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Gao M, Hua T, Niu G, Masabni J, Dewalt W. A locus-dependent mixed inheritance in the segmental allohexaploid sweetpotato ( Ipomoea batatas [L.] Lam). FRONTIERS IN PLANT SCIENCE 2024; 15:1398081. [PMID: 38863536 PMCID: PMC11165125 DOI: 10.3389/fpls.2024.1398081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024]
Abstract
Two interrelated aspects of the sweetpotato genome, its polyploid origin and inheritance type, remain uncertain. We recently proposed a segmental allohexaploid sweetpotato and thus sought to clarify its inheritance type by direct analyses of homoeolog segregations at selected single-copy loci. For such analyses, we developed a digital quantitative PCR genotyping method using one nondiscriminatory and three discriminatory probes for each selected locus to discriminate and quantify three homoeolog-differentiating variation types (homoeolog-types) in genomic DNA samples for genotype fitting and constructed a F2 population for segregation analyses. We confirmed inter-subgenomic distinctions of three identified homoeolog-types at each of five selected loci by their interspecific differentiations among 14 species in Ipomoea section batatas and genotyped the loci in 549 F2 lines, selected F1 progenies, and their founding parents. Segregation and genotype analyses revealed a locus-dependent mixed inheritance (disomic, polysomic, and intermediate types) of the homoeolog-types at 4 loci in the F2 population, displaying estimated disomic-inheritance frequencies of 0, 2.72%, 14.52%, and 36.92%, and probably in the F1 population too. There were also low-frequency non-hexaploid F1 and F2 genotypes that were probably derived from double-reduction recombination or partially unreduced gametes, and F2 genotypes of apparent aneuploids/dysploids with neopolyploid-like frequencies. Additional analyses of homoeolog-type genotypes at the 5 loci in 46 lines from various regions revealed locus-dependent selection biases, favoring genotypes having more of one homoeolog-type, i.e. more of di- or homogenized homoeolog-type composition, and one-direction ploidy trending among apparent aneuploids/dysploids. These inheritance features pointed to an evolving segmental allohexaploid sweetpotato impacted by selection biases.
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Affiliation(s)
- Ming Gao
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Tien Hua
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Genhua Niu
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Joe Masabni
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Willie Dewalt
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
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Nishio S, Shirasawa K, Nishimura R, Takeuchi Y, Imai A, Mase N, Takada N. A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17. FRONTIERS IN PLANT SCIENCE 2024; 15:1360185. [PMID: 38504898 PMCID: PMC10948449 DOI: 10.3389/fpls.2024.1360185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), '415-1', by using γ-irradiated pollen. '415-1' carries the S-genotype S4dS5S5, with "d" indicating a duplication of S 5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between '515-20' (S1S3) and '415-1'. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.
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Affiliation(s)
- Sogo Nishio
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Ryotaro Nishimura
- Fruit Tree Smart Production Group, Division of Fruit Tree Production Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Higashihiroshima, Japan
| | - Yukie Takeuchi
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Atsushi Imai
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Nobuko Mase
- Citrus Breeding and Production Group, Division of Citrus Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Shizuoka, Japan
| | - Norio Takada
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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Lv Z, Addo Nyarko C, Ramtekey V, Behn H, Mason AS. Defining autopolyploidy: Cytology, genetics, and taxonomy. AMERICAN JOURNAL OF BOTANY 2024:e16292. [PMID: 38439575 DOI: 10.1002/ajb2.16292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 03/06/2024]
Abstract
Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker-segregation-based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.
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Affiliation(s)
- Zhenling Lv
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Charles Addo Nyarko
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Vinita Ramtekey
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- ICAR-Indian Institute of Seed Science, 275103, Mau, India
| | - Helen Behn
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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Duan T, Sicard A, Glémin S, Lascoux M. Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris. eLife 2024; 12:RP88398. [PMID: 38189348 PMCID: PMC10945474 DOI: 10.7554/elife.88398] [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] [Indexed: 01/09/2024] Open
Abstract
Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural SciencesUppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
- UMR CNRS 6553 ECOBIO, Campus BeaulieuRennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [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: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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Bird KA, Pires JC, VanBuren R, Xiong Z, Edger PP. Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus. Genetics 2023; 225:iyad114. [PMID: 37338008 PMCID: PMC10471226 DOI: 10.1093/genetics/iyad114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/10/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.
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Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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Mangena P. Cell Mutagenic Autopolyploidy Enhances Salinity Stress Tolerance in Leguminous Crops. Cells 2023; 12:2082. [PMID: 37626892 PMCID: PMC10453822 DOI: 10.3390/cells12162082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/30/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Salinity stress affects plant growth and development by causing osmotic stress and nutrient imbalances through excess Na+, K+, and Cl- ion accumulations that induce toxic effects during germination, seedling development, vegetative growth, flowering, and fruit set. However, the effects of salt stress on growth and development processes, especially in polyploidized leguminous plants, remain unexplored and scantly reported compared to their diploid counterparts. This paper discusses the physiological and molecular response of legumes towards salinity stress-based osmotic and ionic imbalances in plant cells. A multigenic response involving various compatible solutes, osmolytes, ROS, polyamines, and antioxidant activity, together with genes encoding proteins involved in the signal transduction, regulation, and response mechanisms to this stress, were identified and discussed. This discussion reaffirms polyploidization as the driving force in plant evolution and adaptation to environmental stress constraints such as drought, feverish temperatures, and, in particular, salt stress. As a result, thorough physiological and molecular elucidation of the role of gene duplication through induced autopolyploidization and possible mechanisms regulating salinity stress tolerance in grain legumes must be further studied.
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Affiliation(s)
- Phetole Mangena
- Department of Biodiversity, School of Molecular and Life Sciences, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
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Katche EI, Schierholt A, Schiessl SV, He F, Lv Z, Batley J, Becker HC, Mason AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus. G3 (BETHESDA, MD.) 2023; 13:jkad136. [PMID: 37313757 PMCID: PMC10411605 DOI: 10.1093/g3journal/jkad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.
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Affiliation(s)
- Elizabeth Ihien Katche
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Antje Schierholt
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Sarah-Veronica Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main D-60325, Germany
| | - Fei He
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
| | - Zhenling Lv
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Heiko C Becker
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. THE NEW PHYTOLOGIST 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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10
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Liu C, Wang YG. Does one subgenome become dominant in the formation and evolution of a polyploid? ANNALS OF BOTANY 2023; 131:11-16. [PMID: 35291007 PMCID: PMC9904339 DOI: 10.1093/aob/mcac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/15/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution. SCOPE In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered. CONCLUSIONS Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.
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Affiliation(s)
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, Queensland, Australia
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Kashyap A, Garg P, Tanwar K, Sharma J, Gupta NC, Ha PTT, Bhattacharya RC, Mason AS, Rao M. Strategies for utilization of crop wild relatives in plant breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4151-4167. [PMID: 36136128 DOI: 10.1007/s00122-022-04220-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Crop wild relatives (CWRs) are weedy and wild relatives of the domesticated and cultivated crops, which usually occur and are maintained in natural forms in their centres of origin. These include the ancestors or progenitors of all cultivated species and comprise rich sources of diversity for many important traits useful in plant breeding. CWRs can play an important role in broadening genetic bases and introgression of economical traits into crops, but their direct use by breeders for varietal improvement program is usually not advantageous due to the presence of crossing or chromosome introgression barriers with cultivated species as well as their high frequencies of agronomically undesirable alleles. Linkage drag may subsequently result in unfavourable traits in the subsequent progeny when segments of the genome linked with quantitative trait loci (QTL), or a phenotype, are introgressed from wild germplasm. Here, we first present an overview in regards to the contribution that wild species have made to improve biotic, abiotic stress tolerances and yield-related traits in crop varieties, and secondly summarise the various challenges which are experienced in interspecific hybridization along with their probable solutions. We subsequently suggest techniques for readily harnessing these wild relatives for fast and effective introgression of exotic alleles in pre-breeding research programs.
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Affiliation(s)
- Anamika Kashyap
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pooja Garg
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Kunal Tanwar
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Jyoti Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Navin C Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pham Thi Thu Ha
- Genomic Research Institute & Seed, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - R C Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | | | - Mahesh Rao
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India.
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12
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Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. FRONTIERS IN PLANT SCIENCE 2022; 13:1057953. [PMID: 36466276 PMCID: PMC9716091 DOI: 10.3389/fpls.2022.1057953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 05/26/2023]
Abstract
In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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13
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Obermeier C, Mason AS, Meiners T, Petschenka G, Rostás M, Will T, Wittkop B, Austel N. Perspectives for integrated insect pest protection in oilseed rape breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3917-3946. [PMID: 35294574 PMCID: PMC9729155 DOI: 10.1007/s00122-022-04074-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/01/2022] [Indexed: 05/02/2023]
Abstract
In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.
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Affiliation(s)
- Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Torsten Meiners
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
| | - Georg Petschenka
- Department of Applied Entomology, University of Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
| | - Michael Rostás
- Division of Agricultural Entomology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany
| | - Torsten Will
- Insitute for Resistance Research and Stress Tolerance, Julius Kühn Insitute, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Nadine Austel
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
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14
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Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202684. [PMID: 36297708 PMCID: PMC9609754 DOI: 10.3390/plants11202684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/12/2023]
Abstract
The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
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Affiliation(s)
- Md Mazharul Islam
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
- Research and Development, Horticultural Crop Breeding, Quality Feeds Limited, Dhaka 1230, Bangladesh
| | - Deen Mohammad Deepo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation (GCER), College of Engineering Science and Environment, The University of Newcastle, Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Abu Bakar Siddique
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Oliul Hassan
- Department of Ecology and Environmental System, College of Ecology and Environmental Sciences, Kyungpook National University, Sangju 37224, Korea
| | - Abu Bakar Siddique
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Narayan Chandra Paul
- Kumho Life Science Laboratory, Department of Integrative Food Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
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15
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Performance and Genetic Parameters of Poplar Hybrids and Clones in a Field Trial Are Modified by Contrasting Environmental Conditions during the Vegetative Propagation Phase. PLANTS 2022; 11:plants11182401. [PMID: 36145802 PMCID: PMC9505758 DOI: 10.3390/plants11182401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/30/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022]
Abstract
This study investigates epigenetics-like phenomena: how performance phenotypic plasticity, genotypic variation, and the heritability of growth traits and total phenolic compounds of Populus hybrids and clones in field trials may be modified by contrasting temperature conditions at their vegetation propagation phase. The significant effect of rooting–growing conditions on further tree performance in field trials was found for height increment in 2020, although the interaction hybrid by rooting–growing conditions was highly significant for phenolic compounds, tree height, and diameter, meaning that the performance of some hybrids was affected by rooting–growing conditions, thus demonstrating epigenetic-like effects. For phenolic compounds, interactions were also significant at the clonal level. High estimates of ecovalency indicate that some hybrids are ecologically sensitive, and epigenetic-like phenomena might occur. Hybrid P. balsamifera × P. trichocarpa is characterized by high ecovalency and specific adaptations according to mean tree height when vegetatively propagated under different rooting–growing conditions. Low estimates of P. deltoides × P. trichocarpa ecovalency demonstrate a general adaptation according to mean tree height in a field trial. Vegetative propagation conditions have also altered the genetic variation of traits in trees being planted in field trials.
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16
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Zhu M, Yang L, Zhang Y, Zhuang M, Ji J, Hou X, Li Z, Han F, Fang Z, Lv H, Wang Y. Introgression of clubroot resistant gene into Brassica oleracea L. from Brassica rapa based on homoeologous exchange. HORTICULTURE RESEARCH 2022; 9:uhac195. [PMID: 37180031 PMCID: PMC10167419 DOI: 10.1093/hr/uhac195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/26/2022] [Indexed: 05/15/2023]
Abstract
Clubroot is a soil-borne disease in cabbage (Brassica oleracea L. var. capitata L.) caused by Plasmodiophora brassicae, which poses a great threat to cabbage production. However, clubroot resistance (CR) genes in Brassica rapa could be introduced into the cabbage via breeding to make it clubroot resistant. In this study, CR genes from B. rapa were introduced into the cabbage genome and the mechanism of gene introgression was explored. Two methods were used to create CR materials: (i) The fertility of CR Ogura CMS cabbage germplasms containing CRa was restored by using an Ogura CMS restorer. After cytoplasmic replacement and microspore culture, CRa-positive microspore individuals were obtained. (ii) Distant hybridization was performed between cabbage and B. rapa, which contained three CR genes (CRa, CRb, and Pb8.1). Finally, BC2 individuals containing all three CR genes were obtained. Inoculation results showed that both CRa-positive microspore individuals and BC2 individuals containing three CR genes were resistant to race 4 of P. brassicae. Sequencing results from CRa-positive microspore individuals with specific molecular markers and genome-wide association study (GWAS) showed penetration at the homologous position of the cabbage genome by a 3.42 Mb CRa containing a fragment from B. rapa; indicating homoeologous exchange (HE) as the theoretical basis for the introgression of CR resistance. The successful introduction of CR into the cabbage genome in the present study can provide useful clues for creating introgression lines within other species of interest.
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Affiliation(s)
- Mingzhao Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Vegetable Science, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhansheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fengqing Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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17
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Roberts EK, Tardif S, Wright EA, Platt RN, Bradley RD, Hardy DM. Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria. Genome Biol 2022; 23:155. [PMID: 35821049 PMCID: PMC9275260 DOI: 10.1186/s13059-022-02721-y] [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] [Received: 11/18/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediates species-specific adhesion to the egg's zona pellucida, is a speciation gene in placental mammals. RESULTS Genomic ontogeny reveals that Zan arose by repurposing of a stem vertebrate gene that was lost in multiple lineages but retained in Eutheria on acquiring a function in egg recognition. A 112-species Zan sequence phylogeny, representing 17 of 19 placental Orders, resolves all species into monophyletic groups corresponding to recognized Orders and Suborders, with <5% unsupported nodes. Three other rapidly evolving germ cell genes (Adam2, Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a mitochondrial gene commonly used for phylogenetic analyses (Cytb) all yield trees with poorer resolution than the Zan tree and inferior topologies relative to a widely accepted mammalian supertree. Zan divergence by intense positive selection produces dramatic species differences in the protein's properties, with ordinal divergence rates generally reflecting species richness of placental Orders consistent with expectations for a speciation gene that acts across a wide range of taxa. Furthermore, Zan's combined phylogenetic utility and divergence exceeds those of all other genes known to have evolved in Eutheria by positive selection, including the only other mammalian speciation gene, Prdm9. CONCLUSIONS Species-specific egg recognition conferred by Zan's functional divergence served as a mode of prezygotic reproductive isolation that promoted the extraordinary adaptive radiation and success of Eutheria.
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Affiliation(s)
- Emma K Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.,Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Steve Tardif
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Reproductive Biology Division, JangoBio, Fitchburg, WI, USA
| | - Emily A Wright
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Roy N Platt
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert D Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.,Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, USA
| | - Daniel M Hardy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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18
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Van Drunen WE, Johnson MTJ. Polyploidy in urban environments. Trends Ecol Evol 2022; 37:507-516. [PMID: 35246321 DOI: 10.1016/j.tree.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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19
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Bolaños-Villegas P, Chen FC. Advances and Perspectives for Polyploidy Breeding in Orchids. PLANTS 2022; 11:plants11111421. [PMID: 35684197 PMCID: PMC9183072 DOI: 10.3390/plants11111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
The orchid market is a dynamic horticultural business in which novelty and beauty command high prices. The two main interests are the development of flowers, from the miniature to the large and showy, and their fragrance. Overall organ size might be modified by doubling the chromosome number, which can be accomplished by careful study of meiotic chromosome disjunction in hybrids or species. Meiosis is the process in which diploid (2n) pollen mother cells recombine their DNA sequences and then undergo two rounds of division to give rise to four haploid (n) cells. Thus, by interfering in chromosome segregation, one can induce the development of diploid recombinant cells, called unreduced gametes. These unreduced gametes may be used for breeding polyploid progenies with enhanced fertility and large flower size. This review provides an overview of developments in orchid polyploidy breeding placed in the large context of meiotic chromosome segregation in the model plants Arabidopsis thaliana and Brassica napus to facilitate molecular translational research and horticultural innovation.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Fabio Baudrit Agricultural Research Station, University of Costa Rica, La Garita District, Alajuela 20101, Costa Rica
- Lankester Botanical Garden, University of Costa Rica, Dulce Nombre District, Cartago 30109, Costa Rica
- Faculty of Food and Agricultural Sciences, Rodrigo Facio Campus, School of Agronomy, University of Costa Rica, Montes de Oca County, San Jose 11503, Costa Rica
- Correspondence:
| | - Fure-Chyi Chen
- General Research Service Center, National Pingtung University of Science and Technology, #1 Shuefu Road, Neipu township, Pingtung 91201, Taiwan;
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20
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Quezada-Martinez D, Zou J, Zhang W, Meng J, Batley J, Mason AS. Allele segregation analysis of F 1 hybrids between independent Brassica allohexaploid lineages. Chromosoma 2022; 131:147-161. [PMID: 35511360 PMCID: PMC9470611 DOI: 10.1007/s00412-022-00774-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022]
Abstract
In the Brassica genus, we find both diploid species (one genome) and allotetraploid species (two different genomes) but no naturally occurring hexaploid species (three different genomes, AABBCC). Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuffling. Whether these genome rearrangements continue in later generations and whether genomic arrangements follow similar, reproducible patterns between different lineages is still unknown. We crossed Brassica hexaploids resulting from different species combinations to produce five F1 hybrids and analyzed the karyotypes of the parents and the F1 hybrids, as well as allele segregation in a resulting test-cross population via molecular karyotyping using SNP array genotyping. Although some genomic regions were found to be more likely to be duplicated, deleted, or rearranged, a consensus pattern was not shared between genotypes. Brassica hexaploids had a high tolerance for fixed structural rearrangements, but which rearrangements occur and become fixed over many generations does not seem to show either strong reproducibility or to indicate selection for stability. On average, we observed 10 de novo chromosome rearrangements contributed almost equally from both parents to the F1 hybrids. At the same time, the F1 hybrid meiosis produced on average 8.6 new rearrangements. Hence, the increased heterozygosity in the F1 hybrid did not significantly improve genome stability in our hexaploid hybrids and might have had the opposite effect. However, hybridization between lineages was readily achieved and may be exploited for future genetics and breeding purposes.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, University of Bonn, 53115, Bonn, Germany.,Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenshan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley 6009, Perth, Australia
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, 53115, Bonn, Germany. .,Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
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21
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Sharbrough J, Conover JL, Gyorfy MF, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Mol Biol Evol 2022; 39:6564157. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA.,Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
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22
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Assou J, Zhang D, Roth KDR, Steinke S, Hust M, Reinard T, Winkelmann T, Boch J. Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:649-663. [PMID: 34784073 DOI: 10.1111/tpj.15584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 05/21/2023]
Abstract
Food allergies are a major health issue worldwide. Modern breeding techniques such as genome editing via CRISPR/Cas9 have the potential to mitigate this by targeting allergens in plants. This study addressed the major allergen Bra j I, a seed storage protein of the 2S albumin class, in the allotetraploid brown mustard (Brassica juncea). Cotyledon explants of an Indian gene bank accession (CR2664) and the German variety Terratop were transformed using Agrobacterium tumefaciens harboring binary vectors with multiple single guide RNAs to induce either large deletions or frameshift mutations in both Bra j I homoeologs. A total of 49 T0 lines were obtained with up to 3.8% transformation efficiency. Four lines had large deletions of 566 up to 790 bp in the Bra j IB allele. Among 18 Terratop T0 lines, nine carried indels in the targeted regions. From 16 analyzed CR2664 T0 lines, 14 held indels and three had all four Bra j I alleles mutated. The majority of the CRISPR/Cas9-induced mutations were heritable to T1 progenies. In some edited lines, seed formation and viability were reduced and seeds showed a precocious development of the embryo leading to a rupture of the testa already in the siliques. Immunoblotting using newly developed Bra j I-specific antibodies revealed the amount of Bra j I protein to be reduced or absent in seed extracts of selected lines. Removing an allergenic determinant from mustard is an important first step towards the development of safer food crops.
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Affiliation(s)
- Juvenal Assou
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Dingbo Zhang
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Kristian D R Roth
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Institute of Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Reinard
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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Martín AC, Alabdullah AK, Moore G. A separation-of-function ZIP4 wheat mutant allows crossover between related chromosomes and is meiotically stable. Sci Rep 2021; 11:21811. [PMID: 34750469 PMCID: PMC8575954 DOI: 10.1038/s41598-021-01379-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Many species, including most flowering plants, are polyploid, possessing multiple genomes. During polyploidisation, fertility is preserved via the evolution of mechanisms to control the behaviour of these multiple genomes during meiosis. On the polyploidisation of wheat, the major meiotic gene ZIP4 duplicated and diverged, with the resulting new gene TaZIP4-B2 being inserted into chromosome 5B. Previous studies showed that this TaZIP4-B2 promotes pairing and synapsis between wheat homologous chromosomes, whilst suppressing crossover between related (homoeologous) chromosomes. Moreover, in wheat, the presence of TaZIP4-B2 preserves up to 50% of grain number. The present study exploits a 'separation-of-function' wheat Tazip4-B2 mutant named zip4-ph1d, in which the Tazip4-B2 copy still promotes correct pairing and synapsis between homologues (resulting in the same pollen profile and fertility normally found in wild type wheat), but which also allows crossover between the related chromosomes in wheat haploids of this mutant. This suggests an improved utility for the new zip4-ph1d mutant line during wheat breeding, compared to the previously described CRISPR Tazip4-B2 and ph1 mutant lines. The results also reveal that loss of suppression of homoeologous crossover between wheat chromosomes does not in itself reduce wheat fertility when promotion of homologous pairing and synapsis by TaZIP4-B2 is preserved.
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Affiliation(s)
- Azahara C Martín
- Crop Genetics Department, John Innes Centre, Colney, Norwich, NR4 7UH, UK.
| | | | - Graham Moore
- Crop Genetics Department, John Innes Centre, Colney, Norwich, NR4 7UH, UK
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24
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Morgan C, White MA, Franklin FCH, Zickler D, Kleckner N, Bomblies K. Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in Arabidopsis arenosa. Curr Biol 2021; 31:4713-4726.e4. [PMID: 34480856 PMCID: PMC8585506 DOI: 10.1016/j.cub.2021.08.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/23/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
Polyploidy is a major driver of evolutionary change. Autopolyploids, which arise by within-species whole-genome duplication, carry multiple nearly identical copies of each chromosome. This presents an existential challenge to sexual reproduction. Meiotic chromosome segregation requires formation of DNA crossovers (COs) between two homologous chromosomes. How can this outcome be achieved when more than two essentially equivalent partners are available? We addressed this question by comparing diploid, neo-autotetraploid, and established autotetraploid Arabidopsis arenosa using new approaches for analysis of meiotic CO patterns in polyploids. We discover that crossover interference, the classical process responsible for patterning of COs in diploid meiosis, is defective in the neo-autotetraploid but robust in the established autotetraploid. The presented findings suggest that, initially, diploid-like interference fails to act effectively on multivalent pairing and accompanying pre-CO recombination interactions and that stable autopolyploid meiosis can emerge by evolution of a “supercharged” interference process, which can now act effectively on such configurations. Thus, the basic interference mechanism responsible for simplifying CO patterns along chromosomes in diploid meiosis has evolved the capability to also simplify CO patterns among chromosomes in autopolyploids, thereby promoting bivalent formation. We further show that evolution of stable autotetraploidy preadapts meiosis to higher ploidy, which in turn has interesting mechanistic and evolutionary implications. In a neo-autotetraploid, aberrant crossover interference confers aberrant meiosis In a stable autotetraploid, regular crossover interference confers regular meiosis Crossover and synaptic patterns point to evolution of “supercharged” interference Accordingly, evolution of stable autotetraploidy preadapts to higher ploidies
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Affiliation(s)
- Chris Morgan
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Martin A White
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | - Denise Zickler
- University Paris-Saclay, Commissariat à l'Energie Atomique at aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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26
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Zhou Y, Zhu L, Sun Y, Zhang H, Wang J, Qin W, He W, Zhou L, Li Q, Zhao R, Luo K, Tang C, Zhang C, Liu S. Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂). Front Genet 2021; 12:717871. [PMID: 34567072 PMCID: PMC8458772 DOI: 10.3389/fgene.2021.717871] [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] [Received: 05/31/2021] [Accepted: 08/03/2021] [Indexed: 11/15/2022] Open
Abstract
Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF1, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF1, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF1. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF1 with significantly different expression levels.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - La Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Yu Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Hui Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Jiaojiao Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Weilin Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Wangchao He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Luojing Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Qi Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
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27
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Soares NR, Mollinari M, Oliveira GK, Pereira GS, Vieira MLC. Meiosis in Polyploids and Implications for Genetic Mapping: A Review. Genes (Basel) 2021; 12:genes12101517. [PMID: 34680912 PMCID: PMC8535482 DOI: 10.3390/genes12101517] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023] Open
Abstract
Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.
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Affiliation(s)
- Nina Reis Soares
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
| | - Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA;
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7555, USA
| | - Gleicy K. Oliveira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
| | - Guilherme S. Pereira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
- Department of Agronomy, Federal University of Viçosa, Viçosa 36570-900, Brazil
| | - Maria Lucia Carneiro Vieira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
- Correspondence:
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28
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Zhang K, Mason AS, Farooq MA, Islam F, Quezada-Martinez D, Hu D, Yang S, Zou J, Zhou W. Challenges and prospects for a potential allohexaploid Brassica crop. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2711-2726. [PMID: 34089067 DOI: 10.1007/s00122-021-03845-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/23/2021] [Indexed: 05/28/2023]
Abstract
The production of a new allohexaploid Brassica crop (2n = AABBCC) is increasingly attracting international interest: a new allohexaploid crop could benefit from several major advantages over the existing Brassica diploid and allotetraploid species, combining genetic diversity and traits from all six crop species with additional allelic heterosis from the extra genome. Although early attempts to produce allohexaploids showed mixed results, recent technological and conceptual advances have provided promising leads to follow. However, there are still major challenges which exist before this new crop type can be realized: (1) incorporation of sufficient genetic diversity to form a basis for breeding and improvement of this potential crop species; (2) restoration of regular meiosis, as most allohexaploids are genetically unstable after formation; and (3) improvement of agronomic traits to the level of "elite" breeding material in the diploid and allotetraploid crop species. In this review, we outline these major prospects and challenges and propose possible plans to produce a stable, diverse and agronomically viable allohexaploid Brassica crop.
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Affiliation(s)
- Kangni Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Muhammad A Farooq
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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29
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Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. BIOLOGY 2021; 10:biology10080771. [PMID: 34440003 PMCID: PMC8389541 DOI: 10.3390/biology10080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Simple Summary The selection of varieties more resilient to disease and climate change requires generating new genetic diversity for breeding. The main mechanism for reshuffling genetic information is through the recombination of chromosomes during meiosis. We showed in oilseed rape (Brassica napus, AACC, 2n = 4x = 38), which is a natural hybrid formed from a cross between turnip (B. rapa, AA, 2n = 2x = 20) and cabbage (B. oleracea, CC, 2n = 2x = 18), that there is significantly more crossovers occurring along the entire A chromosomes in allotriploid AAC (crossbetween B. napus and B. rapa) than in diploid AA or allotetraploid AACC hybrids. We demonstrated that these allotriploid AAC hybrids are highly efficient to introduce new variability within oilseed rape varieties, notably by enabling the introduction of small genomic regions carrying genes controlling agronomically interesting traits. Abstract Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Coleen Tanguy
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Maryse Lodé-Taburel
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Régine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Correspondence: ; Tel.: +33-2-23-48-51-31
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Roy SW. CRISPR-Cas Toxin-Antitoxin Systems: Selfishness as a Constructive Evolutionary Force. Trends Microbiol 2021; 29:869-870. [PMID: 34376346 DOI: 10.1016/j.tim.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
A recent paper (Li et al.) reports a novel RNA-based Cas-dependent toxin-antitoxin system with the effect of 'addicting' cells to the cassette. Broadly-defined addiction systems could stabilize diverse genomic features, raising the question of the role of selfish elements and intragenomic conflict in the evolution of biological complexity.
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Katche E, Gaebelein R, Idris Z, Vasquez-Teuber P, Lo YT, Nugent D, Batley J, Mason AS. Stable, fertile lines produced by hybridization between allotetraploids Brassica juncea (AABB) and Brassica carinata (BBCC) have merged the A and C genomes. THE NEW PHYTOLOGIST 2021; 230:1242-1257. [PMID: 33476056 DOI: 10.1111/nph.17225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Many flowering plant taxa contain allopolyploids that share one or more genomes in common. In the Brassica genus, crop species Brassica juncea and Brassica carinata share the B genome, with 2n = AABB and 2n = BBCC genome complements, respectively. Hybridization results in 2n = BBAC hybrids, but the fate of these hybrids over generations of self-pollination has never been reported. We produced and characterized B. juncea × B. carinata (2n = BBAC) interspecific hybrids over six generations of self-pollination under selection for high fertility using a combination of genotyping, fertility phenotyping, and cytogenetics techniques. Meiotic pairing behaviour improved from 68% bivalents in the F1 to 98% in the S5 /S6 generations, and initially low hybrid fertility also increased to parent species levels. The S5 /S6 hybrids contained an intact B genome (16 chromosomes) plus a new, stable A/C genome (18-20 chromosomes) resulting from recombination and restructuring of A and C-genome chromosomes. Our results provide the first experimental evidence that two genomes can come together to form a new, restructured genome in hybridization events between two allotetraploid species that share a common genome. This mechanism should be considered in interpreting phylogenies in taxa with multiple allopolyploid species.
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Affiliation(s)
- Elvis Katche
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Roman Gaebelein
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zurianti Idris
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paula Vasquez-Teuber
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
| | - Yu-Tzu Lo
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David Nugent
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, Perth, WA, 6009, Australia
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany
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Alabdullah AK, Moore G, Martín AC. A Duplicated Copy of the Meiotic Gene ZIP4 Preserves up to 50% Pollen Viability and Grain Number in Polyploid Wheat. BIOLOGY 2021; 10:biology10040290. [PMID: 33918149 PMCID: PMC8065865 DOI: 10.3390/biology10040290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022]
Abstract
Simple Summary On wheat polyploidisation, the major meiotic gene ZIP4, duplicated and diverged, such that tetraploid and hexaploid wheat each carry three and four copies of ZIP4, respectively. Surprisingly, this study demonstrates that, in hexaploid wheat, despite the presence of the other three ZIP4 copies, the duplicated ZIP4 copy is required to prevent major abnormalities during meiosis. Although there is greater disruption of subsequent male rather than female fertility, the duplicated ZIP4 copy preserves up to 50% of the grain number. High wheat fertility is important since it is consumed by over 4.5 billion people on the planet, of whom 2.5 billion are dependent on it. This study highlights the potentially extraordinary value of the wheat ZIP4 duplication, mandating further studies to unravel the complexity of the ZIP4 phenotype in this global crop. Abstract Although most flowering plants are polyploid, little is known of how the meiotic process evolves after polyploidisation to stabilise and preserve fertility. On wheat polyploidisation, the major meiotic gene ZIP4 on chromosome 3B duplicated onto 5B and diverged (TaZIP4-B2). TaZIP4-B2 was recently shown to promote homologous pairing, synapsis and crossover, and suppress homoeologous crossover. We therefore suspected that these meiotic stabilising effects could be important for preserving wheat fertility. A CRISPR Tazip4-B2 mutant was exploited to assess the contribution of the 5B duplicated ZIP4 copy in maintaining pollen viability and grain setting. Analysis demonstrated abnormalities in 56% of meiocytes in the Tazip4-B2 mutant, with micronuclei in 50% of tetrads, reduced size in 48% of pollen grains and a near 50% reduction in grain number. Further studies showed that most of the reduced grain number occurred when Tazip4-B2 mutant plants were pollinated with the less viable Tazip4-B2 mutant pollen rather than with wild type pollen, suggesting that the stabilising effect of TaZIP4-B2 on meiosis has a greater consequence in subsequent male, rather than female gametogenesis. These studies reveal the extraordinary value of the wheat chromosome 5B TaZIP4-B2 duplication to agriculture and human nutrition. Future studies should further investigate the role of TaZIP4-B2 on female fertility and assess whether different TaZIP4-B2 alleles exhibit variable effects on meiotic stabilisation and/or resistance to temperature change.
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Huang K, Huber G, Ritland K, Dunn DW, Li B. Performing parentage analysis for polysomic inheritances based on allelic phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6080682. [PMID: 33585871 PMCID: PMC8022955 DOI: 10.1093/g3journal/jkaa064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Polyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (1) double-reduction, (2) null alleles, (3) negative amplification, (4) genotyping errors and (5) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the genotyping error rate and the sample rate. We make our new methods freely available in the software package polygene, at http://github.com/huangkang1987/polygene.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Gwendolyn Huber
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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Tränkner C, Günther K, Sahr P, Engel F, Hohe A. Targeted generation of polyploids in Hydrangea macrophylla through cross-based breeding. BMC Genet 2020; 21:147. [PMID: 33287693 PMCID: PMC7720383 DOI: 10.1186/s12863-020-00954-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/17/2020] [Indexed: 11/29/2022] Open
Abstract
Background Up to now, diploid and triploid cultivars were reported for the ornamental crop Hydrangea macrophylla. Especially, the origin of triploids and their crossing behaviors are unknown, but the underlying mechanisms are highly relevant for breeding polyploids. Results By screening a cultivar collection, we identified diploid, triploid, tetraploid and even aneuploid H. macrophylla varieties. The pollen viability of triploids and tetraploids was comparable to that of diploids. Systematic crosses with these cultivars resulted in viable diploid, triploid, tetraploid and aneuploid offspring. Interestingly, crosses between diploids produced diploid and 0 or 1–94% triploid offspring, depending on the cultivars used as pollen parent. This finding suggests that specific diploids form unreduced pollen, either at low or high frequencies. In contrast, crosses of triploids with diploids or tetraploids produced many viable aneuploids, whose 2C DNA contents ranged between the parental 2C values. As expected, crosses between diploid and tetraploid individuals generated triploid offspring. Putative tetraploid plants were obtained at low frequencies in crosses between diploids and in interploid crosses of triploids with either diploid or tetraploid plants. The analysis of offspring populations indicated the production of 1n = 2x gametes for tetraploid plants, whereas triploids produced obviously reduced, aneuploid gametes with chromosome numbers ranging between haploid and diploid level. While euploid offspring grew normally, aneuploid plants showed mostly an abnormal development and a huge phenotypic variation within offspring populations, most likely due to the variation in chromosome numbers. Subsequent crosses with putative diploid, triploid and aneuploid offspring plants from interploid crosses resulted in viable offspring and germination rates ranging from 21 to 100%. Conclusions The existence of diploids that form unreduced pollen and of tetraploids allows the targeted breeding of polyploid H. macrophylla. Different ploidy levels can be addressed by combining the appropriate crossing partners. In contrast to artificial polyploidization, cross-based polyploidization is easy, cheap and results in genetically variable offspring that allows the direct selection of more robust and stress tolerant polyploid varieties. Furthermore, the generation of polyploid H. macrophylla plants will favor interspecific breeding programs within the genus Hydrangea. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00954-z.
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Affiliation(s)
- Conny Tränkner
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany. .,Present address: Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt, Kühnhäuser Straße 101, 99090, Erfurt, Germany.
| | - Kristina Günther
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Peter Sahr
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany.,Present address: Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Frauke Engel
- Gartenbau Kötterheinrich-Hortensienkulturen, Hohner Mark 20, 49525, Lengerich, Germany
| | - Annette Hohe
- Faculty of Landscape Architecture, Horticulture and Forestry, University of Applied Sciences Erfurt, Leipziger Straße 77, 99085, Erfurt, Germany
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Yin L, Zhu Z, Luo X, Huang L, Li Y, Mason AS, Yang J, Ge X, Long Y, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny. G3 (BETHESDA, MD.) 2020; 10:3687-3699. [PMID: 32753368 PMCID: PMC7534442 DOI: 10.1534/g3.120.401493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/01/2020] [Indexed: 01/27/2023]
Abstract
Whole genome duplications (WGDs) have played a major role in angiosperm species evolution. Polyploid plants have undergone multiple cycles of ancient WGD events during their evolutionary history. However, little attention has been paid to the additional WGD of the existing allopolyploids. In this study, we explored the influences of additional WGD on the allopolyploid Brassica napus Compared to tetraploid B. napus, octoploid B. napus (AAAACCCC, 2n = 8x =76) showed significant differences in phenotype, reproductive ability and the ploidy of self-pollinated progeny. Genome duplication also altered a key reproductive organ feature in B. napus, that is, increased the number of pollen apertures. Unlike autopolyploids produced from the diploid Brassica species, the octoploid B. napus produced from allotetraploid B. napus had a relatively stable meiotic process, high pollen viability and moderate fertility under self-pollination conditions, indicating that sub-genomic interactions may be important for the successful establishment of higher-order polyploids. Doubling the genome of B. napus provided us with an opportunity to gain insight into the flexibility of the Brassica genomes. The genome size of self-pollinated progeny of octoploid B. napus varied greatly, and was accompanied by extensive genomic instability, such as aneuploidy, mixed-ploidy and mitotic abnormality. The octoploid B. napus could go through any of genome reduction, equilibrium or expansion in the short-term, thus providing a novel karyotype library for the Brassica genus. Our results reveal the short-term evolutionary consequences of recurrent polyploidization events, and help to deepen our understanding of polyploid plant evolution.
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Affiliation(s)
- Liqin Yin
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yu Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35396 Giessen, Germany
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yan Long
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
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Mason AS, Wendel JF. Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution. Front Genet 2020; 11:1014. [PMID: 33005183 PMCID: PMC7485112 DOI: 10.3389/fgene.2020.01014] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication - deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.
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Affiliation(s)
- Annaliese S. Mason
- Plant Breeding Department, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan F. Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, United States
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Svačina R, Sourdille P, Kopecký D, Bartoš J. Chromosome Pairing in Polyploid Grasses. FRONTIERS IN PLANT SCIENCE 2020; 11:1056. [PMID: 32733528 PMCID: PMC7363976 DOI: 10.3389/fpls.2020.01056] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Polyploids are species in which three or more sets of chromosomes coexist. Polyploidy frequently occurs in plants and plays a major role in their evolution. Based on their origin, polyploid species can be divided into two groups: autopolyploids and allopolyploids. The autopolyploids arise by multiplication of the chromosome sets from a single species, whereas allopolyploids emerge from the hybridization between distinct species followed or preceded by whole genome duplication, leading to the combination of divergent genomes. Having a polyploid constitution offers some fitness advantages, which could become evolutionarily successful. Nevertheless, polyploid species must develop mechanism(s) that control proper segregation of genetic material during meiosis, and hence, genome stability. Otherwise, the coexistence of more than two copies of the same or similar chromosome sets may lead to multivalent formation during the first meiotic division and subsequent production of aneuploid gametes. In this review, we aim to discuss the pathways leading to the formation of polyploids, the occurrence of polyploidy in the grass family (Poaceae), and mechanisms controlling chromosome associations during meiosis, with special emphasis on wheat.
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Affiliation(s)
- Radim Svačina
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Pierre Sourdille
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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Lunerová J, Herklotz V, Laudien M, Vozárová R, Groth M, Kovařík A, Ritz CM. Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa. ANNALS OF BOTANY 2020; 125:1025-1038. [PMID: 32095807 PMCID: PMC7262465 DOI: 10.1093/aob/mcaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. METHODS To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. KEY RESULTS A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5-20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. CONCLUSIONS The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.
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Affiliation(s)
- Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Melanie Laudien
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute Zittau (IHI), Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
- Masaryk University, Faculty of Science, Brno, Czech Republic
| | - Marco Groth
- Leibniz Institute on Ageing – Fritz Lipmann Institute, Jena, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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Prusicki MA, Keizer EM, Van Rosmalen RP, Fleck C, Schnittger A. Live Cell Imaging of Male Meiosis in Arabidopsis by a Landmark-based System. Bio Protoc 2020; 10:e3611. [PMID: 33659575 DOI: 10.21769/bioprotoc.3611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Live cell imaging has tremendously promoted our understanding of cellular and subcellular processes such as cell division. Here, we present a step-by-step protocol for a robust and easy-to-use live cell imaging approach to study male meiosis in the plant Arabidopsis thaliana as recently established. Our method relies on the concomitant analysis of two reporter genes that highlight chromosome configurations and microtubule dynamics. In combination, these reporter genes allowed the discrimination of five cellular parameters: cell shape, microtubule array, nucleus position, nucleolus position, and chromatin condensation. These parameters can adopt different states, e.g., the nucleus position can be central or lateral. Analyzing how tightly these states are associated gives rise to landmark stages that in turn allow a quantitative and qualitative dissection of meiotic progression. We envision that such an approach can also provide valuable criteria for the analysis of cell differentiation processes outside of meiosis.
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Affiliation(s)
- Maria Ada Prusicki
- Department of Developmental Biology, University of Hamburg, Hamburg, Germany
| | - Emma Mathilde Keizer
- Department of Mathematical and Statistical Methods, Wageningen University and Research, Wageningen, The Netherlands
| | - Rik Peter Van Rosmalen
- Department of Agrotechnology and Food Sciences, Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, The Netherlands
| | - Christian Fleck
- Department of Agrotechnology and Food Sciences, Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, The Netherlands
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, Germany
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Oleszczuk S, Grzechnik N, Mason AS, Zimny J. Heritability of meiotic restitution and fertility restoration in haploid triticale. PLANT CELL REPORTS 2019; 38:1515-1525. [PMID: 31473791 PMCID: PMC6825030 DOI: 10.1007/s00299-019-02462-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/19/2019] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE A single division meiosis mechanism of meiotic restitution is incompletely penetrant but significantly associated with restored fertility in triticale haploids (n = 21, genome formula ABR). Meiotic restitution, or failure of meiosis to produce gametes with a reduced chromosome number, can lead to the restoration of fertility in allohaploids. Meiotic restitution is of major interest for producing doubled haploids, as haploid plants undergoing meiotic restitution can often form seeds without the need to apply mitosis inhibitors to double chromosome number. We aimed to characterize meiotic restitution in a population of 183 haploids (n = 21, genome formula ABR) derived from an F1 wheat-rye hybrid where one parent was known to carry factors responsible for restoration of fertility in wide-cross haploids. Based on cytological analysis, approximately half of the plants analyzed were characterized by normal meiosis, while half showed at least some cytological evidence of meiotic restitution. However, this mechanism was incompletely penetrant in the population, with no individual plant showing 100% unreduced gamete formation: restitution occurred sectorially within each anther and was not observed in all the anthers of a given plant. Hence, the absence of meiotic restitution could not be confirmed conclusively for any individual plant, confounding this analysis. However, cytological observation of meiotic restitution was significantly associated with seed set, further confirming the role of meiotic restitution in fertility restoration. Our results provide insight into this mechanism of unreduced gamete formation, and provide a basis for future work identifying the genetic factors responsible for this trait.
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Affiliation(s)
- Sylwia Oleszczuk
- Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Natalia Grzechnik
- Department of Robotics and Mechatronics, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Krakow, Poland
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Research Center for Biosystems, Land Use and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Janusz Zimny
- Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870, Blonie, Poland
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Lekhapan P, Anamthawat-Jónsson K, Chokchaichamnankit P. Chromosome Evolution Based on Variation in Chromosome Number and Chiasma Frequency in the Genus Ocimum L. from Thailand. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Kesara Anamthawat-Jónsson
- Institute of Life and Environmental Sciences, School of Engineering and Natural Science, University of Iceland
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Mwathi MW, Schiessl SV, Batley J, Mason AS. "Doubled-haploid" allohexaploid Brassica lines lose fertility and viability and accumulate genetic variation due to genomic instability. Chromosoma 2019; 128:521-532. [PMID: 31377850 DOI: 10.1007/s00412-019-00720-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023]
Abstract
Microspore culture stimulates immature pollen grains to develop into plants via tissue culture and is used routinely in many crop species to produce "doubled haploids": homozygous, true-breeding lines. However, microspore culture is also often used on material that does not have stable meiosis, such as interspecific hybrids. In this case, the resulting progeny may lose their "doubled haploid" homozygous status as a result of chromosome missegregation and homoeologous exchanges. However, little is known about the frequency of these effects. We assessed fertility, meiosis and genetic variability in self-pollinated progeny sets (the MDL2 population) resulting from first-generation plants (the MDL1 population) derived from microspores of a near-allohexaploid interspecific hybrid from the cross (Brassica napus × B. carinata) × B. juncea. Allelic inheritance and copy number variation were predicted using single nucleotide polymorphism marker data from the Illumina Infinium 60K Brassica array. Seed fertility and viability decreased substantially from the MDL1 to the MDL2 generation. In the MDL2 population, 87% of individuals differed genetically from their MDL1 parent. These genetic differences resulted from novel homoeologous exchanges between chromosomes, chromosome loss and gain, and segregation and instability of pre-existing karyotype abnormalities. Novel karyotype change was extremely common, with 2.2 new variants observed per MDL2 individual. Significant differences between progeny sets in the number of novel genetic variants were also observed. Meiotic instability clearly has the potential to dramatically change karyotypes (often without detectable effects on the presence or absence of alleles) in putatively homozygous, microspore-derived lines, resulting in loss of fertility and viability.
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Affiliation(s)
- Margaret W Mwathi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Sarah V Schiessl
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Annaliese S Mason
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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43
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Gaebelein R, Schiessl SV, Samans B, Batley J, Mason AS. Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids. THE NEW PHYTOLOGIST 2019; 223:965-978. [PMID: 30887525 DOI: 10.1111/nph.15804] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/13/2019] [Indexed: 05/22/2023]
Abstract
Synthetic allohexaploid Brassica hybrids (2n = AABBCC) do not exist naturally, but can be synthesized by crosses between diploid and/or allotetraploid Brassica species. Using these hybrids, we aimed to identify how novel allohexaploids restore fertility and normal meiosis after formation. Chromosome inheritance, genome structure, fertility and meiotic behaviour were assessed in three segregating allohexaploid populations derived from the cross (B. napus × B. carinata) × B. juncea using a combination of molecular marker genotyping, phenotyping and cytogenetics. Plants with unbalanced A-C translocations in one direction (where a C-genome chromosome fragment replaces an A-genome fragment) but not the other (where an A-genome fragment replaces a C-genome fragment) showed significantly reduced fertility across all populations. Genomic regions associated with fertility contained several meiosis genes with putatively causal mutations inherited from the parents (copies of SCC2 in the A genome, PAIR1/PRD3, PRD1 and ATK1/KATA/KIN14a in the B genome, and MSH2 and SMC1/TITAN8 in the C genome). Reduced seed fertility associated with the loss of chromosome fragments from only one subgenome following homoeologous exchanges could comprise a mechanism for biased genome fractionation in allopolyploids. Pre-existing meiosis gene variants present in allotetraploid parents may help to stabilize meiosis in novel allohexaploids.
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Affiliation(s)
- Roman Gaebelein
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Sarah V Schiessl
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Birgit Samans
- Faculty of Health Science, Technische Hochschule Mittelhessen, Wiesenstrasse 14, Giessen, 35390, Germany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, 35 Stirling Hwy, Perth, WA, 6009, Australia
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
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Baurens FC, Martin G, Hervouet C, Salmon F, Yohomé D, Ricci S, Rouard M, Habas R, Lemainque A, Yahiaoui N, D'Hont A. Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes. Mol Biol Evol 2019; 36:97-111. [PMID: 30403808 PMCID: PMC6340459 DOI: 10.1093/molbev/msy199] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as “AB,” “AAB,” or “ABB” based on morphological characters. We used NGS sequence data to characterize the A versus B chromosome composition of nine diploid and triploid interspecific cultivars, to compare the chromosome structures of A and B genomes and analyze A/B chromosome segregations in a polyploid context. We showed that interspecific recombination occurred frequently between A and B chromosomes. We identified two large structural variations between A and B genomes, a reciprocal translocation and an inversion that locally affected recombination and led to segregation distortion and aneuploidy in a triploid progeny. Interspecific recombination and large structural variations explained the mosaic genomes observed in edible bananas. The unprecedented resolution in deciphering their genome structure allowed us to start revisiting the origins of banana cultivars and provided new information to gain insight into the impact of interspecificity on genome evolution. It will also facilitate much more effective assessment of breeding strategies.
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Affiliation(s)
- Franc-Christophe Baurens
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Salmon
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France
| | | | - Sébastien Ricci
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France.,CARBAP, Bonanjo, Douala, Cameroon
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, Cedex 5, France
| | - Remy Habas
- CIRAD, UMR BGPI, F-34398 Montpellier, France.,BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François-Jacob, Genoscope, Evry, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Kryvokhyzha D, Milesi P, Duan T, Orsucci M, Wright SI, Glémin S, Lascoux M. Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris). PLoS Genet 2019; 15:e1008131. [PMID: 31083657 PMCID: PMC6532933 DOI: 10.1371/journal.pgen.1008131] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/23/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load. Most plant species have a polyploid at some stage of their ancestry. Polyploidy, genome doubling through either multiple copies of a single species or through genomes of different species coming into the same nucleus, is therefore a crucial step in plant evolution. Understanding its impact on basic biological functions is thus a matter of interest. Shepherd’s purse (Capsella bursa-pastoris) is a major weed that appeared about 100,000 years ago through hybridization of two diploid species of the same genus. In the present project, we measured genetic diversity and analyzed gene expression patterns in flowers, roots, and leaves of C. bursa-pastoris individuals as well as in its two parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Our data shows that, after 100,000 generations of evolution, the origin of the two subgenomes can still be seen: the genome inherited from C. grandiflora still differs from the one inherited from self-fertilizing C. orientalis. However, there are also signs that the two genomes have started to work together and are jointly regulated, and the way expression pattern varied across the three tissues indicates that the evolution of gene expression was adaptive.
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Affiliation(s)
- Dmytro Kryvokhyzha
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tianlin Duan
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marion Orsucci
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Sylvain Glémin
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- CNRS, Univ. Rennes, ECOBIO [(Ecosystèmes, biodiversité, évolution)] - UMR 6553, Rennes, France
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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