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Rohner M, Manzanares C, Yates S, Thorogood D, Copetti D, Lübberstedt T, Asp T, Studer B. Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses. Mol Biol Evol 2022; 40:6882748. [PMID: 36477354 PMCID: PMC9825253 DOI: 10.1093/molbev/msac259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.
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Affiliation(s)
- Marius Rohner
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland,Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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Herridge R, McCourt T, Jacobs JME, Mace P, Brownfield L, Macknight R. Identification of the genes at S and Z reveals the molecular basis and evolution of grass self-incompatibility. FRONTIERS IN PLANT SCIENCE 2022; 13:1011299. [PMID: 36330270 PMCID: PMC9623065 DOI: 10.3389/fpls.2022.1011299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Self-incompatibility (SI) is a feature of many flowering plants, whereby self-pollen is recognized and rejected by the stigma. In grasses (Poaceae), the genes controlling this phenomenon have not been fully elucidated. Grasses have a unique two-locus system, in which two independent genetic loci (S and Z) control self-recognition. S and Z are thought to have arisen from an ancient duplication, common to all grasses. With new chromosome-scale genome data, we examined the genes present at S- and Z-loci, firstly in ryegrass (Lolium perenne), and subsequently in ~20 other grass species. We found that two DUF247 genes and a short unstructured protein (SP/ZP) were present at both S- and Z- in all SI species, while in self-compatible species these genes were often lost or mutated. Expression data suggested that DUF247 genes acted as the male components and SP/ZP were the female components. Consistent with their role in distinguishing self- from non-self, all genes were hypervariable, although key secondary structure features were conserved, including the predicted N-terminal cleavage site of SP/ZP. The evolutionary history of these genes was probed, revealing that specificity groups at the Z-locus arose before the advent of various grass subfamilies/species, while specificity groups at the S-locus arose after the split of Panicoideae, Chloridoideae, Oryzoideae and Pooideae. Finally, we propose a model explaining how the proteins encoded at the S and Z loci might function to specify self-incompatibility.
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Affiliation(s)
- Rowan Herridge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tyler McCourt
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Peter Mace
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Richard Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Laugerotte J, Baumann U, Sourdille P. Genetic control of compatibility in crosses between wheat and its wild or cultivated relatives. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:812-832. [PMID: 35114064 PMCID: PMC9055826 DOI: 10.1111/pbi.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 01/20/2022] [Indexed: 05/16/2023]
Abstract
In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilisers. For this purpose, one possible issue is to cross-elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review, we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat (Triticum aestivum L.) and rye (Secale cereale), which lead to the creation of Triticale (x Triticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.
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Affiliation(s)
- Julie Laugerotte
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
| | - Ute Baumann
- School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Pierre Sourdille
- Genetics, Diversity and Ecophysiology of CerealsINRAEUniversité Clermont‐AuvergneClermont‐FerrandFrance
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Cropano C, Place I, Manzanares C, Do Canto J, Lübberstedt T, Studer B, Thorogood D. Characterization and practical use of self-compatibility in outcrossing grass species. ANNALS OF BOTANY 2021; 127:841-852. [PMID: 33755100 PMCID: PMC8225281 DOI: 10.1093/aob/mcab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Self-incompatibility (SI) systems prevent self-fertilization in several species of Poaceae, many of which are economically important forage, bioenergy and turf grasses. Self-incompatibility ensures cross-pollination and genetic diversity but restricts the ability to fix useful genetic variation. In most inbred crops it is possible to develop high-performing homozygous parental lines by self-pollination, which then enables the creation of F1 hybrid varieties with higher performance, a phenomenon known as heterosis. The inability to fully exploit heterosis in outcrossing grasses is partially responsible for lower levels of improvement in breeding programmes compared with inbred crops. However, SI can be overcome in forage grasses to create self-compatible populations. This is generating interest in understanding the genetical basis of self-compatibility (SC), its significance for reproductive strategies and its exploitation for crop improvement, especially in the context of F1 hybrid breeding. SCOPE We review the literature on SI and SC in outcrossing grass species. We review the currently available genomic tools and approaches used to discover and characterize novel SC sources. We discuss opportunities barely explored for outcrossing grasses that SC facilitates. Specifically, we discuss strategies for wide SC introgression in the context of the Lolium-Festuca complex and the use of SC to develop immortalized mapping populations for the dissection of a wide range of agronomically important traits. The germplasm available is a valuable practical resource and will aid understanding the basis of inbreeding depression and hybrid vigour in key temperate forage grass species. CONCLUSIONS A better understanding of the genetic control of additional SC loci offers new insight into SI systems, their evolutionary origins and their reproductive significance. Heterozygous outcrossing grass species that can be readily selfed facilitate studies of heterosis. Moreover, SC introduction into a range of grass species will enable heterosis to be exploited in innovative ways in genetic improvement programmes.
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Affiliation(s)
- Claudio Cropano
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Deutsche Saatveredelung AG, Lippstadt, Germany
| | - Iain Place
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Javier Do Canto
- Instituto Nacional de Investigación Agropecuaria (INIA), 4500 Tacuarembó, Uruguay
| | | | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Manzanares C, Barth S, Thorogood D, Byrne SL, Yates S, Czaban A, Asp T, Yang B, Studer B. A Gene Encoding a DUF247 Domain Protein Cosegregates with the S Self-Incompatibility Locus in Perennial Ryegrass. Mol Biol Evol 2015; 33:870-84. [PMID: 26659250 DOI: 10.1093/molbev/msv335] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The grass family (Poaceae), the fourth largest family of flowering plants, encompasses the most economically important cereal, forage, and energy crops, and exhibits a unique gametophytic self-incompatibility (SI) mechanism that is controlled by at least two multiallelic and independent loci, S and Z. Despite intense research efforts over the last six decades, the genes underlying S and Z remain uncharacterized. Here, we report a fine-mapping approach to identify the male component of the S-locus in perennial ryegrass (Lolium perenne L.) and provide multiple evidence that a domain of unknown function 247 (DUF247) gene is involved in its determination. Using a total of 10,177 individuals from seven different mapping populations segregating for S, we narrowed the S-locus to a genomic region containing eight genes, the closest recombinant marker mapping at a distance of 0.016 cM. Of the eight genes cosegregating with the S-locus, a highly polymorphic gene encoding for a protein containing a DUF247 was fully predictive of known S-locus genotypes at the amino acid level in the seven mapping populations. Strikingly, this gene showed a frameshift mutation in self-compatible darnel (Lolium temulentum L.), whereas all of the self-incompatible species of the Festuca-Lolium complex were predicted to encode functional proteins. Our results represent a major step forward toward understanding the gametophytic SI system in one of the most important plant families and will enable the identification of additional components interacting with the S-locus.
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Affiliation(s)
- Chloé Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland Teagasc Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Susanne Barth
- Teagasc Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Stephen L Byrne
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Steven Yates
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Adrian Czaban
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Bicheng Yang
- BGI-Shenzhen, Building 1, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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Whitford R, Fleury D, Reif JC, Garcia M, Okada T, Korzun V, Langridge P. Hybrid breeding in wheat: technologies to improve hybrid wheat seed production. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5411-28. [PMID: 24179097 DOI: 10.1093/jxb/ert333] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Global food security demands the development and delivery of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. There are several options for boosting wheat yields, but most offer only small yield increases. Wheat is an inbred plant, and hybrids hold the potential to deliver a major lift in yield and will open a wide range of new breeding opportunities. A series of technological advances are needed as a base for hybrid wheat programmes. These start with major changes in floral development and architecture to separate the sexes and force outcrossing. Male sterility provides the best method to block self-fertilization, and modifying the flower structure will enhance pollen access. The recent explosion in genomic resources and technologies provides new opportunities to overcome these limitations. This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a prerequisite for a commercial hybrid wheat system.
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Affiliation(s)
- Ryan Whitford
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
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ANNERSTEDT INGRID, LUNDQVIST ARNE. GENETICS OF SELF-INCOMPATIBILITY IN TRADESCANTIA PALUDOSA (COMMELINACEAE). Hereditas 2009. [DOI: 10.1111/j.1601-5223.1967.tb02139.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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LUNDQVIST ARNE, ØSTERBYE ULLA, LARSEN KNUD, LINDE-LAURSEN IB. Complex self-incompatibility systems in Ranunculus acris L. and Beta vulgaris L. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1973.tb01118.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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QARAEEN ARIFM. Lack of S-allele interaction in monocot Tradescantia paludosa, evidenced by pollen behaviour. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1980.tb01685.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hinata K, Watanabe M, Toriyama K, Isogai A. A Review of Recent Studies on Homomorphic Self-Incompatibility. INTERNATIONAL REVIEW OF CYTOLOGY 1993. [DOI: 10.1016/s0074-7696(08)61877-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Mutations affecting self-incompatibility in Phalaris coerulescens Desf. (Poaceae). Heredity (Edinb) 1992. [DOI: 10.1038/hdy.1992.72] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Dickinson HG, Crabbe MJ, Gaude T. Sporophytic self-incompatibility systems: S gene products. INTERNATIONAL REVIEW OF CYTOLOGY 1992; 140:525-61. [PMID: 1446983 DOI: 10.1016/s0074-7696(08)61108-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- H G Dickinson
- Department of Plant Sciences, University of Oxford, England
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The genetic control of self-compatibility in an inbred line of Lolium perenne L. Heredity (Edinb) 1991. [DOI: 10.1038/hdy.1991.77] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Ebert PR, Anderson MA, Bernatzky R, Altschuler M, Clarke AE. Genetic polymorphism of self-incompatibility in flowering plants. Cell 1989; 56:255-62. [PMID: 2643480 DOI: 10.1016/0092-8674(89)90899-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- P R Ebert
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Victoria, Australia
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Bernatzky R, Anderson MA, Clarke AE. Molecular genetics of self-incompatibility in flowering plants. ACTA ACUST UNITED AC 1988. [DOI: 10.1002/dvg.1020090102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fearon CH, Hayward MD, Lawrence MJ. Self-incompatibility in ryegrass VII. the determination of incompatibility genotypes in autotetraploid families of Lolium perenne L. Heredity (Edinb) 1984. [DOI: 10.1038/hdy.1984.97] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Sharma JR, Murty BR. Changes in genetic background under selection influencing the expression of self-incompatibility in Brassica campestris var. brown sarson. Genetica 1979. [DOI: 10.1007/bf00139497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wricke G. [Investigations on the inheritance of self-fertility in rye (Secale cereale)]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1969; 39:371-378. [PMID: 24435628 DOI: 10.1007/bf00290876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/1969] [Indexed: 06/03/2023]
Abstract
The cross between the rye variety 'Petkuser Kurzstroh' and self-fertile plants of the North-American variety 'Dakold' was carried out and seed setting of the F 1-generation and of the F 2- and F 3-generation produced by selfing was studied. In most cases seed setting was very high, only a few plants were self sterile, with fertile seeds ranging from 0-5 percent. Differences in the degree of fertility in the group of self-fertile plants are inherited and explained by subvital genes, which are not necessarily connected with the incompatibility system. To get more information on the inheritance of the self-fertility introduced by the variety 'Dakold' pollen tube growth after selfing and crossing within the progenies was studied with the help of the petri dish technique. On the basis of the results it is concluded that self-fertility is not caused by an allele of one of the incompatibility loci but by a third factor. Synergic action of this factor with the incompatibility genes and the possible interaction between the alleles of the incompatibility loci of the two different parents are discussed.
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Affiliation(s)
- G Wricke
- Institut für Angewandte Genetik der Technischen, Universität Hannover, Germany
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Gustafsson A. Reproduction mode and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1968; 38:109-117. [PMID: 24442135 DOI: 10.1007/bf00934200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The author has tried to accumulate data on the reproduction modes of crop plants: autogamy and allogamy in the case of sexuality, involving self-fertility and self-sterility, and different means of vegetative propagation and apomixis. In combination with the state of ploidy and the basic chromosome number the different modes of reproduction exert a considerable influence on population structure and the success or failure of different methods applied in plant breeding. This relates to the use of selection, hybrid vigour (F1 heterosis), gene recombination, as well as polyploidy and induced or spontaneous mutation. It is pointed out that extranuclear (cytoplasmic) inheritance should not be neglected as a device also in the case of polyploidy and mutation.Transitional stages exist between autogamy and allogamy. Autogamy is obligate in no or at least very few cases. In allogamous species inbreeding and subsequent outcrossing are important features in their improvement by breeding. In dioecious, monoecious and hermaphroditic species the modes of reproduction can be switched into one another by appropriate methods of gene recombination, mutation and selection. Apomictic species, for instance several grasses, display a series of transitions between more or less obligatory apomixis (parthenogenesis and vivipary) and partial or complete sexuality.At the end of the article data are presented to indicate how various modes of reproduction influence the methods applied in the exploration and conservation of plant gene pools.Finally, the pioneer work on plant exploration carried out byVAVILOV, ZHUKOVSKY and their co-workers is emphasized. Favourable genes, chromosomes and cytoplasms present in natural populations have to be preserved. New favourable genes etc. should be continually produced by mutation. Preservation of old genes and induction of new genes are means of augmenting the breeders' resources in their efforts of continuous crop plant improvement.
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Affiliation(s)
- A Gustafsson
- Department of Forest Genetics, Royal College of Forestry, Stockholm
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