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Saubin M, Tellier A, Stoeckel S, Andrieux A, Halkett F. Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population. Mol Ecol 2024; 33:e16965. [PMID: 37150947 DOI: 10.1111/mec.16965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.
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Affiliation(s)
- Méline Saubin
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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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] [Grants] [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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Sun Y, Shen E, Hu Y, Wu D, Feng Y, Lao S, Dong C, Du T, Hua W, Ye CY, Zhu J, Zhu QH, Cai D, Skuza L, Qiu J, Fan L. Population genomic analysis reveals domestication of cultivated rye from weedy rye. MOLECULAR PLANT 2022; 15:552-561. [PMID: 34971791 DOI: 10.1016/j.molp.2021.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.
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Affiliation(s)
- Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China
| | - Enhui Shen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China
| | - Yiyu Hu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yu Feng
- Institute of Ecology, Zhejiang University, Hangzhou 310058, China
| | - Sangting Lao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chenfeng Dong
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Tianyu Du
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Wei Hua
- Institute of Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 322105, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jinhuan Zhu
- Institute of Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 322105, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Daguang Cai
- Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 71-415 Szczecin, Poland
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China.
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Schreiber M, Himmelbach A, Börner A, Mascher M. Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing. Evol Appl 2019; 12:66-77. [PMID: 30622636 PMCID: PMC6304746 DOI: 10.1111/eva.12624] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/19/2018] [Indexed: 12/20/2022] Open
Abstract
Rye (Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale. Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale. We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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Mousavi S, Mariotti R, Bagnoli F, Costantini L, Cultrera NGM, Arzani K, Pandolfi S, Vendramin GG, Torkzaban B, Hosseini-Mazinani M, Baldoni L. The eastern part of the Fertile Crescent concealed an unexpected route of olive (Olea europaea L.) differentiation. ANNALS OF BOTANY 2017; 119:1305-1318. [PMID: 28387783 PMCID: PMC5604562 DOI: 10.1093/aob/mcx027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/28/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. METHODS Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeo-botanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. KEY RESULTS The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. CONCLUSIONS Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication.
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Affiliation(s)
- Soraya Mousavi
- CNR - Institute for Agricultural and Forest Systems in the Mediterranean, via Madonna Alta, 128, 06128 Perugia, Italy
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- Co-first authors: These authors contributed equally to this work
| | - Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- Co-first authors: These authors contributed equally to this work
| | - Francesca Bagnoli
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Costantini
- ISMEO - International Association of Mediterranean and Oriental Studies, Corso Vittorio Emanuele II, 244, 00186 Rome, Italy
| | - Nicolò G. M. Cultrera
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Kazem Arzani
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Giovanni Giuseppe Vendramin
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Bahareh Torkzaban
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
| | - Mehdi Hosseini-Mazinani
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- For correspondence. E-mail or
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- For correspondence. E-mail or
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7
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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8
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Unterseer S, Pophaly SD, Peis R, Westermeier P, Mayer M, Seidel MA, Haberer G, Mayer KFX, Ordas B, Pausch H, Tellier A, Bauer E, Schön CC. A comprehensive study of the genomic differentiation between temperate Dent and Flint maize. Genome Biol 2016; 17:137. [PMID: 27387028 PMCID: PMC4937532 DOI: 10.1186/s13059-016-1009-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/15/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far. Understanding the genomic differences between germplasm pools may contribute to a better understanding of the complementarity in heterotic patterns exploited in hybrid breeding and of mechanisms involved in adaptation to different environments. RESULTS We perform whole-genome screens for signatures of selection specific to temperate Dent and Flint maize by comparing high-density genotyping data of 70 American and European Dent and 66 European Flint inbred lines. We find 2.2 % and 1.4 % of the genes are under selective pressure, respectively, and identify candidate genes associated with agronomic traits known to differ between the two pools. Taking flowering time as an example for the differentiation between Dent and Flint, we investigate candidate genes involved in the flowering network by phenotypic analyses in a Dent-Flint introgression library and find that the Flint haplotypes of the candidates promote earlier flowering. Within the flowering network, the majority of Flint candidates are associated with endogenous pathways in contrast to Dent candidate genes, which are mainly involved in response to environmental factors like light and photoperiod. The diversity patterns of the candidates in a unique panel of more than 900 individuals from 38 European landraces indicate a major contribution of landraces from France, Germany, and Spain to the candidate gene diversity of the Flint elite lines. CONCLUSIONS In this study, we report the investigation of pool-specific differences between temperate Dent and Flint on a genome-wide scale. The identified candidate genes represent a promising source for the functional investigation of pool-specific haplotypes in different genetic backgrounds and for the evaluation of their potential for future crop improvement like the adaptation to specific environments.
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Affiliation(s)
- Sandra Unterseer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Saurabh D Pophaly
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Regina Peis
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Peter Westermeier
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.,Present Address: Institute for Crop Science and Plant Breeding, Bavarian State Research Center, 85354, Freising, Germany
| | - Manfred Mayer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Michael A Seidel
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Georg Haberer
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bernardo Ordas
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), 36080, Pontevedra, Spain
| | - Hubert Pausch
- Animal Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Eva Bauer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
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9
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Monteiro F, Vidigal P, Barros AB, Monteiro A, Oliveira HR, Viegas W. Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources. FRONTIERS IN PLANT SCIENCE 2016; 7:1334. [PMID: 27630658 PMCID: PMC5006150 DOI: 10.3389/fpls.2016.01334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/18/2016] [Indexed: 05/21/2023]
Abstract
Rye (Secale cereale L.) is a cereal crop of major importance in many parts of Europe and rye breeders are presently very concerned with the restrict pool of rye genetic resources available. Such narrowing of rye genetic diversity results from the presence of "Petkus" pool in most modern rye varieties as well as "Petkus" × "Carsten" heterotic pool in hybrid rye breeding programs. Previous studies on rye's genetic diversity revealed moreover a common genetic background on landraces (ex situ) and cultivars, regardless of breeding level or geographical origin. Thus evaluation of in situ populations is of utmost importance to unveil "on farm" diversity, which is largely undervalued. Here, we perform the first comprehensive assessment of rye's genetic diversity and population structuring using cultivars, ex situ landraces along a comprehensive sampling of in situ accessions from Portugal, through a molecular-directed analysis using SSRs markers. Rye genetic diversity and population structure analysis does not present any geographical trend but disclosed marked differences between genetic backgrounds of in situ accessions and those of cultivars/ex situ collections. Such genetic distinctiveness of in situ accessions highlights their unexplored potential as new genetic resources, which can be used to boost rye breeding strategies and the production of new varieties. Overall, our study successfully demonstrates the high prospective impact of comparing genetic diversity and structure of cultivars, ex situ, and in situ samples in ascertaining the status of plant genetic resources (PGR).
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Affiliation(s)
- Filipa Monteiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
- *Correspondence: Filipa Monteiro
| | - Patrícia Vidigal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - André B. Barros
- Colégio F3 Food, Farming and Forestry, Universidade de LisboaLisboa, Portugal
| | - Ana Monteiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Hugo R. Oliveira
- Plant Biology/Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoPorto, Portugal
- Faculty of Life Sciences, Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Wanda Viegas
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
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