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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Suma A, Joseph John K, Bhat KV, Latha M, Lakshmi CJ, Pitchaimuthu M, Nissar VAM, Thirumalaisamy PP, Pandey CD, Pandey S, Kumar A, Gautam RK, Singh GP. Genetic enhancement of okra [ Abelmoschus esculentus (L.) Moench] germplasm through wide hybridization. FRONTIERS IN PLANT SCIENCE 2023; 14:1284070. [PMID: 38023890 PMCID: PMC10654990 DOI: 10.3389/fpls.2023.1284070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction The introgression of genetic material from one species to another through wide hybridization and repeated back-crossing, plays an important role in genetic modification and enriching the cultivated gene-pool with novel genetic variations. Okra (Abelmoschus esculentus [(L.) Moench)] is a popular vegetable crop with high dietary fibre and protein, rich in essential amino acids, lysine and tryptophan. The wild Abelmoschus genepool has many desirable traits like ornamental value, short internodal length, more number of productive branches, extended bearing, perennation tendency, reduced fruit length (more consumer preferred trait), high mucilage content (medicinal value), abiotic stress tolerances such as drought, high temperature and biotic stress resistances such as okra Yellow Vein Mosaic Virus (YVMV) and Enation Leaf Curl Virus (ELCV) diseases. The repeated use of elite breeding lines led to narrowing of the genetic base of the okra crop, one of the major factors attributed to breakdown of resistance/ tolerance to biotic stresses. YVMV and ELCV are the two major diseases, causing significant yield loss in okra. Hence, wide hybridization was attempted to transfer tolerance genes from wild species to the cultivated genepool to widen the genetic base. Material and methods The screening of germplasm of wild Abelmoschus species at hotspots led to the identification of tolerant species (Abelmoschus pungens var. mizoramensis, A. enbeepeegeearensis, A. caillei, A. tetraphyllus and A. angulosus var. grandiflorus), which were further used in a wide-hybridization programme to generate interspecific hybrids with the cultivated okra. Presence of pre- and post-zygotic barriers to interspecific geneflow, differences in ploidy levels and genotype specific variations in chromosome numbers led to varying degrees of sterility in F1 plants of interspecific crosses. This was overcome by doubling the chromosome number of interspecific hybrids by applying Colchicine at the seedling stage. The 113 cross derivatives generated comprising amphidiploids in the F1 generation (30), F3 (14), one each in F2 and F4 generations, back cross generation in BC1F2 (03), BC1F3 (25), and BC2F3 (02), crosses between amphidiploids (27), multi-cross combinations (07) and inter-specific cross (between A. sagittifolius × A. moschatus subsp. moschatus) selfed derivatives at F8 generation (03) were characterized in the present study. Besides they were advanced through selfing and backcrossing. Results and Discussion The amphidiploids were found to possess many desirable genes with a considerable magnitude of linkage drag. Majority of the wide cross derivatives had an intermediate fruit morphology and dominance of wild characters viz., hispid fruits, stem, leaves, tough fruit fibre, vigorous perennial growth habit and prolonged flowering and fruiting. The fruit morphology of three BC progenies exhibited a high morphological resemblance to the cultivated okra, confirming successful transfer of useful genes to the cultivated okra genepool. The detailed morphological characteristics of the various combinations of Abelmoschus amphidiploids and the genetic enhancement of the genepool achieved in this process is reported here.
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Affiliation(s)
- A. Suma
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | - K. Joseph John
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | - Madhavan Latha
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | | | - V. A. M. Nissar
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, India
| | | | | | - Sushil Pandey
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Raj Kumar Gautam
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Hao Y, Su X, Li W, Li L, Zhang Y, Mumtaz MA, Shu H, Cheng S, Zhu G, Wang Z. The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach ( Ipomoea aquatica Forsk). FRONTIERS IN PLANT SCIENCE 2023; 14:1155531. [PMID: 37123819 PMCID: PMC10140364 DOI: 10.3389/fpls.2023.1155531] [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: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Water spinach (Ipomoea aquatica Forsk) is an essential green leafy vegetable in Asia. In this study, we induced autotetraploid water spinach by colchicine. Furthermore, DNA methylation and transcriptome of tetraploid and diploid were compared using Whole Genome Bisulfite Sequencing (WGBS) and RNA-sequencing techniques. Autotetraploid water spinach was created for the first time. Compared with the diploid parent, autotetraploid water spinach had wider leaves, thicker petioles and stems, thicker and shorter adventitious roots, longer stomas, and larger parenchyma cells. The whole genome methylation level of the autotetraploid was slightly higher than that of the diploid. Compared with the diploid, 12281 Differentially Methylated Regions (DMRs)were found in the autotetraploid, including 2356 hypermethylated and 1310 hypomethylated genes, mainly enriched in 'Arginine and Proline metabolism', 'beta - Alanine metabolism', 'Plant homone signal translation', 'Ribome', and 'Plant - pathgen interaction' pathways. Correlation analysis of transcriptome and DNA methylation data showed that 121 differentially expressed genes undergone differential methylation, related to four pathways 'Other types of O-glycan biosynthesis', 'Terpenoid backbone biosynthesis', 'Biosynthesis of secondary metabolites', and 'Metabolic paths'. This work obtained important autotetraploid resources of water spinach and revealed the genomic DNA methylation changes after genome doubling, being helpful for further studying the molecular mechanism of variations caused by polyploids of the Ipomoea genus.
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Affiliation(s)
- Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiao Su
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Wen Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Lin Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Yu Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Muhammad Ali Mumtaz
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Zhiwei Wang,
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Jia L, Yang Y, Zhai H, He S, Xin G, Zhao N, Zhang H, Gao S, Liu Q. Production and characterization of a novel interspecific somatic hybrid combining drought tolerance and high quality of sweet potato and Ipomoea triloba L. PLANT CELL REPORTS 2022; 41:2159-2171. [PMID: 35943560 DOI: 10.1007/s00299-022-02912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
A novel interspecific somatic hybrid combining drought tolerance and high quality of sweet potato and Ipomoea triloba L. was obtained and its genetic and epigenetic variations were studied. Somatic hybridization can be used to overcome the cross-incompatibility between sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives and transfer useful and desirable genes from wild relatives to cultivated plants. However, most of the interspecific somatic hybrids obtained to date cannot produce storage roots and do not exhibit agronomic characters. In the present study, a novel interspecific somatic hybrid, named XT1, was obtained through protoplast fusion between sweet potato cv. Xushu 18 and its wild relative I. triloba. This somatic hybrid produced storage roots and exhibited significantly higher drought tolerance and quality compared with its cultivated parent Xushu 18. Transcriptome and real-time quantitative PCR (qRT-PCR) analyses revealed that the well-known drought stress-responsive genes in XT1 and I. triloba were significantly up-regulated under drought stress. The genomic structural reconstructions between the two genomes of the fusion parents in XT1 were confirmed using genomic in situ hybridization (GISH) and specific nuclear and cytoplasmic DNA markers. The DNA methylation variations were characterized by methylation-sensitive amplified polymorphism (MSAP). This study not only reveals the significance of somatic hybridization in the genetic improvement of sweet potato but also provides valuable materials and knowledge for further investigating the mechanism of storage root formation in sweet potato.
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Affiliation(s)
- Licong Jia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Yufeng Yang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Guosheng Xin
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China.
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Shin H, Park JE, Park HR, Choi WL, Yu SH, Koh W, Kim S, Soh HY, Waminal NE, Belandres HR, Lim JY, Yi G, Ahn JH, Kim J, Kim Y, Koo N, Kim K, Perumal S, Kang T, Kim J, Jang H, Kang DH, Kim YS, Jeong H, Yang J, Song S, Park S, Kim JA, Lim YP, Park B, Hsieh T, Yang T, Choi D, Kim HH, Lee S, Huh JH. Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae. THE NEW PHYTOLOGIST 2022; 235:743-758. [PMID: 35403705 PMCID: PMC9320894 DOI: 10.1111/nph.18155] [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: 11/25/2021] [Accepted: 03/28/2022] [Indexed: 05/15/2023]
Abstract
Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.
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Affiliation(s)
- Hosub Shin
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jeong Eun Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hye Rang Park
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Woo Lee Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seung Hwa Yu
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Wonjun Koh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Seungill Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504South Korea
| | - Hye Yeon Soh
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Nomar Espinosa Waminal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Hadassah Roa Belandres
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Joo Young Lim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Gibum Yi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Jong Hwa Ahn
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - June‐Sik Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Yong‐Min Kim
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Namjin Koo
- Korea Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141South Korea
| | - Kyunghee Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Sampath Perumal
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Taegu Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Junghyo Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Hosung Jang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
| | - Dong Hyun Kang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Ye Seul Kim
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyeon‐Min Jeong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
| | - Junwoo Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Somin Song
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Suhyoung Park
- Department of Horticultural Crop ResearchNational Institute of Horticultural and Herbal ScienceRural Development AdministrationWanjuJeollabuk‐do55365South Korea
| | - Jin A. Kim
- Department of Agricultural BiotechnologyNational Academy of Agricultural ScienceRural Development AdministrationJeonjuJeollabuk‐do54874South Korea
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeon34134South Korea
| | | | - Tzung‐Fu Hsieh
- Plants for Human Health InstituteNorth Carolina State UniversityNorth Carolina Research CampusKannapolisNC27695USA
| | - Tae‐Jin Yang
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Doil Choi
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
| | - Hyun Hee Kim
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoul01795South Korea
| | - Soo‐Seong Lee
- BioBreeding InstituteAnseongGyeonggi‐do17544South Korea
| | - Jin Hoe Huh
- Department of Agriculture, Forestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826South Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826South Korea
- Research Institute of Agriculture and Life ScienceSeoul National UniversitySeoul08826South Korea
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Zhang W, Shi H, Zhou Y, Liang X, Luo X, Xiao C, Li Y, Xu P, Wang J, Gong W, Zou Q, Tao L, Kang Z, Tang R, Li Z, Yang J, Fu S. Rapid and Synchronous Breeding of Cytoplasmic Male Sterile and Maintainer Line Through Mitochondrial DNA Rearrangement Using Doubled Haploid Inducer in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:871006. [PMID: 35557722 PMCID: PMC9087798 DOI: 10.3389/fpls.2022.871006] [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: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
When homozygously fertile plants were induced using doubled haploid (DH) induction lines Y3380 and Y3560, the morphology of the induced F1 generation was basically consistent with the female parent, but the fertility was separated, showing characteristics similar to cytoplasmic male sterile (CMS) and maintainer lines. In this study, the morphology, fertility, ploidy, and cytoplasm genotype of the induced progeny were identified, and the results showed that the sterile progeny was polima cytoplasm sterile (pol CMS) and the fertile progeny was nap cytoplasm. The molecular marker and test-cross experimental results showed that the fertile progeny did not carry the restorer gene of pol CMS and the genetic distance between the female parent and the offspring was 0.002. This suggested that those inductions which produced sterile and fertile progeny were coordinated to CMS and maintainer lines. Through the co-linearity analysis of the mitochondrial DNA (mtDNA), it was found that the rearrangement of mtDNA by DH induction was the key factor that caused the transformation of fertility (nap) into sterility (pol). Also, when heterozygous females were induced with DH induction lines, the induction F2 generation also showed the segregation of fertile and sterile lines, and the genetic distance between sterile and fertile lines was approximately 0.075. Therefore, the induction line can induce different types of female parents, and the breeding of the sterile line and the maintainer line can be achieved through the rapid synchronization of sister crosses and self-crosses. The induction of DH inducer in B. napus can provide a new model for the innovation of germplasm resources and open up a new way for its application.
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Affiliation(s)
- Wei Zhang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Ying Zhou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Xingyu Liang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuan Luo
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaowen Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yun Li
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jisheng Wang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Wanzhuo Gong
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Qiong Zou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Lanrong Tao
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zeming Kang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Rong Tang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zhuang Li
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Jin Yang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Shaohong Fu
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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8
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Blasio F, Prieto P, Pradillo M, Naranjo T. Genomic and Meiotic Changes Accompanying Polyploidization. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11010125. [PMID: 35009128 PMCID: PMC8747196 DOI: 10.3390/plants11010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.
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Affiliation(s)
- Francesco Blasio
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4048, 14080 Cordova, Spain;
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
- Correspondence:
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9
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Xiao L, Lu L, Zeng W, Shang X, Cao S, Yan H. DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava. FRONTIERS IN PLANT SCIENCE 2022; 13:915056. [PMID: 35860527 PMCID: PMC9289687 DOI: 10.3389/fpls.2022.915056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 05/16/2023]
Abstract
Whole genome duplication (WGD) increases the dosage of all coding and non-coding genes, yet the molecular implications of genome-dosage effects remain elusive. In this study, we generated integrated maps of the methylomes and lncRNAomes for diploid and artificially generated autotetraploid cassava (Manihot esculenta Crantz). We found that transposable elements (TEs) suppressed adjacent protein coding gene (PCG)-expression levels, while TEs activated the expression of nearby long non-coding RNAs (lncRNAs) in the cassava genome. The hypermethylation of DNA transposons in mCG and mCHH sites may be an effective way to suppress the expression of nearby PCGs in autotetraploid cassava, resulting in similar expression levels for most of PCGs between autotetraploid and diploid cassava. In the autotetraploid, decreased methylation levels of retrotransposons at mCHG and mCHH sites contributed to reduced methylation of Gypsy-neighboring long intergenic non-coding RNAs, potentially preserving diploid-like expression patterns in the major of lncRNAs. Collectively, our study highlighted that WGD-induced DNA methylation variation in DNA transposons and retrotransposons may be as direct adaptive responses to dosage of all coding-genes and lncRNAs, respectively.
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Affiliation(s)
- Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- *Correspondence: Huabing Yan,
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R, Robinson MD. ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics 2021; 22:547. [PMID: 34273949 PMCID: PMC8285871 DOI: 10.1186/s12864-021-07845-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid's parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. RESULTS We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC's performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO's output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. CONCLUSIONS The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO .
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Affiliation(s)
- Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Tony Kuo
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Samuele Decarli
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Lucas Mohn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jun Sese
- AIST Artificial Intelligence Research Center, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke 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
| | - 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
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, 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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13
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Esposito S, Aversano R, Tripodi P, Carputo D. Whole-Genome Doubling Affects Pre-miRNA Expression in Plants. PLANTS 2021; 10:plants10051004. [PMID: 34069771 PMCID: PMC8157229 DOI: 10.3390/plants10051004] [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: 01/13/2021] [Revised: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano, Italy;
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
- Correspondence: ; Tel.: +39-08-1252-9225
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Zhang Q, Guan P, Zhao L, Ma M, Xie L, Li Y, Zheng R, Ouyang W, Wang S, Li H, Zhang Y, Peng Y, Cao Z, Zhang W, Xiao Q, Xiao Y, Fu T, Li G, Li X, Shen J. Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus. MOLECULAR PLANT 2021; 14:604-619. [PMID: 33387675 DOI: 10.1016/j.molp.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/28/2020] [Accepted: 12/28/2020] [Indexed: 05/20/2023]
Abstract
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization, which drives genome evolution and contributes to the increased adaptability to diverse environments. However, a comprehensive epigenome map of Brassica napus is still unavailable. In this study, we performed integrative analysis of five histone modifications, RNA polymerase II occupancy, DNA methylation, and transcriptomes in two B. napus lines (2063A and B409), and established global maps of regulatory elements, chromatin states, and their dynamics for the whole genome (including the An and Cn subgenomes) in four tissue types (young leaf, flower bud, silique, and root) of these two lines. Approximately 65.8% of the genome was annotated with different epigenomic signals. Compared with the Cn subgenome, the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks. Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes. Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns. We identified a novel bivalent chromatin state (with H3K4me1 and H3K27me3) in B. napus that is associated with tissue-specific gene expression. Furthermore, we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels. Collectively, our findings provide a valuable epigenetic resource for allopolyploid plants.
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Affiliation(s)
- Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengpeng Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqin Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shunyao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmeijuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanling Xiao
- National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Heyduk K, McAssey EV, Grimwood J, Shu S, Schmutz J, McKain MR, Leebens-Mack J. Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae). FRONTIERS IN PLANT SCIENCE 2021; 11:573767. [PMID: 33519836 PMCID: PMC7843428 DOI: 10.3389/fpls.2020.573767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/17/2020] [Indexed: 05/23/2023]
Abstract
Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ∼11 kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from 41 accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case-Copia LTR transposons-did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Edward V. McAssey
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Biological Sciences, Quinnipiac University, Hamden, CT, United States
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shengqiang Shu
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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Gimenez MD, Vazquez DV, Trepat F, Cambiaso V, Rodríguez GR. Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato. PLANT CELL REPORTS 2021; 40:171-186. [PMID: 33079280 DOI: 10.1007/s00299-020-02624-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.
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Affiliation(s)
- Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- CIGEOBIO, (CONICET-UNSJ), Complejo Universitario "Islas Malvinas", FCEFN, Universidad de San Juan, Av. Ignacio de la Roza 590, J5402DCS, Rivadavia, San Juan, Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Felipe Trepat
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
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Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis. Genes (Basel) 2020; 11:genes11121500. [PMID: 33322817 PMCID: PMC7763881 DOI: 10.3390/genes11121500] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S14), its diploid parents, and the F1 hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in C. hytivus, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S14, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.
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18
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Zagorski D, Hartmann M, Bertrand YJK, Paštová L, Slavíková R, Josefiová J, Fehrer J. Characterization and Dynamics of Repeatomes in Closely Related Species of Hieracium (Asteraceae) and Their Synthetic and Apomictic Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:591053. [PMID: 33224172 PMCID: PMC7667050 DOI: 10.3389/fpls.2020.591053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/09/2020] [Indexed: 05/05/2023]
Abstract
The repetitive content of the plant genome (repeatome) often represents its largest fraction and is frequently correlated with its size. Transposable elements (TEs), the main component of the repeatome, are an important driver in the genome diversification due to their fast-evolving nature. Hybridization and polyploidization events are hypothesized to induce massive bursts of TEs resulting, among other effects, in an increase of copy number and genome size. Little is known about the repeatome dynamics following hybridization and polyploidization in plants that reproduce by apomixis (asexual reproduction via seeds). To address this, we analyzed the repeatomes of two diploid parental species, Hieracium intybaceum and H. prenanthoides (sexual), their diploid F1 synthetic and their natural triploid hybrids (H. pallidiflorum and H. picroides, apomictic). Using low-coverage next-generation sequencing (NGS) and a graph-based clustering approach, we detected high overall similarity across all major repeatome categories between the parental species, despite their large phylogenetic distance. Medium and highly abundant repetitive elements comprise ∼70% of Hieracium genomes; most prevalent were Ty3/Gypsy chromovirus Tekay and Ty1/Copia Maximus-SIRE elements. No TE bursts were detected, neither in synthetic nor in natural hybrids, as TE abundance generally followed theoretical expectations based on parental genome dosage. Slight over- and under-representation of TE cluster abundances reflected individual differences in genome size. However, in comparative analyses, apomicts displayed an overabundance of pararetrovirus clusters not observed in synthetic hybrids. Substantial deviations were detected in rDNAs and satellite repeats, but these patterns were sample specific. rDNA and satellite repeats (three of them were newly developed as cytogenetic markers) were localized on chromosomes by fluorescence in situ hybridization (FISH). In a few cases, low-abundant repeats (5S rDNA and certain satellites) showed some discrepancy between NGS data and FISH results, which is due partly to the bias of low-coverage sequencing and partly to low amounts of the satellite repeats or their sequence divergence. Overall, satellite DNA (including rDNA) was markedly affected by hybridization, but independent of the ploidy or reproductive mode of the progeny, whereas bursts of TEs did not play an important role in the evolutionary history of Hieracium.
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19
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Lu H, Xue L, Cheng J, Yang X, Xie H, Song X, Qiang S. Polyploidization-driven differentiation of freezing tolerance in Solidago canadensis. PLANT, CELL & ENVIRONMENT 2020; 43:1394-1403. [PMID: 32092164 DOI: 10.1111/pce.13745] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Solidago canadensis, originating from the temperate region of North America, has expanded southward to subtropical regions through polyploidization. Here we investigated whether freezing tolerance of S. canadensis was weakened during expansion. Measurement of the temperature causing 50% ruptured cells (LT50 ) in 35 S. canadensis populations revealed ploidy-related differentiation in freezing tolerance. Freezing tolerance was found to decrease with increasing ploidy. The polyploid populations of S. canadensis had lower ScICE1 gene expression levels but more ScICE1 gene copies than the diploids. Furthermore, more DNA methylation sites in the ScICE1 gene promoter were detected in the polyploids than in the diploids. The results suggest that promoter methylation represses the expression of multi-copy ScICE1 genes, leading to weaker freezing tolerance in polyploid S. canadensis compared to the diploids. The study provides empirical evidence that DNA methylation regulates expression of the gene copies and supports polyploidization-driven adaptation to new environments.
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Affiliation(s)
- Huan Lu
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Lifang Xue
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Jiliang Cheng
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Xianghong Yang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Xie
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Xiaoling Song
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Sheng Qiang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, China
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20
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Li M, Wang R, Wu X, Wang J. Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. BMC Genomics 2020; 21:330. [PMID: 32349676 PMCID: PMC7191788 DOI: 10.1186/s12864-020-6747-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
Background Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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21
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Pan Q, Zhu B, Zhang D, Tong C, Ge X, Liu S, Li Z. Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus. Front Genet 2020; 10:1279. [PMID: 31921314 PMCID: PMC6931035 DOI: 10.3389/fgene.2019.01279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 11/21/2022] Open
Abstract
Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.
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Affiliation(s)
- Qi Pan
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Zhu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dawei Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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22
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Yan H, Bombarely A, Xu B, Wu B, Frazier TP, Zhang X, Chen J, Chen P, Sun M, Feng G, Wang C, Cui C, Li Q, Zhao B, Huang L. Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5673-5686. [PMID: 31419288 DOI: 10.1093/jxb/erz325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/18/2019] [Indexed: 05/16/2023]
Abstract
Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Life Sciences, University of Milan, Milan, Italy
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Bingchao Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Taylor P Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chenming Cui
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Qi Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
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23
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Zhang L, Zou J, Li S, Wang B, Raboanatahiry N, Li M. Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa. BMC Genomics 2019; 20:649. [PMID: 31412776 PMCID: PMC6694508 DOI: 10.1186/s12864-019-6001-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. RESULTS Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid. CONCLUSIONS This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
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24
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Li N, Xu C, Zhang A, Lv R, Meng X, Lin X, Gong L, Wendel JF, Liu B. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. THE NEW PHYTOLOGIST 2019; 223:979-992. [PMID: 30919978 DOI: 10.1111/nph.15820] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.
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Affiliation(s)
- Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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25
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Wang R, Li M, Wu X, Wang J. The Gene Structure and Expression Level Changes of the GH3 Gene Family in Brassica napus Relative to Its Diploid Ancestors. Genes (Basel) 2019; 10:genes10010058. [PMID: 30658516 PMCID: PMC6356818 DOI: 10.3390/genes10010058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
The GH3 gene family plays a vital role in the phytohormone-related growth and developmental processes. The effects of allopolyploidization on GH3 gene structures and expression levels have not been reported. In this study, a total of 38, 25, and 66 GH3 genes were identified in Brassica rapa (ArAr), Brassica oleracea (CoCo), and Brassica napus (AnACnCn), respectively. BnaGH3 genes were unevenly distributed on chromosomes with 39 on An and 27 on Cn, in which six BnaGH3 genes may appear as new genes. The whole genome triplication allowed the GH3 gene family to expand in diploid ancestors, and allopolyploidization made the GH3 gene family re-expand in B. napus. For most BnaGH3 genes, the exon-intron compositions were similar to diploid ancestors, while the cis-element distributions were obviously different from its ancestors. After allopolyploidization, the expression patterns of GH3 genes from ancestor species changed greatly in B. napus, and the orthologous gene pairs between An/Ar and Cn/Co had diverged expression patterns across four tissues. Our study provides a comprehensive analysis of the GH3 gene family in B. napus, and these results could contribute to identifying genes with vital roles in phytohormone-related growth and developmental processes.
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Affiliation(s)
- Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiaoming Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430072, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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26
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Goswami G, Nath UK, Park JI, Hossain MR, Biswas MK, Kim HT, Kim HR, Nou IS. Transcriptional regulation of anthocyanin biosynthesis in a high-anthocyanin resynthesized Brassica napus cultivar. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2018; 25:19. [PMID: 30505808 PMCID: PMC6258291 DOI: 10.1186/s40709-018-0090-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/09/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Anthocyanins are plant secondary metabolites with key roles in attracting insect pollinators and protecting against biotic and abiotic stresses. They have potential health-promoting effects as part of the human diet. Anthocyanin biosynthesis has been elucidated in many species, enabling the development of anthocyanin-enriched fruits, vegetables, and grains; however, few studies have investigated Brassica napus anthocyanin biosynthesis. RESULTS We developed a high-anthocyanin resynthesized B. napus line, Rs035, by crossing anthocyanin-rich B. rapa (A genome) and B. oleracea (C genome) lines, followed by chromosome doubling. We identified and characterized 73 and 58 anthocyanin biosynthesis genes in silico in the A and C genomes, respectively; these genes showed syntenic relationships with 41 genes in Arabidopsis thaliana and B. napus. Among the syntenic genes, twelve biosynthetic and six regulatory genes showed transgressively higher expression in Rs035, and eight structural genes and one regulatory gene showed additive expression. We identified three early-, four late-biosynthesis pathways, three transcriptional regulator genes, and one transporter as putative candidates enhancing anthocyanin accumulation in Rs035. Principal component analysis and Pearson's correlation coefficients corroborated the contribution of these genes to anthocyanin accumulation. CONCLUSIONS Our study lays the foundation for producing high-anthocyanin B. napus cultivars. The resynthesized lines and the differentially expressed genes we have identified could be used to transfer the anthocyanin traits to other commercial rapeseed lines using molecular and conventional breeding.
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Affiliation(s)
- Gayatri Goswami
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Mohammad Rashed Hossain
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hye Ran Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
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Zhang H, Ali A, Hou F, Wu T, Guo D, Zeng X, Wang F, Zhao H, Chen X, Xu P, Wu X. Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2018; 18:314. [PMID: 30497392 PMCID: PMC6267922 DOI: 10.1186/s12870-018-1553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. RESULTS In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). CONCLUSIONS We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
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Affiliation(s)
- Hongyu Zhang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Asif Ali
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Feixue Hou
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Tingkai Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Daiming Guo
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiufeng Zeng
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Fangfang Wang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Huixia Zhao
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiaoqiong Chen
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Peizhou Xu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xianjun Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
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Duan CG, Zhu JK, Cao X. Retrospective and perspective of plant epigenetics in China. J Genet Genomics 2018; 45:621-638. [PMID: 30455036 DOI: 10.1016/j.jgg.2018.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 01/21/2023]
Abstract
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Xia J, Ma YJ, Wang Y, Wang JW. Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:112-126. [PMID: 29982168 DOI: 10.1016/j.plaphy.2018.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
To investigate on the effects of autopolyploidization on growth and artemisinin biosynthesis in Artemisia annua, we performed a comprehensive transcriptomic characterization of diploid and induced autotetraploid A. annua. The polyploidization treatment not only enhanced photosynthetic capacity and endogenous contents of indole-3-acetic acid (IAA), abscisic acid (ABA) and jasmonic acid (JA), oxidative stress, but increased the average level of artemisinin in tetraploids from 42.0 to 63.6%. The obvious phenotypic alterations in tetraploids were observed including shorter stems, larger size of stomata and glandular secretory trichomes (GSTs), larger leaves, more branches and roots. A total of 8763 (8.85%) differentially expressed genes (DEGs) were identified in autotetraploids and mainly involved in carbohydrate metabolic processes, cell wall organization and defense responses. Both the up-regulated expression of DNA methylation unigenes and enhanced level of DNA methylation in autotetraploids indicated a possible role of DNA methylation on transcriptomic remodeling and phenotypic alteration. The up-regulated genes were enriched in response to extracellular protein biosynthesis, photosynthesis and hormone stimulus for cell enlargement and phenotypic alteration. The genomic shock induced by chromosome duplication stimulated the expression of transcripts related to oxidative stress, biosynthesis and signal transduction of ABA and JA, and key enzymes in artemisinin biosynthetic pathway, leading to the increased accumulation of artemisinin. This is the first transcriptomic research that identifies DEGs involved in the polyploidization of A. annua. The results provide novel information for understanding the complexity of polyploidization and for further identification of the factors and genes involve in artemisinin biosynthesis.
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Affiliation(s)
- Jing Xia
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yan Jun Ma
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yue Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jian Wen Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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Wu J, Lin L, Xu M, Chen P, Liu D, Sun Q, Ran L, Wang Y. Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus. BMC Genomics 2018; 19:586. [PMID: 30081834 PMCID: PMC6080508 DOI: 10.1186/s12864-018-4966-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/30/2018] [Indexed: 01/08/2023] Open
Abstract
Background Allopolyploids require rapid genetic and epigenetic modifications to reconcile two or more sets of divergent genomes. To better understand the fate of duplicate genes following genomic mergers and doubling during allopolyploid formation, in this study, we explored the global gene expression patterns in resynthesized allotetraploid Brassica napus (AACC) and its diploid parents B. rapa (AA) and B. oleracea (CC) using RNA sequencing of leaf transcriptomes. Results We found that allopolyploid B. napus formation was accompanied by extensive changes (approximately one-third of the expressed genes) in the parental gene expression patterns (‘transcriptome shock’). Interestingly, the majority (85%) of differentially expressed genes (DEGs) were downregulated in the allotetraploid. Moreover, the homoeolog expression bias (relative contribution of homoeologs to the transcriptome) and expression level dominance (total expression level of both homoeologs) were thoroughly investigated by monitoring the expression of 23,766 B. oleracea-B. rapa orthologous gene pairs. Approximately 36.5% of the expressed gene pairs displayed expression bias with a slight preference toward the A-genome. In addition, 39.6, 4.9 and 9.0% of the expressed gene pairs exhibited expression level dominance (ELD), additivity expression and transgressive expression, respectively. The genome-wide ELD was also biased toward the A-genome in the resynthesized B. napus. To explain the ELD phenomenon, we compared the individual homoeolog expression levels relative to those of the diploid parents and found that ELD in the direction of the higher-expression parent can be explained by the downregulation of homoeologs from the dominant parent or upregulation of homoeologs from the nondominant parent; however, ELD in the direction of the lower-expression parent can be explained only by the downregulation of the nondominant parent or both homoeologs. Furthermore, Gene Ontology (GO) enrichment analysis suggested that the alteration in the gene expression patterns could be a prominent cause of the phenotypic variation between the newly formed B. napus and its parental species. Conclusions Collectively, our data provide insight into the rapid repatterning of gene expression at the beginning of Brassica allopolyploidization and enhance our knowledge of allopolyploidization processes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4966-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Li Lin
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Meiling Xu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Peipei Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Dongxiao Liu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Qinfu Sun
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Liping Ran
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
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31
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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32
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de Jong TJ, Escobedo Quevedo K, van der Veen-van Wijk CAM, Moshgani M. Performance of aneuploid backcross hybrids between the crop Brassica napus and its wild relative B. rapa. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:67-74. [PMID: 28921773 DOI: 10.1111/plb.12629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Crossings between the diploid wild Brassica rapa (AA, 2n = 20) and the tetraploid cultivar B. napus (AACC, 2n = 38) can readily be made. Backcrosses to the wild B. rapa (BC1 ) produce aneuploids with variable chromosome numbers between 20 and 29. How does survival and performance relate to DNA content of plants? Growth of the BC1 plants was measured in the lab. One plant in the F1 self-pollinated spontaneously and produced abundant F2 seeds that were also examined. The number of C-chromosomes was estimated from DNA values obtained with flow cytometry. Average DNA value of the BC1 was similar to that of the parents, which shows that C-chromosomes do not reduce success of pollen or embryos. The average DNA value in the F2 was 13% higher than in the F1 , suggesting that extra C-chromosomes facilitated gamete success and/or embryo survival. Under both optimal and drought stress conditions growth and survival of BC1 hybrids was similar to that of B. rapa. No significant correlations existed between growth or survival and DNA value. Aneuploid plants were not inferior under the conditions of the growth room and may persist in nature. We discuss other factors, such as herbivory, that could prevent hybrid establishment in the field.
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Affiliation(s)
- T J de Jong
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | | | | | - M Moshgani
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
- Department of Environmental Science, Faculty of Agriculture, University of Birjand, Birjand, Iran
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Qi X, Wang H, Song A, Jiang J, Chen S, Chen F. Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense× Tanacetum vulgare hybrid and allopolyploid (Asteraceae). HORTICULTURE RESEARCH 2018; 5:5. [PMID: 29423235 PMCID: PMC5802763 DOI: 10.1038/s41438-017-0003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/22/2017] [Accepted: 11/26/2017] [Indexed: 05/05/2023]
Abstract
Allopolyploid formation involves two major events: interspecific hybridization and polyploidization. A number of species in the Asteraceae family are polyploids because of frequent hybridization. The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported. In this study, we obtained allopolyploids by applying a colchicine treatment to a synthesized C. nankingense×T. vulgare hybrid. Sequence-related amplified polymorphism (SRAP), methylation-sensitive amplification polymorphism (MSAP), and high-throughput RNA sequencing (RNA-Seq) technologies were used to investigate the genomic, epigenetic, and transcriptomic alterations in both the hybrid and allopolyploids. The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments. The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization. There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent. Most differentially expressed genes (DEGs) showed down-regulation in the hybrid/allopolyploid relative to the parents. Among the non-additive genes, transgressive patterns appeared to be dominant, especially repression patterns. Maternal expression dominance was observed specifically for down-regulated genes. Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents. Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids. The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.
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Affiliation(s)
- Xiangyu Qi
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Haibin Wang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Aiping Song
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Jiafu Jiang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Sumei Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
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Vicient CM, Casacuberta JM. Impact of transposable elements on polyploid plant genomes. ANNALS OF BOTANY 2017; 120:195-207. [PMID: 28854566 PMCID: PMC5737689 DOI: 10.1093/aob/mcx078] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. SCOPE This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. CONCLUSIONS TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes.
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Affiliation(s)
- Carlos M. Vicient
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
- For correspondence. E-mail
| | - Josep M. Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Pelé A, Trotoux G, Eber F, Lodé M, Gilet M, Deniot G, Falentin C, Nègre S, Morice J, Rousseau-Gueutin M, Chèvre AM. The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate. THE NEW PHYTOLOGIST 2017; 213:1886-1897. [PMID: 27575298 DOI: 10.1111/nph.14147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Gwenaelle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, 35650, Le Rheu, France
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Raman R, Qiu Y, Coombes N, Song J, Kilian A, Raman H. Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L. FRONTIERS IN PLANT SCIENCE 2017; 8:1765. [PMID: 29250080 PMCID: PMC5716317 DOI: 10.3389/fpls.2017.01765] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/27/2017] [Indexed: 05/05/2023]
Abstract
Seed lost due to easy pod dehiscence at maturity (pod shatter) is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata) and identified quantitative trait loci (QTL) for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE). In comparison to B. napus (RE = 2.16 mJ), B. carinata accessions had higher RE values (2.53 to 20.82 mJ). A genetic linkage map of an F2 population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE) and BC73524 (shatter prone with low RE) comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F2 and F2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3) that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools.
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Affiliation(s)
- Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
- *Correspondence: Rosy Raman,
| | - Yu Qiu
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Neil Coombes
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Jie Song
- Diversity Arrays Technology Pty. Ltd., University of Canberra, Canberra, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty. Ltd., University of Canberra, Canberra, ACT, Australia
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica. Sci Rep 2016; 6:37416. [PMID: 27874043 PMCID: PMC5118723 DOI: 10.1038/srep37416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/27/2016] [Indexed: 11/08/2022] Open
Abstract
Raphanobrassica is an allopolyploid species derived from inter-generic hybridization that combines the R genome from R. sativus and the C genome from B. oleracea var. alboglabra. In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles in Raphanobrassica and its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed in Raphanobrassica. Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected in Raphanobrassica. In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term 'metabolic processes'. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.
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Gutierrez-Gonzalez JJ, Garvin DF. Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2147-2157. [PMID: 27135276 PMCID: PMC5096403 DOI: 10.1111/pbi.12571] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/13/2016] [Accepted: 04/23/2016] [Indexed: 05/05/2023]
Abstract
Vitamin E is essential for humans and thus must be a component of a healthy diet. Among the cereal grains, hexaploid oats (Avena sativa L.) have high vitamin E content. To date, no gene sequences in the vitamin E biosynthesis pathway have been reported for oats. Using deep sequencing and orthology-guided assembly, coding sequences of genes for each step in vitamin E synthesis in oats were reconstructed, including resolution of the sequences of homeologs. Three homeologs, presumably representing each of the three oat subgenomes, were identified for the main steps of the pathway. Partial sequences, likely representing pseudogenes, were recovered in some instances as well. Pairwise comparisons among homeologs revealed that two of the three putative subgenome-specific homeologs are almost identical for each gene. Synonymous substitution rates indicate the time of divergence of the two more similar subgenomes from the distinct one at 7.9-8.7 MYA, and a divergence between the similar subgenomes from a common ancestor 1.1 MYA. A new proposed evolutionary model for hexaploid oat formation is discussed. Homeolog-specific gene expression was quantified during oat seed development and compared with vitamin E accumulation. Homeolog expression largely appears to be similar for most of genes; however, for some genes, homoeolog-specific transcriptional bias was observed. The expression of HPPD, as well as certain homoeologs of VTE2 and VTE4, is highly correlated with seed vitamin E accumulation. Our findings expand our understanding of oat genome evolution and will assist efforts to modify vitamin E content and composition in oats.
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Affiliation(s)
| | - David F Garvin
- USDA-ARS Plant Science Research Unit, St. Paul, MN, USA.
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Fu Y, Xiao M, Yu H, Mason AS, Yin J, Li J, Zhang D, Fu D. Small RNA changes in synthetic Brassica napus. PLANTA 2016; 244:607-622. [PMID: 27107747 DOI: 10.1007/s00425-016-2529-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/09/2016] [Indexed: 06/05/2023]
Abstract
Small RNAs and microRNAs were found to vary extensively in synthetic Brassica napus and subsequent generations, accompanied by the activation of transposable elements in response to hybridization and polyploidization. Resynthesizing B. napus by hybridization and chromosome doubling provides an approach to create novel polyploids and increases the usable genetic variability in oilseed rape. Although many studies have shown that small RNAs (sRNAs) act as important factor during hybridization and polyploidization in plants, much less is known on how sRNAs change in synthetic B. napus, particularly in subsequent generations after formation. We performed high-throughput sequencing of sRNAs in S1-S4 generations of synthetic B. napus and in the homozygous B. oleracea and B. rapa parent lines. We found that the number of small RNAs (sRNAs) and microRNAs (miRNAs) doubled in synthetic B. napus relative to the parents. The proportions of common sRNAs detected varied from the S1 to S4 generations, suggesting sRNAs are unstable in synthetic B. napus. The majority of miRNAs (67.2 %) were non-additively expressed in the synthesized Brassica allotetraploid, and 33.3 % of miRNAs were novel in the resynthesized B. napus. The percentage of miRNAs derived from transposable elements (TEs) also increased, indicating transposon activation and increased transposon-associated miRNA production in response to hybridization and polyploidization. The number of target genes for each miRNA in the synthesized Brassica allotetraploid was doubled relative to the parents, enhancing the complexity of gene expression regulation. The potential roles of miRNAs and their targets are discussed. Our data demonstrate generational changes in sRNAs and miRNAs in synthesized B. napus.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meili Xiao
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jiaming Yin
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dongqing Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum. Mol Genet Genomics 2016; 291:1871-83. [PMID: 27295958 DOI: 10.1007/s00438-016-1225-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference Sorghum bicolor genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of S. bicolor and its close relative S. propinquum. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of S. propinquum reads to the S. bicolor database failed to fully describe TE content in S. propinquum, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons.
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Gautam M, Dang Y, Ge X, Shao Y, Li Z. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus. FRONTIERS IN PLANT SCIENCE 2016; 7:438. [PMID: 27148282 PMCID: PMC4828432 DOI: 10.3389/fpls.2016.00438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/21/2016] [Indexed: 05/24/2023]
Abstract
Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent.
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Affiliation(s)
- Mayank Gautam
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yanwei Dang
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yujiao Shao
- College of Chemistry and Life Science, Hubei University of EducationWuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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Zhang X, Liu T, Li X, Duan M, Wang J, Qiu Y, Wang H, Song J, Shen D. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables. Sci Rep 2016; 6:18618. [PMID: 26727246 PMCID: PMC4698638 DOI: 10.1038/srep18618] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops.
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Affiliation(s)
- Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Tongjin Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Mengmeng Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jinglei Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
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Cheng S, Huang Z, Li Y, Liao T, Suo Y, Zhang P, Wang J, Kang X. Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:1031-1045. [PMID: 25557321 DOI: 10.1111/jipb.12328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.
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Affiliation(s)
- Shiping Cheng
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Huang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Liao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. Proc Natl Acad Sci U S A 2015; 112:E7022-9. [PMID: 26621743 DOI: 10.1073/pnas.1515170112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a "genome shock" response factor to help neoautopolyploids adapt to genome-dosage effects.
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Liu C, Yang X, Zhang H, Wang X, Zhang Z, Bian Y, Zhu B, Dong Y, Liu B. Genetic and epigenetic modifications to the BBAA component of common wheat during its evolutionary history at the hexaploid level. PLANT MOLECULAR BIOLOGY 2015; 88:53-64. [PMID: 25809554 DOI: 10.1007/s11103-015-0307-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/12/2015] [Indexed: 05/11/2023]
Abstract
The formation and evolution of common wheat (Triticum aestivum L., genome BBAADD) involves allopolyploidization events at two ploidy levels. Whether the two ploidy levels (tetraploidy and hexaploidy) have impacted the BBAA subgenomes differentially remains largely unknown. We have reported recently that extensive and distinct modifications of transcriptome expression occurred to the BBAA component of common wheat relative to the evolution of gene expression at the tetraploid level in Triticum turgidum. As a step further, here we analyzed the genetic and cytosine DNA methylation differences between an extracted tetraploid wheat (ETW) harboring genome BBAA that is highly similar to the BBAA subgenomes of common wheat, and a set of diverse T. turgidum collections, including both wild and cultivated genotypes. We found that while ETW had no significantly altered karyotype from T. turgidum, it diverged substantially from the later at both the nucleotide sequence level and in DNA methylation based on molecular marker assay of randomly sampled loci across the genome. In particular, ETW is globally less cytosine-methylated than T. turgidum, consistent with earlier observations of a generally higher transcriptome expression level in ETW than in T. turgidum. Together, our results suggest that genome evolution at the allohexaploid level has caused extensive genetic and DNA methylation modifications to the BBAA subgenomes of common wheat, which are distinctive from those accumulated at the tetraploid level in both wild and cultivated T. turgidum genotypes.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Song Q, Chen ZJ. Epigenetic and developmental regulation in plant polyploids. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:101-9. [PMID: 25765928 PMCID: PMC4395545 DOI: 10.1016/j.pbi.2015.02.007] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic structure and gene expression after polyploid formation. Growing evidence suggests that epigenetic modifications can alter homoeologous gene expression and reprogram gene expression networks, which allows polyploids to establish new cytotypes, grow vigorously and promote adaptation in local environments. Sequence and gene expression changes in polyploids have been well documented and reviewed elsewhere. This review is focused on developmental regulation and epigenetic changes including DNA methylation and histone modifications in polyploids.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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48
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Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C, Paux E. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Genome Biol 2015; 16:29. [PMID: 25853487 PMCID: PMC4355351 DOI: 10.1186/s13059-015-0601-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022] Open
Abstract
Background Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. Results By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Conclusions Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0601-9) contains supplementary material, which is available to authorized users.
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Buggs RJA, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0354. [PMID: 24958927 DOI: 10.1098/rstb.2013.0354] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.
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Affiliation(s)
- Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR 97202, USA
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