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Munguambe NE, Inoue S, Demeter Z, Yamagata Y, Yasui H, Zheng SH, Fujita D. Substitution Mapping of a Locus Responsible for Hybrid Breakdown in Populations Derived From Interspecific Introgression Line. Front Plant Sci 2021; 12:633247. [PMID: 33968097 PMCID: PMC8097182 DOI: 10.3389/fpls.2021.633247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/22/2021] [Indexed: 05/27/2023]
Abstract
Hybrid breakdown, a form of postzygotic reproductive barrier, has been reported to hinder gene flow in many crosses between wild and cultivated rice. Here, the phenomenon of hybrid breakdown was observed as low-tillering (i.e., low tiller number) in some progeny of an interspecific cross produced in an attempt to introduce Oryza meridionalis Ng (W1625) chromosomal segments into Oryza sativa L. ssp. japonica "Taichung 65" (T65). Low-tillering lines were obtained in BC4-derived progeny from a cross between W1625 and "Taichung 65," but the locus for low-tillering could not be mapped in segregating populations. As a second approach to map the locus for low-tillering, we analyzed an F2 population derived from a cross between the low-tillering lines and a high-yielding indica cultivar, "Takanari." A major QTL for low-tillering, qLTN4, was detected between PCR-based markers MS10 and RM307 on the long arm of chromosome 4, with a LOD score of 15.6. The low-tillering phenotype was associated with weak growth and pale yellow phenotype; however, low-tillering plant had less reduction of grain fertility. In an F4 population (4896 plants), 563 recombinant plants were identified and the low-tillering locus was delimited to a 4.6-Mbp region between markers W1 and C5-indel3729. This region could not be further delimited because recombination is restricted in this region of qLTN4, which is near the centromere. Understanding the genetic basis of hybrid breakdown, including the low-tillering habit, will be important for improving varieties in rice breeding.
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Affiliation(s)
- Nilsa Emilia Munguambe
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Shouta Inoue
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Zita Demeter
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shao-Hui Zheng
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Daisuke Fujita
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
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Hou J, Cao C, Ruan Y, Deng Y, Liu Y, Zhang K, Tan L, Zhu Z, Cai H, Liu F, Sun H, Gu P, Sun C, Fu Y. ESA1 Is Involved in Embryo Sac Abortion in Interspecific Hybrid Progeny of Rice. Plant Physiol 2019; 180:356-366. [PMID: 30770460 PMCID: PMC6501066 DOI: 10.1104/pp.18.01374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/02/2019] [Indexed: 05/13/2023]
Abstract
The emergence of sterile individuals in the hybrid backcross progeny of wild and cultivated rice limits the use of wild rice alleles for improving cultivated rice, but the molecular mechanisms underlying this sterility remain unclear. Here, we identified the semisterile introgression line YIL42, derived from a cross between the indica rice variety Teqing (Oryza sativa) and Oryza rufipogon accession YJCWR (Yuanjiang common wild rice), which exhibits semisterility. Using positional cloning, we isolated EMBRYO SAC ABORTION 1 (ESA1), which encodes a nuclear-membrane localized protein containing an armadillo repeat domain. A mutation in ESA1 at position 1819 (T1819C) converts a stop codon into an Arg (R) codon, causing delayed termination of protein translation. Analysis of transgenic lines indicated that the difference in ESA1 protein structure between O. rufipogon-derived ESA1 and Teqing-derived esa1 affects female gamete abortion during early mitosis. Fertility investigation and expression analysis indicated that the interaction between ESA1 T1819 and unknown gene(s) of Teqing affects spikelet fertility of the hybrid backcross progeny. The ESA1 T1819 allele is present in O. rufipogon but absent in O. sativa, suggesting that variation in ESA1 may be associated with interspecific hybrid incompatibility between wild and cultivated rice. Our findings provide insight into the molecular mechanism underlying female sterility, which is useful for improving the panicle seed setting rate of rice and for developing a strategy to overcome interspecific hybrid sterility between cultivated rice and wild rice.
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Affiliation(s)
- Jingjing Hou
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Caihong Cao
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yini Ruan
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yanyan Deng
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yaxin Liu
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Kun Zhang
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Lubin Tan
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Zuofeng Zhu
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Hongwei Cai
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Fengxia Liu
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Hongying Sun
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Ping Gu
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yongcai Fu
- Ministry of Education Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/ bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int J Mol Sci 2019; 20:E1773. [PMID: 30974846 PMCID: PMC6480052 DOI: 10.3390/ijms20071773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/09/2023] Open
Abstract
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
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Affiliation(s)
- Eliška Nováková
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Lenka Zablatzká
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Viktorie Nesrstová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 78371 Olomouc, Czech Republic.
| | - Pavel Hanáček
- Department of Plant Biology, Faculty of Agronomy, Mendel University, 61300 Brno, Czech Republic.
| | - Ruslan Kalendar
- National Center for Biotechnology, Astana 010000, Kazakhstan.
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, 12844 Prague, Czech Republic.
| | - Ľuboš Majeský
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
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Abstract
Hybrids between flowering plant species often exhibit reduced fitness, including sterility and inviability. Such hybrid incompatibilities create barriers to genetic exchange that can promote reproductive isolation between diverging populations and, ultimately, speciation. Additionally, hybrid breakdown opens a window into hidden molecular and evolutionary processes occurring within species. Here, we review recent work on the mechanisms and origins of hybrid incompatibility in flowering plants, including both diverse genic interactions and chromosomal incompatibilities. Conflict and coevolution among and within plant genomes contributes to the evolution of some well-characterized genic incompatibilities, but duplication and drift also play important roles. Inversions, while contributing to speciation by suppressing recombination, rarely cause underdominant sterility. Translocations cause severe F1 sterility by disrupting meiosis in heterozygotes, making their fixation in outcrossing sister species a paradox. Evolutionary genomic analyses of both genic and chromosomal incompatibilities, in the context of population genetic theory, can explicitly test alternative scenarios for their origins.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
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Kerwin RE, Sweigart AL. Mechanisms of Transmission Ratio Distortion at Hybrid Sterility Loci Within and Between Mimulus Species. G3 (Bethesda) 2017; 7:3719-3730. [PMID: 28935753 PMCID: PMC5677164 DOI: 10.1534/g3.117.300148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/09/2017] [Indexed: 12/28/2022]
Abstract
Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2) in the closely related yellow monkeyflower species Mimulus guttatus and M. nasutus By performing reciprocal backcrosses with introgression lines (ILs), we find evidence for gametic expression of the hms1-hms2 incompatibility. Surprisingly, however, hybrid transmission ratios at hms1 do not reflect this incompatibility, suggesting that additional mechanisms counteract the effects of gametic sterility. Indeed, our backcross experiment shows hybrid transmission bias toward M. guttatus through both pollen and ovules, an effect that is particularly strong when hms2 is homozygous for M. nasutus alleles. In contrast, we find little evidence for hms1 transmission bias in crosses within M. guttatus, providing no indication of selfish evolution at this locus. Although we do not yet have sufficient genetic resolution to determine if hybrid sterility and transmission ratio distortion (TRD) map to the same loci, our preliminary fine-mapping uncovers a genetically independent hybrid lethality system involving at least two loci linked to hms1 This fine-scale dissection of TRD at hms1 and hms2 provides insight into genomic differentiation between closely related Mimulus species and reveals multiple mechanisms of hybrid dysfunction.
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Affiliation(s)
- Rachel E Kerwin
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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Chen C, E Z, Lin HX. Evolution and Molecular Control of Hybrid Incompatibility in Plants. Front Plant Sci 2016; 7:1208. [PMID: 27563306 PMCID: PMC4980391 DOI: 10.3389/fpls.2016.01208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/29/2016] [Indexed: 05/09/2023]
Abstract
Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with "parasitic" selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- *Correspondence: Chen Chen,
| | - Zhiguo E
- China National Rice Research InstituteHangzhou, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics and CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
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Bogdanova VS, Zaytseva OO, Mglinets AV, Shatskaya NV, Kosterin OE, Vasiliev GV. Nuclear-cytoplasmic conflict in pea (Pisum sativum L.) is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits. PLoS One 2015; 10:e0119835. [PMID: 25789472 PMCID: PMC4366379 DOI: 10.1371/journal.pone.0119835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022] Open
Abstract
In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized.
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Affiliation(s)
- Vera S. Bogdanova
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga O. Zaytseva
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Anatoliy V. Mglinets
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V. Shatskaya
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E. Kosterin
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Gennadiy V. Vasiliev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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