genome was determined based on three independent experiments with different genetic backgrounds: genome-wide association mapping in a diverse set of inbred oat lines and binary phenotype mapping in two bi-parental populations. Powdery mildew resistance was assessed in the field as well as by detached leaf tests in the laboratory. Genotyping-by-sequencing was conducted to establish comprehensive genetic fingerprints for subsequent genetic mapping experiments. All three mapping approaches located the gene to the distal part of the long arm of chromosome 5D in the hexaploid oat genome sequences of OT3098 and 'Sang.' Markers from this region were homologous to a region of chromosome 2Ce of the C-genome species, Avena eriantha, the donor of Pm7, which appears to be the ancestral source of a translocated region on the hexaploid chromosome 5D.
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Affiliation(s)
- Sophie Brodführer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany
- I.G. Saatzucht GmbH & Co KG, Am Park 3, 18276, Gülzow-Prüzen OT Boldebuck, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 6, 85354, Freising, Germany
| | - Melanie Stadlmeier
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 6, 85354, Freising, Germany
| | - Sylwia Okoń
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Steffen Beuch
- Nordsaat Saatzucht GmbH, Saatzucht Granskevitz, Granskevitz 3, 18569, Schaprode, Germany
| | - Martin Mascher
- Research Group Domestication Genomics, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstraße 3, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Nicholas A Tinker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Wubishet A Bekele
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Bernd Hackauf
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany
| | - Matthias Heinrich Herrmann
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany.
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5
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Hackauf B, Siekmann D, Fromme FJ. Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:2666. [PMID: 36235531 PMCID: PMC9571156 DOI: 10.3390/plants11192666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature.
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Affiliation(s)
- Bernd Hackauf
- Julius Kühn Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190 Sanitz, Germany
| | - Dörthe Siekmann
- Hybro Saatzucht GmbH & Co. KG, Langlinger Straße 3, 29565 Wriedel, Germany
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Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale. Int J Mol Sci 2022; 23:ijms231911106. [PMID: 36232406 PMCID: PMC9569962 DOI: 10.3390/ijms231911106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic diversity of rye will assist both the improvement of this crop and facilitate the introgression of more valuable traits into wheat. Here, we isolated and sequenced the short arm of rye chromosome 7 (7RS) from Triticale 380SD using flow cytometry and compared it to the public Lo7 rye whole genome reference assembly. We identify 2747 Lo7 genes present on the isolated chromosome arm and two clusters containing seven and sixty-five genes that are present on Triticale 380SD 7RS, but absent from Lo7 7RS. We identified 29 genes that are not assigned to chromosomal locations in the Lo7 assembly but are present on Triticale 380SD 7RS, suggesting a chromosome arm location for these genes. Our study supports the Lo7 reference assembly and provides a repertoire of genes on Triticale 7RS.
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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8
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Gruner P, Schmitt AK, Flath K, Piepho HP, Miedaner T. Mapping and validating stem rust resistance genes directly in self-incompatible genetic resources of winter rye. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1989-2003. [PMID: 33688982 PMCID: PMC8263455 DOI: 10.1007/s00122-021-03800-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/20/2021] [Indexed: 06/03/2023]
Abstract
Individual stem rust resistance genes could be directly mapped within self-incompatible rye populations. Genetic resources of rye (Secale cereale L.) are cross-pollinating populations that can be highly diverse and are naturally segregating. In this study, we show that this segregation could be used for mapping stem rust resistance. Populations of pre-selected donors from the Russian Federation, the USA and Austria were tested on a single-plant basis for stem rust resistance by a leaf-segment test with three rust isolates. Seventy-four plants per population were genotyped with a 10 K-SNP chip. Using cumulative logit models, significant associations between the ordinal infection score and the marker alleles could be found. Three different loci (Pgs1, Pgs2, Pgs3) in three populations were highly significant, and resistance-linked markers could be validated with field experiments of an independent seed sample from the original population and were used to fix two populations for resistance. We showed that it is possible to map monogenically inherited seedling resistance genes directly in genetic resources, thus providing a competitive alternative to linkage mapping approaches that require a tedious and time-consuming inbreeding over several generations.
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Affiliation(s)
- Paul Gruner
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - Anne-Kristin Schmitt
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - Kerstin Flath
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, 70593, Stuttgart, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
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9
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Vidakovic DO, Perovic D, Semilet TV, Börner A, Khlestkina EK. The consensus rye microsatellite map with EST-SSRs transferred from wheat. Vavilovskii Zhurnal Genet Selektsii 2021; 24:459-464. [PMID: 33659829 PMCID: PMC7716552 DOI: 10.18699/vj20.48-o] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.
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Affiliation(s)
- D O Vidakovic
- Julius Kuehn-Institute (JKI), Quedlinburg, Germany University of Novi Sad, Department of Biology and Ecology, Novi Sad, Serbia
| | - D Perovic
- Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - T V Semilet
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - A Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - E K Khlestkina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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10
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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nat Genet 2021; 53:564-573. [PMID: 33737754 PMCID: PMC8035072 DOI: 10.1038/s41588-021-00807-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
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11
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Li G, Wang L, Yang J, He H, Jin H, Li X, Ren T, Ren Z, Li F, Han X, Zhao X, Dong L, Li Y, Song Z, Yan Z, Zheng N, Shi C, Wang Z, Yang S, Xiong Z, Zhang M, Sun G, Zheng X, Gou M, Ji C, Du J, Zheng H, Doležel J, Deng XW, Stein N, Yang Q, Zhang K, Wang D. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nat Genet 2021; 53:574-584. [PMID: 33737755 PMCID: PMC8035075 DOI: 10.1038/s41588-021-00808-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
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Affiliation(s)
- Guangwei Li
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Lijian Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Jianping Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Hang He
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Huaibing Jin
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xuming Li
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Tianheng Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Zhenglong Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Feng Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xue Han
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiaoge Zhao
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lingli Dong
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhongping Song
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zehong Yan
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Nannan Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Cuilan Shi
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zhaohui Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Shuling Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zijun Xiong
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Menglan Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Guanghua Sun
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xu Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Mingyue Gou
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Changmian Ji
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Junkai Du
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Hongkun Zheng
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Jaroslav Doležel
- grid.454748.eInstitute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Xing Wang Deng
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Qinghua Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Kunpu Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
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12
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Góralska M, Bińkowski J, Lenarczyk N, Bienias A, Grądzielewska A, Czyczyło-Mysza I, Kapłoniak K, Stojałowski S, Myśków B. How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data. Int J Mol Sci 2020; 21:E7501. [PMID: 33053706 PMCID: PMC7593958 DOI: 10.3390/ijms21207501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.
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Affiliation(s)
- Magdalena Góralska
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Jan Bińkowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Natalia Lenarczyk
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Anna Bienias
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Agnieszka Grądzielewska
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, ul. Akademicka, 20–950 Lublin, Poland;
| | - Ilona Czyczyło-Mysza
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Kamila Kapłoniak
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland; (I.C.-M.); (K.K.)
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland; (M.G.); (J.B.); (N.L.); (A.B.); (S.S.)
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13
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Gruner P, Schmitt AK, Flath K, Schmiedchen B, Eifler J, Gordillo A, Schmidt M, Korzun V, Fromme FJ, Siekmann D, Tratwal A, Danielewicz J, Korbas M, Marciniak K, Krysztofik R, Niewińska M, Koch S, Piepho HP, Miedaner T. Mapping Stem Rust ( Puccinia graminis f. sp. secalis) Resistance in Self-Fertile Winter Rye Populations. FRONTIERS IN PLANT SCIENCE 2020; 11:667. [PMID: 32528509 PMCID: PMC7265987 DOI: 10.3389/fpls.2020.00667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 06/03/2023]
Abstract
Rye stem rust caused by Puccinia graminis f. sp. secalis can be found in all European rye growing regions. When the summers are warm and dry, the disease can cause severe yield losses over large areas. To date only little research was done in Europe to trigger resistance breeding. To our knowledge, all varieties currently registered in Germany are susceptible. In this study, three biparental populations of inbred lines and one testcross population developed for mapping resistance were investigated. Over 2 years, 68-70 genotypes per population were tested, each in three locations. Combining the phenotypic data with genotyping results of a custom 10k Infinium iSelect single nucleotide polymorphism (SNP) array, we identified both quantitatively inherited adult plant resistance and monogenic all-stage resistance. A single resistance gene, tentatively named Pgs1, located at the distal end of chromosome 7R, could be identified in two independently developed populations. With high probability, it is closely linked to a nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene homolog. A marker for a competitive allele-specific polymerase chain reaction (KASP) genotyping assay was designed that could explain 73 and 97% of the genetic variance in each of both populations, respectively. Additional investigation of naturally occurring rye leaf rust (caused by Puccinia recondita ROEBERGE) revealed a gene complex on chromosome 7R. The gene Pgs1 and further identified quantitative trait loci (QTL) have high potential to be used for breeding stem rust resistant rye.
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Affiliation(s)
- Paul Gruner
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Anne-Kristin Schmitt
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Kleinmachnow, Germany
| | - Kerstin Flath
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Kleinmachnow, Germany
| | | | | | | | | | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, Kazan, Russia
| | | | | | - Anna Tratwal
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | - Jakub Danielewicz
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | - Marek Korbas
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | | | | | | | - Silvia Koch
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
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14
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Masojć P, Kruszona P, Bienias A, Milczarski P. A complex network of QTL for thousand-kernel weight in the rye genome. J Appl Genet 2020; 61:337-348. [PMID: 32356077 PMCID: PMC7413868 DOI: 10.1007/s13353-020-00559-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 11/26/2022]
Abstract
Here, QTL mapping for thousand-kernel weight carried out within a 541 × Ot1-3 population of recombinant inbred lines using high-density DArT-based map and three methods (single-marker analysis with F parametric test, marker analysis with the Kruskal–Wallis K* nonparametric test, and the recently developed analysis named genes interaction assorting by divergent selection with χ2 test) revealed 28 QTL distributed over all seven rye chromosomes. The first two methods showed a high level of consistency in QTL detection. Each of 13 QTL revealed in the course of gene interaction assorting by divergent selection analysis coincided with those detected by the two other methods, confirming the reliability of the new approach to QTL mapping. Its unique feature of discriminating QTL classes might help in selecting positively acting QTL and alleles for marker-assisted selection. Also, interaction among seven QTL for thousand-kernel weight was analyzed using gene interaction assorting by the divergent selection method. Pairs of QTL showed a predominantly additive relationship, but epistatic and complementary types of two-loci interactions were also revealed.
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Affiliation(s)
- Piotr Masojć
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Piotr Kruszona
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Anna Bienias
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland.
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15
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Borzęcka E, Hawliczek-Strulak A, Bolibok L, Gawroński P, Tofil K, Milczarski P, Stojałowski S, Myśków B, Targońska-Karasek M, Grądzielewska A, Smolik M, Kilian A, Bolibok-Brągoszewska H. Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye. Sci Rep 2018; 8:8428. [PMID: 29849048 PMCID: PMC5976670 DOI: 10.1038/s41598-018-26541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.
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Affiliation(s)
- Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Anna Hawliczek-Strulak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Małgorzata Targońska-Karasek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Agnieszka Grądzielewska
- Institute of Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Miłosz Smolik
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari st, ACT 2617, Bruce, Australia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
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16
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Tyrka M, Oleszczuk S, Rabiza-Swider J, Wos H, Wedzony M, Zimny J, Ponitka A, Ślusarkiewicz-Jarzina A, Metzger RJ, Baenziger PS, Lukaszewski AJ. Populations of doubled haploids for genetic mapping in hexaploid winter triticale. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:46. [PMID: 29623004 PMCID: PMC5878199 DOI: 10.1007/s11032-018-0804-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9 cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics.
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Affiliation(s)
- M. Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Poland
| | - S. Oleszczuk
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - J. Rabiza-Swider
- Department of Ornamental Plants, Warsaw University of Life Sciences, Warsaw, Poland
| | - H. Wos
- Plant Breeding Strzelce Ltd., Co. - IHAR-PIB Group, Strzelce, Poland
| | - M. Wedzony
- Department of Cell Biology and Genetics, Pedagogical University of Cracow, Kraków, Poland
| | - J. Zimny
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - A. Ponitka
- Institute of Plant Genetics, Poznan, Poland
| | | | - R. J. Metzger
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002 USA
| | - P. S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE USA
| | - A. J. Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
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