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Batiru G, Lübberstedt T. Polyploidy in maize: from evolution to breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:182. [PMID: 39001883 DOI: 10.1007/s00122-024-04688-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/29/2024] [Indexed: 07/15/2024]
Abstract
Polyploidy played an important role in the evolution of the three most important crops: wheat, maize and rice, each of them providing a unique model for studying allopolyploidy, segmental alloploidy or paleopolyploidy. However, its genetic and evolutionary role is still vague. The undelying mechanisms and consequences of polyploidy remain fundamental objectives in the study of eukaryotes. Maize is one of the underutilized crops at the polyploid level. This species has no stable natural polyploids, the existing ones being artificially obtained. From the experimental polyploid series of maize, only the tetraploid forms (4n = 40) are of interest. They are characterized by some valuable morphological, physiological and biochemical features, superior to the diploid forms from which they originated, but also by some drawbacks such as: reduced fertility, slower development, longer vegetation period, low productivity and adaptedness. Due to these barriers to using tetraploids in field production, maize tetraploids primarily found utility in scientific studies regarding genetic variability, inbreeding, heterosis and gene dosage effect. Since the first mention of a triploid maize plant to present, many scientists and schools, devoted their efforts to capitalize on the use of polyploidy in maize. Despite its common disadvantages as a crop, significant progress in developing tetraploid maize with good agronomic performance was achieved leading to registered tetraploid maize varieties. In this review we summarize and discuss the different aspects of polyploidy in maize, such as evolutionary context, methods of induction, morphology, fertility issue, inheritance patterns, gene expression and potential use.
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Affiliation(s)
- Grigorii Batiru
- Department of Agronomy and Environment, Technical University of Moldova, MD-2049, Chisinau, Republic of Moldova.
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1051, USA
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Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [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] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
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Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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Li Y, Yan X, Cheng M, Wu Z, Zhang Q, Duan S, Zhou Y, Li H, Yang S, Cheng Y, Li W, Xu L, Li X, He R, Zhou Y, Yang C, Iqbal MZ, He J, Rong T, Tang Q. Genome dosage alteration caused by chromosome pyramiding and shuffling effects on karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:28. [PMID: 38252297 DOI: 10.1007/s00122-023-04540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE We developed an array of Zea-Tripsacum tri-hybrid allopolyploids with multiple ploidies. We unveiled that changes in genome dosage due to the chromosomes pyramiding and shuffling of three species effects karyotypic heterogeneity, reproductive diversity, and phenotypic variation in Zea-Tripsacum allopolyploids. Polyploidy, or whole genome duplication, has played a major role in evolution and speciation. The genomic consequences of polyploidy have been extensively studied in many plants; however, the extent of chromosomal variation, genome dosage, phenotypic diversity, and heterosis in allopolyploids derived from multiple species remains largely unknown. To address this question, we synthesized an allohexaploid involving Zea mays, Tripsacum dactyloides, and Z. perennis by chromosomal pyramiding. Subsequently, an allooctoploid and an allopentaploid were obtained by hybridization of the allohexaploid with Z. perennis. Moreover, we constructed three populations with different ploidy by chromosomal shuffling (allopentaploid × Z. perennis, allohexaploid × Z. perennis, and allooctoploid × Z. perennis). We have observed 3 types of sexual reproductive modes and 2 types of asexual reproduction modes in the tri-species hybrids, including 2n gamete fusion (2n + n), haploid gamete fusion (n + n), polyspermy fertilization (n + n + n) or 2n gamete fusion (n + 2n), haploid gametophyte apomixis, and asexual reproduction. The tri-hybrids library presents extremely rich karyotype heterogeneity. Chromosomal compensation appears to exist between maize and Z. perennis. A rise in the ploidy of the trihybrids was linked to a higher frequency of chromosomal translocation. Variation in the degree of phenotypic diversity observed in different segregating populations suggested that genome dosage effects phenotypic manifestation. These findings not only broaden our understanding of the mechanisms of polyploid formation and reproductive diversity but also provide a novel insight into genome pyramiding and shuffling driven genome dosage effects and phenotypic diversity.
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Affiliation(s)
- Yingzheng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xu Yan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000, China
| | - Mingjun Cheng
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Zizhou Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000, China
| | - Qiyuan Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Saifei Duan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaxiong Li
- Neijiang Municipal Bureau of Agriculture and Rural Affairs, Neijiang, 641000, China
| | - Shipeng Yang
- Zigong Academy of Agricultural Sciences, Zigong, 643000, China
| | - Yulin Cheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wansong Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaofeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ruyu He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunyan Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Guizhou Prataculture Institute, Guiyang, Guizhou, China
| | - Muhammad Zafar Iqbal
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianmei He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qilin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Comai L. Unlikely heroes on the long and winding road to potato inbreeding. ABIOTECH 2023; 4:267-271. [PMID: 37970470 PMCID: PMC10638346 DOI: 10.1007/s42994-023-00109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 11/17/2023]
Abstract
Conversion of potato from a tetraploid, heterozygous, vegetatively propagated crop to a diploid F1 hybrid, propagated via botanical seed, would constitute a considerable advance for global agriculture, but faces multiple challenges. One such challenge is the difficulty in inbreeding potato, which involves purging deleterious alleles from its genome. This commentary discusses possible reasons for this difficulty and highlights a recent sequence-based effort to classify SNP variation, in potato germplasm, according to its deleterious potential. Tools and strategies connected to this database may facilitate development of F1 hybrids.
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Affiliation(s)
- Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616 USA
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Labroo MR, Endelman JB, Gemenet DC, Werner CR, Gaynor RC, Covarrubias-Pazaran GE. Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:147. [PMID: 37291402 DOI: 10.1007/s00122-023-04377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 05/05/2023] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.
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Affiliation(s)
- Marlee R Labroo
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dorcus C Gemenet
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Christian R Werner
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Giovanny E Covarrubias-Pazaran
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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Mackay IJ, Cockram J, Howell P, Powell W. Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:26-34. [PMID: 32996672 PMCID: PMC7769232 DOI: 10.1111/pbi.13481] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 05/12/2023]
Abstract
Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation - and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders' ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.
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Affiliation(s)
- Ian J. Mackay
- SRUC (Scotland’s Rural College)EdinburghUK
- IMplant ConsultancyChelmsfordUK
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Yao H, Srivastava S, Swyers N, Han F, Doerge RW, Birchler JA. Inbreeding Depression in Genotypically Matched Diploid and Tetraploid Maize. Front Genet 2020; 11:564928. [PMID: 33329701 PMCID: PMC7734256 DOI: 10.3389/fgene.2020.564928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023] Open
Abstract
The genetic and molecular basis of heterosis has long been studied but without a consensus about mechanism. The opposite effect, inbreeding depression, results from repeated self-pollination and leads to a reduction in vigor. A popular explanation for this reaction is the homozygosis of recessive, slightly deleterious alleles upon inbreeding. However, extensive studies in alfalfa indicated that inbreeding between diploids and autotetraploids was similar despite the fact that homozygosis of alleles would be dramatically different. The availability of tetraploid lines of maize generated directly from various inbred lines provided the opportunity to examine this issue in detail in perfectly matched diploid and tetraploid hybrids and their parallel inbreeding regimes. Identical hybrids at the diploid and tetraploid levels were inbred in triplicate for seven generations. At the conclusion of this regime, F1 hybrids and selected representative generations (S1, S3, S5, S7) were characterized phenotypically in randomized blocks during the same field conditions. Quantitative measures of the multiple generations of inbreeding provided little evidence for a distinction in the decline of vigor between the diploids and the tetraploids. The results suggest that the homozygosis of completely recessive, slightly deleterious alleles is an inadequate hypothesis to explain inbreeding depression in general.
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Affiliation(s)
- Hong Yao
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sanvesh Srivastava
- Department of Statistics and Actuarial Science, University of Iowa, Iowa City, IA, United States
| | - Nathan Swyers
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Fangpu Han
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Rebecca W Doerge
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, United States
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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