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Bente H, Köhler C. Molecular basis and evolutionary drivers of endosperm-based hybridization barriers. PLANT PHYSIOLOGY 2024; 195:155-169. [PMID: 38298124 PMCID: PMC11060687 DOI: 10.1093/plphys/kiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
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Affiliation(s)
- Heinrich Bente
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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Tezuka T, Nagai S, Matsuo C, Okamori T, Iizuka T, Marubashi W. Genetic Cause of Hybrid Lethality Observed in Reciprocal Interspecific Crosses between Nicotiana simulans and N. tabacum. Int J Mol Sci 2024; 25:1226. [PMID: 38279225 PMCID: PMC10817076 DOI: 10.3390/ijms25021226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Hybrid lethality, a type of postzygotic reproductive isolation, is an obstacle to wide hybridization breeding. Here, we report the hybrid lethality that was observed in crosses between the cultivated tobacco, Nicotiana tabacum (section Nicotiana), and the wild tobacco species, Nicotiana simulans (section Suaveolentes). Reciprocal hybrid seedlings were inviable at 28 °C, and the lethality was characterized by browning of the hypocotyl and roots, suggesting that hybrid lethality is due to the interaction of nuclear genomes derived from each parental species, and not to a cytoplasmic effect. Hybrid lethality was temperature-sensitive and suppressed at 36 °C. However, when hybrid seedlings cultured at 36 °C were transferred to 28 °C, all of them showed hybrid lethality. After crossing between an N. tabacum monosomic line missing one copy of the Q chromosome and N. simulans, hybrid seedlings with or without the Q chromosome were inviable and viable, respectively. These results indicated that gene(s) on the Q chromosome are responsible for hybrid lethality and also suggested that N. simulans has the same allele at the Hybrid Lethality A1 (HLA1) locus responsible for hybrid lethality as other species in the section Suaveolentes. Haplotype analysis around the HLA1 locus suggested that there are at least six and two haplotypes containing Hla1-1 and hla1-2 alleles, respectively, in the section Suaveolentes.
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Affiliation(s)
- Takahiro Tezuka
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan;
- Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan;
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Shota Nagai
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan;
| | - Chihiro Matsuo
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Toshiaki Okamori
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Takahiro Iizuka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan;
| | - Wataru Marubashi
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
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Kim J, Jang H, Huh SM, Cho A, Yim B, Jeong SH, Kim H, Yu HJ, Mun JH. Effect of structural variation in the promoter region of RsMYB1.1 on the skin color of radish taproot. FRONTIERS IN PLANT SCIENCE 2024; 14:1327009. [PMID: 38264015 PMCID: PMC10804855 DOI: 10.3389/fpls.2023.1327009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Accumulation of anthocyanins in the taproot of radish is an agronomic trait beneficial for human health. Several genetic loci are related to a red skin or flesh color of radish, however, the functional divergence of candidate genes between non-red and red radishes has not been investigated. Here, we report that a novel genetic locus on the R2 chromosome, where RsMYB1.1 is located, is associated with the red color of the skin of radish taproot. A genome-wide association study (GWAS) of 66 non-red-skinned (nR) and 34 red-skinned (R) radish accessions identified three nonsynonymous single nucleotide polymorphisms (SNPs) in the third exon of RsMYB1.1. Although the genotypes of SNP loci differed between the nR and R radishes, no functional difference in the RsMYB1.1 proteins of nR and R radishes in their physical interaction with RsTT8 was detected by yeast-two hybrid assay or in anthocyanin accumulation in tobacco and radish leaves coexpressing RsMYB1.1 and RsTT8. By contrast, insertion- or deletion-based GWAS revealed that one large AT-rich low-complexity sequence of 1.3-2 kb was inserted in the promoter region of RsMYB1.1 in the nR radishes (RsMYB1.1nR), whereas the R radishes had no such insertion; this represents a presence/absence variation (PAV). This insertion sequence (RsIS) was radish specific and distributed among the nine chromosomes of Raphanus genomes. Despite the extremely low transcription level of RsMYB1.1nR in the nR radishes, the inactive RsMYB1.1nR promoter could be functionally restored by deletion of the RsIS. The results of a transient expression assay using radish root sections suggested that the RsIS negatively regulates the expression of RsMYB1.1nR, resulting in the downregulation of anthocyanin biosynthesis genes, including RsCHS, RsDFR, and RsANS, in the nR radishes. This work provides the first evidence of the involvement of PAV in an agronomic trait of radish.
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Affiliation(s)
- Jiin Kim
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Hoyeol Jang
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Sun Mi Huh
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Ara Cho
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Bomi Yim
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Seung-Hoon Jeong
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Hee-Ju Yu
- Department of Life Sciences, Institute of Convergence Science & Technology, The Catholic University of Korea, Bucheon, Republic of Korea
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Republic of Korea
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Zumajo-Cardona C, Gabrieli F, Anire J, Albertini E, Ezquer I, Colombo L. Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development. ANNALS OF BOTANY 2023; 132:383-400. [PMID: 37467144 PMCID: PMC10667011 DOI: 10.1093/aob/mcad097] [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: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND AND AIMS The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review. METHODS Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions. KEY RESULTS TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage. CONCLUSIONS The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Flavio Gabrieli
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
- Dipartimento di Ingegneria Industriale DII, University of Padua, via Gradenigo, 6/a, Padova, Italy
| | - Jovannemar Anire
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- National Coconut Research Center – Visayas, Visayas State University, Baybay City, Leyte, Philippines
| | - Emidio Albertini
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
| | - Ignacio Ezquer
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Lucia Colombo
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Zhang X, Chen Y, Wang L, Yuan Y, Fang M, Shi L, Lu R, Comes HP, Ma Y, Chen Y, Huang G, Zhou Y, Zheng Z, Qiu Y. Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization. HORTICULTURE RESEARCH 2023; 10:uhad203. [PMID: 38046854 PMCID: PMC10689057 DOI: 10.1093/hr/uhad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.
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Affiliation(s)
- Xinyi Zhang
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yang Chen
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Lingyun Wang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ye Yuan
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016, Zhejiang, China
| | - Mingya Fang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Lin Shi
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, 5020, Austria
| | - Yazhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yuanyuan Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Guizhou Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Zhaisheng Zheng
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Yingxiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
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He H, Shiragaki K, Tezuka T. Understanding and overcoming hybrid lethality in seed and seedling stages as barriers to hybridization and gene flow. FRONTIERS IN PLANT SCIENCE 2023; 14:1219417. [PMID: 37476165 PMCID: PMC10354522 DOI: 10.3389/fpls.2023.1219417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hybrid lethality is a type of reproductive isolation barrier observed in two developmental stages, hybrid embryos (hybrid seeds) and hybrid seedlings. Hybrid lethality has been reported in many plant species and limits distant hybridization breeding including interspecific and intergeneric hybridization, which increases genetic diversity and contributes to produce new germplasm for agricultural purposes. Recent studies have provided molecular and genetic evidence suggesting that underlying causes of hybrid lethality involve epistatic interaction of one or more loci, as hypothesized by the Bateson-Dobzhansky-Muller model, and effective ploidy or endosperm balance number. In this review, we focus on the similarities and differences between hybrid seed lethality and hybrid seedling lethality, as well as methods of recovering seed/seedling activity to circumvent hybrid lethality. Current knowledge summarized in our article will provides new insights into the mechanisms of hybrid lethality and effective methods for circumventing hybrid lethality.
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Affiliation(s)
- Hai He
- School of Agriculture, Sun Yat-sen University, Shenzhen, China
| | - Kumpei Shiragaki
- Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Takahiro Tezuka
- Laboratory of Breeding and Genetics, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
- Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
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